Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
Peptide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Any of a variety of procedures which use biomolecular probes to measure the presence or concentration of biological molecules, biological structures, microorganisms, etc., by translating a biochemical interaction at the probe surface into a quantifiable physical signal.
Molecules of DNA that possess enzymatic activity.
Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen-antibody binding.
Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
The rate dynamics in chemical or physical systems.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
A 60-kDa extracellular protein of Streptomyces avidinii with four high-affinity biotin binding sites. Unlike AVIDIN, streptavidin has a near neutral isoelectric point and is free of carbohydrate side chains.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
Ribonucleic acid that makes up the genetic material of viruses.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The relationships of groups of organisms as reflected by their genetic makeup.
Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)
High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages.
A technology, in which sets of reactions for solution or solid-phase synthesis, is used to create molecular libraries for analysis of compounds on a large scale.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The functional hereditary units of BACTERIA.
Inorganic compounds that contain fluorine as an integral part of the molecule.
Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Genotypic differences observed among individuals in a population.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.
Established cell cultures that have the potential to propagate indefinitely.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Deoxyribonucleic acid that makes up the genetic material of viruses.
The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Proteins found in any species of bacterium.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.
A collection of cloned peptides, or chemically synthesized peptides, frequently consisting of all possible combinations of amino acids making up an n-amino acid peptide.
An enzyme formed from PROTHROMBIN that converts FIBRINOGEN to FIBRIN.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
A guanine nucleotide containing one phosphate group esterified to the sugar moiety and found widely in nature.
A group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in MOLECULAR GENETICS to detect the presence of a complementary sequence by NUCLEIC ACID HYBRIDIZATION.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The processes of RNA tertiary structure formation.
A guanine nucleotide containing two phosphate groups esterified to the sugar moiety.
Adenine nucleotide containing one phosphate group esterified to the sugar moiety in the 2'-, 3'-, or 5'-position.
Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A family of RNA plant viruses that infect a wide range of herbaceous and woody plant species. There are at least eight genera including POTEXVIRUS and CARLAVIRUS, both of which are highly immunogenic.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The functional hereditary units of VIRUSES.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The development and use of techniques to study physical phenomena and construct structures in the nanoscale size range or smaller.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Proteins prepared by recombinant DNA technology.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The study of fluid channels and chambers of tiny dimensions of tens to hundreds of micrometers and volumes of nanoliters or picoliters. This is of interest in biological MICROCIRCULATION and used in MICROCHEMISTRY and INVESTIGATIVE TECHNIQUES.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Systems for the delivery of drugs to target sites of pharmacological actions. Technologies employed include those concerning drug preparation, route of administration, site targeting, metabolism, and toxicity.
A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of PROTEINS; NUCLEIC ACIDS; and CARBOHYDRATES. (Segen, Dictionary of Modern Medicine, 1992)
Proteins found in any species of virus.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
Adenine nucleotides which contain deoxyribose as the sugar moiety.
Uridine 5'-(tetrahydrogen triphosphate). A uracil nucleotide containing three phosphate groups esterified to the sugar moiety.
Any method used for determining the location of and relative distances between genes on a chromosome.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Methods utilizing the principles of MICROFLUIDICS for sample handling, reagent mixing, and separation and detection of specific components in fluids.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Agents that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags.
Guanine nucleotides which contain deoxyribose as the sugar moiety.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.

Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. (1/893)

Aptamers are powerful candidates for molecular imaging applications due to a number of attractive features, including rapid blood clearance and tumor penetration. We carried out structure-activity relationship (SAR) studies with the Tenascin-C binding aptamer TTA1, which is a promising candidate for application in tumor imaging with radioisotopes. The aim was to improve its in vivo stability and target binding. We investigated the effect of thermal stabilization of the presumed non-binding double-stranded stem region on binding affinity and resistance against nucleolytic degradation. To achieve maximal thermal stem stabilization melting experiments with model hexanucleotide duplexes consisting of unmodified RNA, 2'-O-methyl RNA (2'-OMe), 2'-Fluoro RNA (2'-F) or Locked Nucleic Acids (LNAs) were initially carried out. Extremely high melting temperatures have been found for an LNA/LNA duplex. TTA1 derivatives with LNA and 2'-OMe modifications within the non-binding stem have subsequently been synthesized. Especially, the LNA-modified TTA1 derivative exhibited significant stem stabilization and markedly improved plasma stability while maintaining its binding affinity to the target. In addition, higher tumor uptake and longer blood retention was found in tumor-bearing nude mice. Thus, our strategy to introduce LNA modifications after the selection procedure is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding properties.  (+info)

Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids. (2/893)

The nucleic acid exchange reaction is a common feature for genetic recombination, DNA replication and transcription. Due to the fact that in the strand-exchange reactions the reactant and product molecules have similar or identical nucleotide sequences, the reaction is undetectable. As a rule, the nucleic acids with radioactive or fluorescence labels are used in such studies. Besides the fact that the labels can perturb the reaction and pose a health risk to the investigators, the assays usually involve extra experimental steps: quenching the reaction, separation, visualization and quantification of the products. Here, we describe a straightforward, direct and precise method to study strand-exchange reaction of unlabeled nucleic acids by real-time measurements of optical absorption. The method takes advantage of the property of some guanine-rich oligonucleotides to adopt monomolecular quadruplex conformation in the presence of certain cations. The conformation is characterized by significant absorption in long-wavelength range of the ultraviolet region where usually other secondary structures are transparent. The 'signal' oligonucleotide is incorporated into reactant duplex by annealing with target sequence. Adding the replacement sequence initiates the release of the 'signal' oligonucleotide into solution, which is accompanied by ultraviolet absorption in long-wavelength range.  (+info)

Pegaptanib for neovascular age-related macular degeneration. (3/893)

BACKGROUND: Pegaptanib, an anti-vascular endothelial growth factor therapy, was evaluated in the treatment of neovascular age-related macular degeneration. METHODS: We conducted two concurrent, prospective, randomized, double-blind, multicenter, dose-ranging, controlled clinical trials using broad entry criteria. Intravitreous injection into one eye per patient of pegaptanib (at a dose of 0.3 mg, 1.0 mg, or 3.0 mg) or sham injections were administered every 6 weeks over a period of 48 weeks. The primary end point was the proportion of patients who had lost fewer than 15 letters of visual acuity at 54 weeks. RESULTS: In the combined analysis of the primary end point (for a total of 1186 patients), efficacy was demonstrated, without a dose-response relationship, for all three doses of pegaptanib (P<0.001 for the comparison of 0.3 mg with sham injection; P<0.001 for the comparison of 1.0 mg with sham injection; and P=0.03 for the comparison of 3.0 mg with sham injection). In the group given pegaptanib at 0.3 mg, 70 percent of patients lost fewer than 15 letters of visual acuity, as compared with 55 percent among the controls (P<0.001). The risk of severe loss of visual acuity (loss of 30 letters or more) was reduced from 22 percent in the sham-injection group to 10 percent in the group receiving 0.3 mg of pegaptanib (P<0.001). More patients receiving pegaptanib (0.3 mg), as compared with sham injection, maintained their visual acuity or gained acuity (33 percent vs. 23 percent; P=0.003). As early as six weeks after beginning therapy with the study drug, and at all subsequent points, the mean visual acuity among patients receiving 0.3 mg of pegaptanib was better than in those receiving sham injections (P<0.002). Among the adverse events that occurred, endophthalmitis (in 1.3 percent of patients), traumatic injury to the lens (in 0.7 percent), and retinal detachment (in 0.6 percent) were the most serious and required vigilance. These events were associated with a severe loss of visual acuity in 0.1 percent of patients. CONCLUSIONS: Pegaptanib appears to be an effective therapy for neovascular age-related macular degeneration. Its long-term safety is not known.  (+info)

NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A. (4/893)

A high affinity RNA aptamer (APT58, 58 nt long) against mammalian initiation factor 4A (eIF4A) requires nearly its entire nucleotide sequence for efficient binding. Since splitting either APT58 or eIF4A into two domains diminishes the affinity for each other, it is suggested that multiple interactions or a global interaction between the two molecules accounts for the high affinity. To understand the structural basis of APT58's global recognition of eIF4A, we determined the solution structure of two essential nucleotide loops (AUCGCA and ACAUAGA) within the aptamer using NMR spectroscopy. The AUCGCA loop is stabilized by a U-turn motif and contains a non-canonical A:A base pair (the single hydrogen bond mismatch: Hoogsteen/Sugar-edge). On the other hand, the ACAUAGA loop is stabilized by an AUA tri-nucleotide loop motif and contains the other type of A:A base pair (single hydrogen bond mismatch: Watson-Crick/Watson-Crick). Considering the known structural and functional properties of APT58, we propose that the AUCGCA loop is directly involved in the interaction with eIF4A, while the flexibility of the ACAUAGA loop is important to support this interaction. The Watson-Crick edges of C7 and C9 in the AUCGCA loop may directly interact with eIF4A.  (+info)

Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. (5/893)

We have developed an automated SELEX (Systematic Evolution of Ligands by EXponential Enrichment) process that allows the execution of in vitro selection cycles without any direct manual intervention steps. The automated selection protocol is designed to provide for high flexibility and versatility in terms of choice of buffers and reagents as well as stringency of selection conditions. Employing the automated SELEX process, we have identified RNA aptamers to the mirror-image configuration (d-peptide) of substance P. The peptide substance P belongs to the tachykinin family and exerts various biologically important functions, such as peripheral vasodilation, smooth muscle contraction and pain transmission. The aptamer that was identified most frequently was truncated to the 44mer SUP-A-004. The mirror-image configuration of SUP-A-004, the so-called Spiegelmer, has been shown to bind to naturally occurring l-substance P displaying a K(d) of 40 nM and to inhibit (IC50 of 45 nM) l-substance P-mediated Ca2+ release in a cell culture assay.  (+info)

Proximity extension of circular DNA aptamers with real-time protein detection. (6/893)

Multivalent circular aptamers or 'captamers' have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the 'proximity extension' assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer-thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier.  (+info)

Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium. (7/893)

The circular dichroism, CD, spectra of the telomere repeats of vertebrates, d(TTAGGG), indicate that parallel type quadruplex structures or disordered single-stranded structures are formed in low salt. Anti-parallel quadruplex structures are favored in the presence of high concentrations, 140 mM, of sodium. External loop, also known as propeller, parallel type structures are favored in the presence of high concentrations, 100 mM, of potassium in the presence of either 5 or 140 mM sodium. The cation dependence of the CD spectra of the vertebrate telomere repeat DNAs is distinctly different from that of the telomere repeats of Tetrahymena and Oxytricha as well as that of the thrombin binding aptamer. These results indicate that the external loop structures may be present in vertebrate telomeres under the conditions of high potassium and low sodium concentration found in nuclei.  (+info)

Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. (8/893)

We recently described the isolation of 2'-fluoropyrimidine-substituted RNA aptamers that bind specifically to the surface glycoprotein (gp 120) of the R5 strain, HIV-1(Ba-L), as presented in a previous study. These aptamers potently neutralize HIV-1 infectivity in human peripheral blood mononuclear cells of both tissue culture lab-adapted strains and diverse R5 clinical isolates from multiple clades. Here, we report a detailed structural characterization of one such neutralizing aptamer, B40, using enzymatic and chemical probing methods. We identify the minimal region of the aptamer essential for binding gp120 and accordingly design a 77-nucleotide truncated aptamer, B40t77. We then quantitatively analyze the binding affinity and neutralization potency of the parental and truncated (minimal) aptamer, and show them to be comparable. Furthermore, using results from secondary structure analysis, RNA mutagenesis and BIAcore surface plasmon resonance (SPR) binding assays, we hypothesize that a folded RNA structure is required to present specific nucleotide sequences to allow gp120-recognition and binding. The information gained from this study may provide leads for development of novel anti-HIV-1 therapies and can be used to extend our understanding of the molecular interactions between the virus and its host cell.  (+info)

Nucleic acid aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with very high affinity and specificity, and are generally selected by a process referred to as systematic evolution of ligands by exponential enrichment. Conventional antibody-based therapeutic and diagnostic approach currently employed against biotoxins pose major limitations such as the requirement of a live animal for the in vivo enrichment of the antibody species, decreased stability, high production cost, and side effects. Aptamer technology is a viable alternative that can be used to combat these problems. Fully sequestered in vitro, aptamers eliminate the need for a living host. Furthermore, one of the key advantages of using aptamers instead of antibodies is that they can be selected against very weakly immunogenic and cytotoxic substances. In this review, we focus on nucleic acid aptamers developed against various biotoxins of plant, microorganism, or animal origin and show how ...
TY - JOUR. T1 - BODIPY-labeled fluorescent aptamer sensors for turn-on sensing of interferon-gamma and adenine compounds on cells. AU - Tsuchiya, Akira. AU - Hashim, Siti N.. AU - Ise, Shoko. AU - Furuhata, Takafumi. AU - Kawai, Kiyohiko. AU - Wakabayashi, Rie. AU - Goto, Masahiro. AU - Kamiya, Noriho. AU - Sando, Shinsuke. PY - 2016/1/1. Y1 - 2016/1/1. N2 - An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-? and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a turn-on detection of the target molecule with improved off/on efficiency.. AB - An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-? and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a ...
TY - JOUR. T1 - Nucleic Acid Aptamers as a Potential Nucleus Targeted Drug Delivery System. AU - Shrivastava, Garima. AU - Bakshi, Hamid A.. AU - Aljabali, Alaa A.. AU - Mishra, Vijay. AU - Faruck, Lukmanul Hakkim. AU - Charbe, Nitin B.. AU - Kesharwani, Prashant. AU - Chellappan, Dinesh Kumar. AU - Dua, Kamal. AU - Tambuwala, Murtaza M.. N1 - Email sent to journal requesting confirmation of publication date - awaiting reply (27/4/20). PY - 2020/1/31. Y1 - 2020/1/31. N2 - Background: Nucleus targeted drug delivery provides several opportunities for the treatment of fatal diseases such as cancer. However, the complex nucleocytoplasmic barriers pose significant challenges for delivering a drug directly and efficiently into the nucleus. Aptamers representing single-stranded DNA and RNA qualify as next-generation highly advanced and personalized medicinal agents that successfully inhibit the expression of certain proteins; possess extraordinary gene-expression for manoeuvring the diseased cells ...
TY - JOUR. T1 - Programmable hydrogels for the controlled release of therapeutic nucleic acid aptamers via reversible DNA hybridization. AU - Zhang, Xiaolong. AU - Battig, Mark R.. AU - Wang, Yong. N1 - Copyright: Copyright 2013 Elsevier B.V., All rights reserved.. PY - 2013/10/25. Y1 - 2013/10/25. N2 - Reversible DNA hybridization can be used as a new mechanism to control the sustained and triggered release of therapeutic oligonucleotides from hydrogels.. AB - Reversible DNA hybridization can be used as a new mechanism to control the sustained and triggered release of therapeutic oligonucleotides from hydrogels.. UR - UR - U2 - 10.1039/c3cc45594g. DO - 10.1039/c3cc45594g. M3 - Article. C2 - 24018965. AN - SCOPUS:84884614812. VL - 49. SP - 9600. EP - 9602. JO - Chemical Communications. JF - Chemical Communications. SN - 1359-7345. IS - 83. ER - ...
Human Immunodeficiency Virus (HIV) reverse transcriptase (RT) is the most common molecular target of current HIV treatments. Oligonucleotide aptamers bind and inhibit the RNA- and DNA-dependent polymerization activities of HIV RT. Libraries consisting of aptamers including 32, 70 or 80 nucleotide variable regions were previously screened by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) against RT. Roughly half of the resulting aptamers were represented by pseudoknots with well defined signature sequences (the Family I), but also additional pseudoknots with little sequence convergence (Family II), and non-pseudoknot aptamers (Family III). Nucleic acid aptamers bind RT in the primer/template binding site. Aptamers are generally non-toxic and non-immunogenic molecules making them enticing drug prospects. Many aptamers inhibit DNA dependent DNA polymerization by RT from several phenotypically different recombinant viruses, but inhibition depends on a single amino acid mutation at ...
RNA APTAMERS AGAINST BAFF-R AS CELL-TYPE SPECIFIC DELIVERY AGENTS AND METHODS FOR THEIR USE - In one embodiment, a B cell specific aptamer-siRNA chimera is provided. The B cell specific aptamer-siRNa chimera may include an RNA aptamer that binds BAFF-R and an siRNA molecule conjugated to the RNA aptamer via a nucleotide linker. In another embodiment, a B cell specific RNA aptamer is provided. The RNA aptamer may be a molecule that binds to BAFF-R that has the sequence SEQ ID NO:37, SEQ ID NO:38 or SEQ ID NO:39. In some embodiments, the RNA aptamer is conjugated, via a nucleotide linker, to an siRNA molecule that suppresses expression of one or more target oncogenes in one or more B cells. In one aspect, the one or more target oncogenes are selected from Bcl6, Bcl2, STAT3, Cyclin D1, Cyclin E2 and c-myc. In another embodiment, methods for treating a B cell malignancy in a cancer patient are provided. Such methods may include administering a therapeutically effective amount of a therapeutic ...
Aptamer Solutions Ltd is a York based Biotechnology Company specialising in the custom selection of high-affinity and highly specific nucleic acid aptamers for use in the life sciences sector. Our proprietary automated high-throughput aptamer selection processes allow us to offer a flexible and competitive pricing structure for the development of RNA and DNA aptamers. In addition, we are about to launch a new complementary technology in the area of biomarker discovery.. Our proprietary aptamer based biomarker discovery platform and proprietary combinatorial libraries contain up to and over 1018 different molecules, this diversity and bespoke library design is fundamental to the success of the screening process. This technology enables us to greatly speed up the identification of novel biomarkers as well as diagnostics and/or therapeutic candidate molecules. This technology builds on one of the most powerful uses of aptamer technology, which is the ability for aptamers to be isolated against ...
Macugen (pegaptanib sodium injection) is a sterile, aqueous solution containing pegaptanib sodium for intravitreous injection. Macugen is supplied in a single-dose, pre-filled syringe.
Anti-thrombin aptamers are G-quadruplex-bearing oligonucleotides, which recognizes the exosites of human thrombin. The first anti-thrombin aptamer, TBA, was generated through via SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology in 1992 by L.C. Bock, J.J. Toole and colleagues. A second thrombin-binding aptamer, HD22, recognizes thrombin exosite II and was discovered in 1997 by NeXstar (now Gilead Sciences). These two aptamers have high affinity and good specificity and have been widely studied and used for the development of aptamer-based therapeutics and diagnostics. The aptamer TBA (also known as G15D, HTQ, HD1 or ARC183) is a 15-mer single-stranded DNA with the sequence 5-GGTTGGTGTGGTTGG-3. It interacts with the exosite I of human alpha-thrombin, which is the binding site of fibrinogen, so this aptamer acts as an anti-coagulant agent inhibiting the activation of fibrinogen as well as platelet aggregation. In addition, TBA shows good affinity and specificity ...
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents.
An L-ribonucleic acid aptamer (L-RNA aptamer, trade name Spiegelmer - from German Spiegel mirror - by Noxxon Pharma) is an RNA-like molecule built from L-ribose units. It is an artificial oligonucleotide named for being a mirror image of natural oligonucleotides. L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. Spiegelmers are considered potential drugs and are currently being tested in clinical trials. Spiegelmers, built using L-ribose, are the enantiomers of natural oligonucleotides, which are made with D-ribose. Nucleic acid aptamers, including L-RNA aptamers, contain adenosine monophosphate, guanosine monophosphate, cytidine monophosphate, uridine monophosphate, a phosphate group, a nucleobase and a ribose sugar. Like other aptamers, L-RNA aptamers are able to bind molecules such as peptides, proteins, and substances of low molecular weight. The affinity of L-RNA aptamers to their target molecules often lies in the ...
70846 Oilseed contains sterols and related compounds with economic potential. The extraction and analysis of these compounds would be aided by the availability of highly selective aptamers with high affinities for their particular sterol ligands. This project will develop aptamers for use in microarrays to analyze and extract sterol contents of oil and other biological extracts. Bacterial expression vectors will be prepared from which the aptamers can be expressed in large quantities. In Phase I, one or more DNA aptamers for sitosterol will be selected. The aptamers will be evaluated for their specificity and affinity for sitosterol and related compounds. A bacterial expression vector will be developed from which aptamers can be prepared. Commercial Applications and Other Benefits as described by the awardee: Commercial applications include (1) the use of aptamers in the analysis and extraction of sitosterol and related compounds, and (2) a general method for economically mass-producing DNA ...
Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B
Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B
Human Neutrophil Elastase (DNA I) , DNA Aptamer, Biotinylated DNA Aptamers AD-155-B Human Neutrophil Elastase (DNA I) , DNA Aptamer, Biotinylated DNA Aptamers AD-155-B
After three decades, the human immunodeficiency virus type 1 (HIV-1) remains a global pandemic. It has been difficult to develop therapeutic agents and vaccines against HIV due partly to the virus s ability to mutate rapidly. As a result, there is a constant need to develop new therapeutic agents that target HIV-1. This research seeks to develop an RNA aptamer that would bind tightly to the Pre-Hairpin Intermediate state of the HIV-1 envelope glycoprotein gp41 to inhibit viral fusion. The project targets the envelope glycoprotein of HIV-1, gp41, with nucleic acid aptamers. Aptamers are selected from random pools (libraries) by an in vitro selection called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The aptamers go through rounds of selection, where the weak binders will be washed off in each round. Once these aptamers are developed, they will be tested for their ability to prevent viral membrane fusion, and their potential use in HIV therapeutics. ...
However, even among aptamers, those nucleic acid aptamers that are polynucleotides (i.e. high-molecular-weight compounds with nucleic acid bases and sugars bound together) are biological high-molecular-weight compounds that offer the below advantages not shown by peptides, proteins or antibodies, and it is hoped that they will be new molecular-targeted agents and molecular-recognition elements.. Advantages of nucleic acid aptamers ...
4DII: High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment). During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometry or microscopy. Some have also been used as drugs by inhibiting or activating functions of their targets in a manner similar to neutralizing or agonistic antibodies. Additionally, it is straightforward to conjugate aptamers to other agents without losing their affinity and they have successfully been used in vitro and in vivo to deliver drugs, siRNA, nanoparticles or contrast agents to target cells. Hence, aptamers identified against cell surface biomarkers represent a promising class of ligands. This review
Aptamers are single-stranded oligonucleotides isolated via in vitro systematic evolution of ligands by exponential enrichment (SELEX),1,2 which can specifically bind to a wide range of targets including proteins, small molecules and metal ions.3 Aptamers offer several advantages as recognition elements for biosensor applications relative to antibodies. First, aptamers can be chemically synthesized with high reproducibility at relatively low cost.4,5 Second, the high chemical stability of DNA aptamers means that they can be used under harsher conditions and stored with a longer shelf life.6 Finally, it is possible to generate unstructured aptamers that form specific secondary structures such as three-way junctions7,8 or tertiary folds such as G-quadruplex structures9,10 upon target binding. Such target-induced conformational changes can be readily exploited for specific target detection in a variety of applications, including medical diagnostics, environmental monitoring and drug screening.11-13 ...
Standard DNA Aptamer Microarray from LC Sciences,Microarrays designed for DNA aptamer screening and binding optimization and built on the flexible and powerful Paraflo microfluidic on-chip synthesis platform. These microarrays are available as part of our comprehensive DNA/RNA Aptamer Microarray Service. Our Standar,biological,biology supply,biology supplies,biology product
ELRIG are busily preparing for the 8th Annual Drug Discovery conference which will be held at Manchester Convention Centre on 2nd & 3rd September 2014. The programme contain presentations from leading scientists across Europe and beyond, covering exciting advances in basic and translational aspects of drug discovery and brings together Academia, Biotech, Vendors and Pharma into a single community.. Aptamer Group are delighted to be invited back to the Innovation Zone (stand IZ12) for the second year running, where we will be exhibiting our new and exciting technologies. We have over 20 years combined expertise in the development of nucleic acid aptamers to peptides, proteins, cells, tissue samples, micro-organisms and small molecules.. Dr David Bunka, CTO, world leading high-throughput aptamer selection expert will be addressing the Target Validation audience on 3 September at 12.00 in Charter 1. Dr Bunka will be discussing how our technology enables us to greatly speed up the identification of ...
Background: RNA aptamers are small RNA molecules that bind antigens like antibodies and are currently being explored as alternatives to antibodies for diagnosis and therapy. A potential merit of aptamers is that they can be generated against native cellular antigens, such as those with unique post-translational modifications or receptor-ligand complexes, for which antibody generation can be difficult. Here, we report the use of a cell-based systematic enrichment approach (SELEX) to develop a novel Treg-binding RNA aptamer specific to IL2Rα-IL2 receptor-ligand complex.. Methods and Results:. A. Generation of Treg-binding aptamers:. We designed a cell-based SELEX strategy to generate RNA aptamers specific to human T regulatory (Treg) cells. The starting library consisted of random RNA aptamers with a structural diversity of ~1012. Aptamers against common T cell antigens were pre-cleared using CD4+CD25- Teff cells. Treg-binding aptamers were then positively selected using CD4+CD25+ Tregs from the ...
Multitasking by Multivalent Circular DNA Aptamers | Daniel A. Di Giusto; Sarah M. Knox; Yuching Lai; Gregory D. Tyrelle; May T. Aung; Garry C. King | download | BookSC. Download books for free. Find books
and / or polyclonal antibodies specific to a particular target for capture and / or quantitative detection. Most ELISAs employ a 96-well plate-based format. ELISAs are currently used in a wide range of industries, with wide-spread application for the detection of protein biomarkers in research, diagnostics and therapeutics. While antibody-based immunoassays have proven to be very sensitive and specific, there are some limitations which can be overcome with the ELASA, or Enzyme-Linked Aptamer Sorbent Assay. Unlike antibodies, aptamers can be selected for specific binding to poorly immunogenic and toxic compounds. Aptamers can also distinguish between highly conserved molecules. Chemical aptamer synthesis enables rapid, low-cost production of new batches with low lot-to-lot variability. As with traditional ELISAs, ELASAs can be direct, indirect, and sandwich assays. Several sandwich ELASA assays have been developed at Base Pair Biotechnologies. Biotinylated capture aptamers are typically bound to ...
Shigdar, Sarah, Lv, Li, Wang, Lifen and Duan, Wei 2016, Application of aptamers in histopathology. In Mayer, Gunter (ed), Nucleic acid aptamers : selection, characterization and application, Humana Press, New York, N.Y., pp.191-196, doi: 10.1007/978-1-4939-3197-2_16. ...
TY - JOUR. T1 - Oligonucleotide-based systems. T2 - DNA, microRNAs, DNA/RNA aptamers. AU - Jolly, Pawan. AU - Estrela, Pedro. AU - Ladomery, Michael. N1 - Special volume Biosensor technologies for detection of biomolecules (Ed: P. Estrela) PY - 2016/6/30. Y1 - 2016/6/30. N2 - There is an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of DNA, RNA or a synthetic analogue to naturally occurring nucleic acids. This chapter will draw light upon various types of nucleic acids such as DNA, RNA (particularly microRNAs), their role and their application in biosensing. Also, it will cover DNA/RNA aptamers, which can be used as bioreceptors to a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides like PNA or LNA has pushed the ...
endothelial progenitor cells in a porcine myocardial infarction model. Nucleic Acid Therapeutics, 25: 20-26.. Ireson, C. and Kelland, L. (2006): Discovery and development of anticancer aptamers. Molecular Cancer Therapeuics, 5: 2957-2962.. Kaittanis, C., Santra, S. and Perez, J. (2010): Emerging nanotechnologybased strategies for the identification of microbial pathogenesis. Advanced Drug Delivery Reviews, 62: 408-442.Kanamori, H., Yuhashi, K., Uchiyama, Y., Kodama, T., and Ohnishi, S. (2009). In vitro selection of RNA aptamers that bind the RNAdependent RNA polymerase of hepatitis C virus: a possible role of GC-rich RNA motifs in NS5B binding. Virology, 388: 91-102.. Keefe, A., Pai, S. and Ellington, A. (2010). Aptamers as therapeutics. Nature Reviews Drug Discovery, 9: 537-550.. Kikuchi, K., Umehara, T., Fukuda, K., Hwang, J., Kuno, A., Hasegawa, T. and Nishikawa, S. (2003): RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region. Journal of ...
The functionality of aptamers is similar to that of antibodies. Aptamer are selected for specific target molecules by an in vitro selection and amplification method called SELEX. They can recognise and bind their targets with high affinity and specificity. As single-stranded oligonucleotides, aptamers are able to fold into complex and stable three-dimensional structures, which allow them to specifically interact with their targets. Aptamers are receiving increasing attention as alternative affinity reagents and represent essential tools in both basic and applied research. Aptamers can be used to detect and characterise their targets but also to modify the activity of their targets. Therefore, they provide a broad range of applications, e.g., affinity enrichment, analytics, medical diagnostics, or therapy.. Research focuses ...
p,To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to ...
Aptamers are typically selected from libraries of random DNA (or RNA) sequences through systematic evolution of ligands by exponential enrichment (SELEX), which involves several rounds of alternating steps of partitioning of candidate oligonucleotides and their PCR amplification. Here we describe a protocol for non-SELEX selection of aptamers - a process that involves repetitive steps of partitioning with no amplification between them. Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), which is a highly efficient affinity method, is used for partitioning. NECEEM also facilitates monitoring of bulk affinity of enriched libraries at every step of partitioning and screening of individual clones for their affinity to the target. NECEEM allows all clones to be screened prior to sequencing, so that only clones with suitable binding parameters are sequenced. The entire protocol can be completed in 1 wk, whereas conventional SELEX protocols take several weeks even in a specialized
Infectious diseases are a subject of public health safety. In case of events such as bioterrorism or food samples tainted with a disease causing bacteria or virus the standard traditional methods of detection of viral or bacterial detection are too slow. We have developed molecular probes known as ?aptamers? to detect infection with high specificity and sensitivity. Aptamer, a word derived from Latin ?aptus? meaning ?to fit?; are molecular probes which are generated using nucleic acids which recognize and bind their target with a very high affinity and specificity. Aptamers are evolved in vitro in a test tube for its target. Aptamers are generated using a screening process known an SELEX, which stands for Systematic Evolution of Ligands by Exponential Enrichment. A library of 10 14 to 10 16 unique sequences is synthesized. These sequences are fractionated based on interactions with the target for which the aptamer is generated. The weaker binding sequences are weeded out after each successive ... 0 0 Prabodhika Mallikaratchy Prabodhika Mallikaratchy2009-07-30 07:30:062019-05-22 19:52:41Cell-specific aptamer probes for membrane protein elucidation in cancer cells ...
The adenosine aptamer was split into two halves and linked to a fluid liposome surface; addition of adenosine resulted in aptamer assembly, which did not occur if the split aptamer was attached to silica nanoparticles, demonstrating the feasibility of using aptamer probes to study diffusion within lipid membranes ...
Aptamers are an interesting class of molecules that have potential in many facets of human health. They are characterized by high affinity and specificity to their targets, are small in size, have similar properties to antibodies, but are made synthetically. All of these properties, among others, give aptamers the potential to diagnose, image and treat like no other molecules. By combining the unique properties of aptamers with the ever expanding field of nanotechnology and all it has to offer, we are entering a very promising new area of targeted nanodelivery treatments. These treatments have found success in the complex disease processes of cancer, eye and inflammatory diseases ...
LC Sciences provides unique aptamer microarray services using a novel µParaflo technology, a list of aptamer sequences, and sequence design software. The
We have recently described the isolation of 2-fluoropyrimidine-substituted RNA aptamers that bind selectively to disease-associated beta-sheet-rich forms of the prion protein, PrP, from a number of mammalian species. These aptamers inhibit the accumulation of protease-resistant forms of PrP in a prion-seeded, in vitro conversion assay. Here we identify the minimal portions of two of these aptamers that retain binding specificity. We determine their secondary structures by a combination of modeling and solution probing. Finally, we identify an internal site for biotinylation of a minimized, synthetic aptamer and use the resultant reagent in the detection of abnormal forms of PrP in vitro.
Aptamers, synthetic oligonucleotide‐based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets
Membrane Accelerator and Membrane Rudder are both post-translational controlling device to regulate metabolic flux of the host cell. To connect this relatively isolated post-translational control system to genetic circuits, we employed RNA signal, which is present in cytoplasm. Rationally designed RNA D0 with MS2 and PP7 aptamer domain is recruited. When RNA molecule with this two aptamer domains is present in cells, their cognate aptamer binding proteins can thus aggregate together. Furthermore, if we place RNA D0 (with PP7 and MS2 aptamer domains) under various promoters regulated by different signals, approaches to induce dimerization would be expanded sharply. Thus, Membrane Rudder could sense much more signals. We constructed our device as demonstrated in Fig.3. In RNA-sensing Membrane Rudder, VioA, VioB, VioE and VioC with interacting Membrane Anchors constitutively aggregate. RNA D0, can aggregate with RNA aptamer binding protein MS2 and PP7. So when RNA D0 is present, VioD with ...
RNA interference (RNAi) is an important biological process that ultimately leads to suppression of gene expression. Activators of RNAi are typically s.. is the marketplace for research antibodies. Find the right antibody for your research needs. Enzymatic conjugation of multiple proteins on a DNA aptamer in a tail-specific manner.
An Aptamer-siRNA Chimera Suppresses HIV-1 Viral Loads and Protects from Helper CD4+ T Cell Decline in Humanized Mice. C. Preston Neff, Jiehua Zhou, Leila Remling, Jes Kuruvilla, Jane Zhang, Haitang Li, David Smith, Piotr Swiderski, John Rossi and Ramesh Akkina. Science Translational Medicine Vol 3: 66ra6. Yes faithful readers of the MIPnews, for the first time in history we have an MIP laboratory who has garnered back-to-back MIPublication of the Month honors! Ramesh Akkina and his collaborators at the City of Hope have come out with a very exciting approach to harness the awesome power of in vitro-evolved RNA aptamers and RNA interference. In this paper in the Science spin off Science Translational Medicine journal, they report on a form of superdrug that not only effectively targets HIV in cells but appears to overcome one of the main hurdles for these RNA-based technologies - effective in vivo delivery.. Ramesh et al make their superdrug in a very straightforward fashion on a ribonucleic ...
Aptamers are single-stranded RNA or DNA oligonucleotides, which could be screened and synthesized for specific target (including any cell type), using systematic evolution of ligands by exponential enrichment (SELEX) technology..... Read More ...
Kit 30500-050 Kit 30500-096 DNA marker 81-0020 DNA marker 81-0100 DNA marker 82-0100 DNA marker 82-0200 DNA marker 82-0500 DNA marker 82-1000 DNA marker 83-2500 DNA marker 83-5000 DNA Aptamers AD-155-B DNA Aptamers AD-155-F DNA Aptamers AD-155-U Peptide Aptamers AP-302-B Peptide Aptamers AP-302-F Peptide Aptamers AP-302-U Peptide Aptamers AP-304-B Peptide Aptamers AP-304-F Peptide Aptamers AP-304-U Peptide Aptamers AP-306-B Peptide Aptamers AP-306-F Peptide Aptamers AP-306-U Peptide Aptamers AP-308-B Peptide Aptamers AP-308-F Peptide Aptamers AP-308-U Peptide Aptamers AP-309-B Peptide Aptamers AP-309-F Peptide Aptamers AP-309-U Peptide Aptamers AP-310-B Peptide Aptamers AP-310-F Peptide Aptamers AP-310-U Peptide Aptamers AP-312-B Peptide Aptamers AP-312-F Peptide Aptamers AP-312-U Peptide Aptamers AP-315-B Peptide Aptamers AP-315-F Peptide Aptamers AP-315-U Peptide Aptamers AP-318-B Peptide Aptamers AP-318-F Peptide Aptamers AP-318-U Peptide Aptamers AP-319-B Peptide Aptamers AP-319-F Peptide Aptamers
TY - JOUR. T1 - Cancer-targeted Nucleic Acid Delivery and Quantum Dot Imaging Using EGF Receptor Aptamer-conjugated Lipid Nanoparticles. AU - Kim, Min Woo. AU - Jeong, Hwa Yeon. AU - Kang, Seong Jae. AU - Choi, Moon Jung. AU - You, Young Myoung. AU - Im, Chan Su. AU - Lee, Tae Sup. AU - Song, In Ho. AU - Lee, Chang Gun. AU - Rhee, Ki Jong. AU - Lee, Yeon Kyung. AU - Park, Yong Serk. PY - 2017/12/1. Y1 - 2017/12/1. N2 - Co-application of fluorescent quantum dot nanocrystals and therapeutics has recently become a promising theranostic methodology for cancer treatment. We developed a tumor-targeted lipid nanocarrier that demonstrates notable efficacy in gene delivery as well as tumor bio-imaging. Coupling of aptamer molecules against the EGF receptor (EGFR) to the distal termini of lipid nanoparticles provided the carrier with tumor-specific recognition capability. The cationic lipid component, referred to as O,O-dimyristyl-N-lysyl glutamate (DMKE), was able to effectively complex with anionic ...
TY - JOUR. T1 - First-in-human experience of an antidote-controlled anticoagulant using RNA aptamer technology. T2 - A phase 1a pharmacodynamic evaluation of a drug-antidote pair for the controlled regulation of factor IXa activity. AU - Dyke, Christopher K.. AU - Steinhubl, Steven R.. AU - Kleiman, Neal S.. AU - Cannon, Richard O.. AU - Aberle, Laura G.. AU - Lin, Min. AU - Myles, Shelley K.. AU - Melloni, Chiara. AU - Harrington, Robert A.. AU - Alexander, John H.. AU - Becker, Richard C.. AU - Rusconi, Christopher P.. N1 - Copyright: Copyright 2010 Elsevier B.V., All rights reserved.. PY - 2006/12. Y1 - 2006/12. N2 - BACKGROUND - Selectivity, titratability, rapidity of onset, and active reversibility are desirable pharmacological properties of anticoagulant therapy administered for acute indications and collectively represent an attractive platform to maximize patient safety. A novel anticoagulation system (REG1, Regado Biosciences), developed using a protein-binding oligonucleotide to factor ...
TY - JOUR. T1 - A novel RNA aptamer identifies plasma membrane ATP synthase beta subunit as an early marker and therapeutic target in aggressive cancer. AU - Speransky, S.. AU - Serafini, Paolo. AU - Caroli, J.. AU - Bicciato, S.. AU - Lippman, M. E.. AU - Bishopric, N. H.. PY - 2019/1/1. Y1 - 2019/1/1. N2 - Purpose: Primary breast and prostate cancers can be cured, but metastatic disease cannot. Identifying cell factors that predict metastatic potential could guide both prognosis and treatment. Methods: We used Cell-SELEX to screen an RNA aptamer library for differential binding to prostate cancer cell lines with high vs. low metastatic potential. Mass spectroscopy, immunoblot, and immunohistochemistry were used to identify and validate aptamer targets. Aptamer properties were tested in vitro, in xenograft models, and in clinical biopsies. Gene expression datasets were queried for target associations in cancer. Results: We identified a novel aptamer (Apt63) that binds to the beta subunit of F 1 ...
TY - JOUR. T1 - DNA aptamer-based sandwich microfluidic assays for dual quantification and multi-glycan profiling of cancer biomarkers. AU - Jolly, Pawan. AU - Damborsky, P.. AU - Madaboosi, N.. AU - Soares, R.R.G.. AU - Chu, V.. AU - Conde, J.P.. AU - Katrlik, J.. AU - Estrela, Pedro. PY - 2016/5/16. Y1 - 2016/5/16. N2 - Two novel sandwich-based immunoassays for prostate cancer (PCa) diagnosis are reported, in which the primary antibody for capture is replaced by a DNA aptamer. The assays, which can be performed in parallel, were developed in a microfluidic device and tested for the detection of free Prostate Specific Antigen (fPSA). A secondary antibody (Aptamer-Antibody Assay) or a lectin (Aptamer-Lectin Assay) is used to quantify, by chemiluminescence, both the amount of fPSA and its glycosylation levels. The use of aptamers enables a more reliable, selective and controlled sensing of the analyte. The dual approach provides sensitive detection of fPSA along with selective fPSA ...
TY - JOUR. T1 - A sensitive method to detect Escherichia coli based on immunomagnetic separation and real-time PCR amplification of aptamers. AU - Lee, Hye Jin. AU - Kim, Byoung Chan. AU - Kim, Kyung Woo. AU - Kim, Young Keun. AU - Kim, Jungbae. AU - Oh, Min Kyu. PY - 2009/8/15. Y1 - 2009/8/15. N2 - Aptamers, single-stranded nucleic acids, provide a unique opportunity as amplifiable molecules using polymerase chain reaction (PCR) as well as recognition molecules like antibodies. We report a highly sensitive detection of Escherichia coli by taking advantage of the aptamer amplification as well as the specific binding of aptamers onto E. coli. This unique approach consists of three steps. First, the target E. coli was captured by antibody-conjugated magnetic beads. Second, the RNA aptamers were bound onto the surface of captured E. coli in a sandwich way. Finally, the heat-released aptamers were amplified by using real-time reverse-transcriptase-PCR (RT-PCR). The aptamer amplification in this ...
Easy capture and easy release! The cover illustrates a nanostructured platform that combines silicon nanowire arrays and targeted DNA aptamers, realizing significant capture and efficient release of T lymphocytes. This method of capture and release provides an artful strategy to fulfill the demands of cell isolation and diagnostics, as reported by Dong Han, Shutao Wang, and co-workers on page 4376.. ...
Article Aptamer-based and DNAzyme-based biosensors for environmental monitoring. Aptamers and DNAzymes are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure with high specificity to various ligands, such as...
Thrombin is an important serine protease in blood and a therapeutic biomarker. The aptamer-based assays for thrombin take advantage of unique features of nucleic acid aptamers in selection, preparation, stability, and modification of functional groups. Aptamer affinity capillary electrophoresis coupled with
Aptamer selection protocols, named cell-SELEX, have been developed to target trans-membrane proteins using whole living cells as target. This technique presents several advantages. (1) It does not...
摘要:A simple approach based on exfoliating and disintegrating treatments for graphite oxide, followed by hydrothermal synthesis, was developed to prepare water-soluble graphene quantum dots (GQDs). The as-prepared GQDs exhibited bright blue emission under ultraviolet irradiation (similar to 365 nm), and showed an excitation-independent photoluminescence feature. More importantly, a newly anodic electrochemiluminescence (ECL) was observed from the water-soluble GQDs with H2O2 as coreactant for the first time, and the ECL induced a strong light emission at a low potential (ca. 0.4 V vs. Ag/AgCl). The ECL mechanism is investigated in detail. Employing SiO2 nanospheres as signal carrier, a novel SiO2/GQDs ECL signal amplification labels were synthesized based on which a ultrasensitive ECL aptamer sensor was proposed. Under the optimized experimental conditions, the proposed ECL aptamer sensor exhibited excellent analytical performance for adenosine triphosphate (ATP) determination, ranging from ...
The present invention provides an aptamer-based calorimetric sensor system for determining the presence and optionally the concentration of an analyte in a sample. Methods of utilizing the sensor syst
There is currently an urgent need for biomarkers that can be used to monitor the efficacy of experimental therapies for Duchenne Muscular Dystrophy (DMD) in clinical trials. Identification of novel protein biomarkers has been limited due to the massive complexity of the serum proteome and the presence of a small number of very highly abundant proteins. Here we have utilised an aptamer-based proteomics approach to profile 1,129 proteins in the serum of wild-type and mdx (dystrophin deficient) mice. The serum levels of 96 proteins were found to be significantly altered (P | 0.001, q | 0.01) in mdx mice. Additionally, systemic treatment with a peptide-antisense oligonucleotide conjugate designed to induce Dmd exon skipping and recover dystrophin protein expression caused many of the differentially abundant serum proteins to be restored towards wild-type levels. Results for five leading candidate protein biomarkers (Pgam1, Tnni3, Camk2b, Cycs and Adamts5) were validated by ELISA in the mouse samples.
Some bioterrorism agents cause disease at very low infective doses and their presence can be masked by the environment. Therefore, ultrasensitive detection is required for homeland defense applications. In this Phase I research project, Operational Technologies Corporation (OpTech) proposes to couple DNA aptamers made by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process to commercially available fluorescent nanoparticles (NPs, composed of chelated europium in polystyrene). OpTech will demonstrate aptamer-NP-mediated detection of a bacterial, viral, and toxin simulant at low levels. Fluorescent NPs are nanometer-sized plastic and metallic ¿beads¿ that endow superior sensitivity in clinical assays (up to zeptomolar [10-21] detection limits). OpTech also will couple the DNA aptamers to magnetic microbeads and demonstrate magnetic separation and purification of the bioterrorism agent simulants from natural water samples in conjunction with aptamer-fluorescent NP ...
For the development of K(+)-responsive RNA aptamers, we proposed a new general strategy that makes use of a G-quadruplex formation in response to K(+). This is the first report of developing an RNA aptamer that demonstrates ON/OFF switching of its target-binding activity by sensing the addition/removal of K(+).. ...
Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Trying to incorporate quantum dots into biological systems has proven difficult due to their lack of biocompatibility and the toxicity of heavy metals inside cells. Recently developed carbon nanodots retain the advantages of quantum dots, but can function in biological media. Xianogang Qu and researchers at the Chinese Academy of Sciences incorporated carbon nanodots in a thrombin detection assay using DNA aptamers. Thrombin contains two binding sites that are recognized by different aptamers on both a silica nanoparticle and carbon nanodot. The multi-binding site capabilities of aptamers allow for greater sensitivity when compared to single site antibodies, and the fluorescent signal of the carbon nanodot is only detected when bound to thrombin on the silica nanoparticle. Click on the paper below to read more, it will be free to read until November 16th.. Aptamer carbon nanodot sandwich used for fluorescent detection of protein ...
Data accumulated over the latest two decades have established that the serine protease urokinase-type plasminogen activator (uPA) is a potential therapeutic target in cancer. When designing inhibitors of the proteolytic activity of serine proteases, obtaining sufficient specificity is problematic, because the topology of the proteases active sites are highly similar. In an effort to generate highly specific uPA inhibitors with new inhibitory modalities, we isolated uPA-binding RNA aptamers by screening a library of 35 nucleotides long 2′-fluoro-pyrimidine RNA molecules using a version of human pro-uPA lacking the epidermal growth factor-like and kringle domains as bait. One pro-uPA-binding aptamer sequence, referred to as upanap-126, proved to be highly specific for human uPA. Upanap-126 delayed the proteolytic conversion of human pro-uPA to active uPA, but did not inhibit plasminogen activation catalyzed by two-chain uPA. The aptamer also inhibited the binding of pro-uPA to uPAR and the ...
Disclosed are single-stranded DNA molecules which bind adenosine or an adenosine-5-phosphate and methods for their production and isolation. Also disclosed are methods for producing and isolating related catalytic DNA molecules.
Pivotal Scientific Ltd and Base Pair Biotechnologies Partner to Expand Access to Novel Aptamer Technologies to Global Markets. Oxfordshire, UK and Texas, US, June 3, 2013 - Pivotal Scientific Ltd, a consultancy company specialising in developing the international growth of biotech SMEs, and Base Pair Biotechnologies, a specialist developer of novel aptamer based technologies for research and diagnostics, are pleased to announce their collaboration to expand the reach of Base Pair Biotechnologies products and services.. A mainstay of bioscience research is the antibody. Yet standard antibody technologies can take months to produce an antibody against a new target; a long time in the fast paced and global arena of the biosciences. Base Pair Biotechnologies patented development process can turn around aptamers - short strands of DNA or RNA that specifically bind a target with equal specificity and affinity to antibodies - in weeks instead of months, getting researchers the reagents they need ...
2. This paper is also talking about how protein arrays can be self-assembled using DNA nanostructures in the shape of a lattice. The biotin-streptavidin interaction provides only one type of protein-ligand interaction; while it is possible to fuse other proteins with streptavidin, this process is both complicated and may affect the functionality of the proteins themselves during the process. They then introduce aptamers, which are DNA or RNA molecules that have the ability to bind to other molecules such as proteins, nucleic acids, organic compounds, and organisms. There are a wide range of aptamers suited to a variety of proteins that guarantee specificity and high affinity. This method has three components: the DNA lattice nanostructure, a DNA-docking site with the aptamer sequence that will bind the protein of interest to the nanostructure, and the protein itself. In the paper, they use the ...
Systemic administration of the noncompetitive NMDA-receptor antagonist, MK-801, has been proposed to model cognitive deficits similar to those seen in patients with schizophrenia. The present work investigated the ability of a dopamine-binding DNA aptamer to regulate these MK-801-induced cognitive deficits when injected into the nucleus accumbens. Rats were trained to bar press for chocolate pellet rewards then randomly assigned to receive an intra-accumbens injection of a DNA aptamer (200 nM; n = 7), tris buffer (n = 6) or a randomized DNA oligonucleotide (n = 7). Animals were then treated systemically with MK-801 (0.1 mg/kg) and tested for their ability to extinguish their bar pressing response. Two control groups were also included that did not receive MK-801. Data revealed that injection of Tris buffer or the random oligonucleotide sequence into the nucleus accumbens prior to treatment with MK-801 did not reduce the MK-801-induced extinction deficit. Animals continued to press at a high rate over
Background SELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection. Methodology/Principal Findings To evaluate SELEX and assess the extent of these effects, we designed and performed a Neutral SELEX experiment omitting the selection step, such that the sequences are under the sole selective pressure of SELEXs amplification steps. Using high-throughput sequencing, we obtained thousands of full-length sequences from the initial genomic library and the pools after each of the 10 rounds of Neutral SELEX. We compared these to sequences obtained from a Genomic SELEX experiment deriving from the same initial library, but screening for RNAs binding with high affinity to the E.
Dynamical systems are often used to model biochemical and biological processes. In Seo et al. (2010, 2014) we studied two mathematical models of the iterative biochemical procedure known as SELEX (Systematic Evolution of Ligands by EXponential Enrichment): multiple target SELEX and alternate SELEX. It is the purpose of this paper to revisit the mathematics of these processes in the language of dynamical systems on compact manifolds but for a dynamical system on a manifold with compact closure. From the experimentalists point of view, multiple target SELEX provides a way of obtaining the best binding ligands to a pool of several fixed targets, whereas alternate SELEX provides a way to specify which of the best binding ligands also bind best to a specified subtarget. Because these procedures are iterative, it is natural to investigate them in the context of the theory of discrete dynamical systems. Although the iterative schemes are nonautonomous, they have the same limiting properties as two closely
CURRENT STEM CELL NEWS. 1. Bioengineered protein -The latest Therapeutic Invention to fight Leukemia. In a fascinating discovery US scientists have reported a bioengineered protein CD19-L, that can target the CD19-positive leukemic stem cells and destroy them Click to read more... 2. Worlds First RNA Aptamer -The chemical Guided missile against cancer. Deakin University medical scientists along with scientists in India and Australia have created the worlds first RNA aptamer which can act as a cell target missile against cancer cells that in future can help in designing Cell Therapy Bombs against Cancer cells Click to read more... 3. Reprogramming Cells may result in Genomic Aberrations, reveal studies. Recent studies have reported that reprogrammed stem cells exhibit a genomic instability that results in genetic mutations akin to mutations found in cancer cells which has lead to the conclusion that reprogrammed stem cells need to be extensively investigated before applied clinically Click to ...
A new Transparency Market Research report states that the global aptamers market stood at US$0.93 bn in 2012 and is predicted to reach US$4.3 bn by 2019. It...
FNAs), as described by Dr. S.K. Silverman, are DNA and RNA aptamers that bind targets, or they are deoxyribozymes (single stranded DNA) and ribozymes (RNA) that have catalytic activity.,cite,Silverman2012,/cite, Aptamers, Ribozymes, and Deoxyribozymes are grouped into three main categories that are further classified into either natural or artificial depending on their origin. The exception being Deoxyribozymes as they have yet to be discovered in a living organism. Although the first ribozyme was discovered only in the 1980s, the search for new and better FNAs continues. This has led the development of new methodologies, such as the SELEX ,cite,Stozack1990, Gold1990 ,/cite, or In vitro selection, as we strive to expand their potential both as tools for exploring biology and solving real world problem solving ...
AgNCs are complexes between few Ag atoms and a specific DNA sequence template to stabilize the clusters. In most cases, AgNCs are synthesized either at the 3 or 5 end of the template. Our results show that AgNCs can successfully be generated from a template embedded in the middle of a hybridization probe, used for the isothermal amplification of aptamers, called rolling circle amplification (RCA). RCA uses circular oligonucleotide probes to generate long, ssDNA molecules containing periodic repeats of the circular probe.[4][5] Previous works show that overexpression of aptamers by RCA increases target binding efficiency compared to monovalent aptamers.[6] The RCA concatemer combines both the aptamer and the fluorescent AgNC template. Subsequently synthetized AgNCs exhibit strong, robust and tunable fluorescence, eliminating the need for labeling.[7] Importantly, it has been shown that aptamer-AgNCs retain the same specificity and affinity for the cognate protein and that target binding results ...
View PROTEIN DETECTION for MB.BS.pptx from AA 1PROTEIN DETECTION Dr.Sajida Parveen Shaikh OBJECTIVES Define proteins List major body proteins in various body fluids. Proteinuria State Principle of
Flow cytometry has gained popularity and demand in the field of biology because of its accurate analysis and high throughput. The use of multiple lasers, affinity ligands and attached fluorophores allows simultaneous analysis of several markers expressed on thousands of cells per second (Figure 1). Some of the most widely used applications include drug testing, microbiological analysis of bacteria and viruses, cell phenotyping, stem cell research and most importantly detecting cancer cells. Aptamers compete with antibodies in many such applications, in which high-affinity and specificity ligands are needed. Moreover, low specificity and inconsistent labelling of antibodies may lead to significant loss of function and reliability in detecting the target of interest. In this regard, fluorescence-tagged aptamers have shown increased use in flow and imaging cytometry for detecting cells expressing distinct antigens.. ...
Riboswitches are defined as RNA domains at the 5-ends of mRNA that recognize small molecules and respond by changing their three-dimensional structure. This change in turn affects the translation of the mRNA or, sometimes, its premature termination, especially during protein synthesis in the cell, including microbial cells. A riboswitch can be defined as an RNA domain, usually in an mRNA molecule, that can bind a specific small molecule and alter its secondary structure. And this alteration in turn controls translation of the mRNA in the affected cell. Riboswitching as explained above is an important process in molecular biology because it helps to control biosynthetic pathways for amino acids and other metabolites in the cell of an organism. Riboswitches are mostly used to control biosynthetic pathways for amino acids, purines, and other metabolites produced in the cells of microbes.. One of the most interesting findings in molecular biology has been the discovery that RNA molecules can carry ...
The integration of anatomic, molecular, and genomic pathology into surgical pathology practice is conspicuous in oncology, where definition of molecular pathways important for specific tumors has enabled development of new biomarkers and innovative approaches to the detection of cancer and metastases. The so-called liquid biopsy includes a wide array of new technologies, including tumor-derived tumor vesicles and aptamer probes. The surgical pathologist will need to understand these new technologies and be aware of their advantages and pitfalls as they are applied into practice. Upon completion of this educational activity, participants should be able to:. ...
In this study, we investigated the efficacy of an LNA (locked nucleic acid)-modified DNA aptamer named RNV66 targeting VEGF against various breast cancer cell lines. Our results demonstrate that RNV66 efficiently inhibits breast cancer cell proliferation both in vitro and in vivo. Introduction of LNA nucleotides were crucial for higher efficacy. Furthermore, the binding interaction of RNV66 with VEGF was investigated using molecular dynamic simulations leading to the first computational model of the LNA aptamer-VEGF complex blocking its interaction with VEGF-receptor.. ...
My research interests lie in the interface of engineering, nanotechnology and biology towards the utilization of the fundamentals of biomolecular recognition in the development of ultra sensitive diagnostic assays to meet the urgent and critical need for the early diagnosis of disease. My research includes the use of standard biophysical techniques such as, fluorescence anisotropy and SPR to acquire a mechanistic understanding of the details of antibody-antigen and DNA aptamer -protein recognition. It extends to the development of nanoparticle-based assays with main focus on optimizing surface chemistry for controlling specificity and fine tuning of the ligand-analyte detection schemes.. ...
There is growing appreciation that small, non-coding RNAs can participate in gene regulation. Can small RNAs inhibit DNA-binding proteins? We have developed an artificial example by performing in vitro genetic selection experiments identifying a small RNA aptamer that competitively inhibits human transcription factor NF-kappaB binding to DNA in vitro. Optimization by yeast in vivo genetic selections resulted in an RNA that inhibits NF-kappaB in living yeast cells. We have solved the X-ray co-crystal structure of this unusual RNA/NF-I ...
The design and implementation of synthetic biological systems often require information on transcription and translation rates and on the impact of both RNA and protein levels on metabolic activities of host cells. Such information is needed when both strong and low levels of expression are desired, depending on the biologists goal, e.g. high production or cell localization of a protein, respectively. To date, however, quantitative information about the expression strength of a promoter is difficult to obtain due to the lack of noninvasive and quick approaches to measure the levels of RNA and protein in cells. Here, we engineer a fluorescence-based sensor that can provide information on both transcription strength and translation efficiency that is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies. The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating ...
There are surprisingly few ways to directly observe how cells and proteins work inside living creatures. Weian Zhao devised simple sensors that let scientists do exactly that.. Zhao starts by identifying a short, single-stranded piece of DNA called an aptamer that selectively binds with a protein or other biomolecule researchers are interested in. He attaches a fluorescent dye to the aptamer and then attaches the aptamer-dye combination to the surface of a type of stem cell, found in bone marrow and fat tissue, that homes in on inflamed tissue and tumors.. When the combination of dye, aptamer, and stem cell is injected into a living organism, the stem cell seeks out the targeted biomolecules. For example, if researchers want to look at unhealthy tissue, the aptamer latches onto the biomolecule suspected of being at the root of the problem, and the dye lights up or changes color.. By putting mice that have been injected with these sensors under a special microscope designed to hold a living ...
Press release - Transparency Market Research - Aptamer Market to Reflect Impressive Growth Rate by 2025 - published on
SPR imaging platform would be a good choice to characterize aptamer -protein interactions. To study the aptamer-protein ... Thiol groups are introduced on DNA nucleotides by N-hydroxysuccinimide (NHS). Target oligonucleotides having a primary amine ... The interaction of thrombin and the aptamer can be monitored on microarray in real-time during injections of thrombin at ... Daniel, C; Roupioz, Y; Gasparutti, D; Livache, T; Buhot, A (2013). "Solution-Phase vs Surface-Phase Aptamer-Protein Affinity ...
Aptamers have emerged as a novel category in the field of bioreceptors due to their wide applications ranging from biosensing ... Nucleotides with chemically modified sugars and bases have been incorporated into SELEX reactions to increase the chemical ... If a good binding affinity for the selected aptamer is not a concern, then an excess of target can be used to increase the ... There are aptamer applications for which a short sequence, and thus primer truncation, is desirable. An advancement on the ...
These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride. Upon binding ...
BNA nucleotides can be incorporated into DNA or RNA oligonucleotides at any desired position. Such oligomers are synthesized ... design and synthesis of RNA aptamers; siRNA; antisense probes; diagnostics; isolation; microarray analysis; Northern blotting; ... A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible ... BNAs are structurally rigid oligo-nucleotides with increased binding affinities and stability. Chemical structures of BNA ...
incorporated modified nucleotides in aptamers to introduce new confrontational features and high affinity interactions from the ... uses ACE to investigate protein-protein interactions using aptamers. A α-thrombin binding aptamer was labeled with 6- ... Aptamer-based affinity capillary electrophoresis is utilized for the analysis and modifications of specific affinity reagents. ... Modified aptamers ideally exhibit and high binding affinity, specificity, and nuclease resistance. Ren et al. ...
Another example of an RNA aptamer therapeutic is NOX-A12, a 45 nucleotide RNA aptamer that is in clinical trials for chronic ... Broadly, aptamers are small molecules composed of either single-stranded DNA or RNA and are typically 20-100 nucleotides in ... In order to combat some of the in vivo limitations of RNA aptamers, various modifications can be added to the nucleotides to ... Originally approved in 2004 to treat age-related macular degeneration, Pegaptanib is a 28 nucleotide RNA aptamer that acts as a ...
Moreover, Chemically modified nucleotides in siRNA therapeutics improve chemical stability and efficacy, assist in targeting ... aptamers, peptides and antibodies have been covalently linked to siRNA in order to improve cellular uptake and target specific ... Oligonucleotides are single or double-stranded sequences of DNA or RNA of less than 30 nucleotides in length. Small interfering ... Elbashir, S M (2011). "Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells". Nature. 411 (6836 ...
PreQ1-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, compared to the structures of PreQ1-II ... with an average of 58 nucleotides composing its aptamer, which forms as many as five base-paired substructures. PreQ1-III ... Binding of preQ1 to the aptamer domain promotes the sequestration of a part of SD sequence at the 5' end to the P2 stem of the ... In the native mRNA structure, binding of preQ1 to the aptamer region in the riboswitch leads to the formation of a terminator ...
... but lacks most of the highly conserved nucleotides of SAM-III class. SAM-VI aptamers bind the cofactor S-adenosylmethinine SAM ...
This would include the evolution of TNA aptamers that can bind to specific small molecule and protein targets, as well as the ... These structures demonstrate imperfect recognition of the incoming TNA nucleotide triphosphate and support the need for further ... 140, 5706-5713, (2018). Rangel, A. E., Chen, Z., Ayele, T. M. & Heemstra, J. M. In vitro selection of an XNA aptamer capable of ... The availability of TNA polymerases have enabled the in vitro selection of biologically stable TNA aptamers to both small ...
Mutagenesis confirmed that changing nucleotides within the loop regions of this riboswitch altered the specificity for ligand ... classed as novel riboswitches as they deviate in sequence and structure within the loops regions that are required in aptamer ...
... aptamers, nucleotide MeSH D13.695.578.424.450 - oligodeoxyribonucleotides MeSH D13.695.578.424.450.275 - dna primers MeSH ... thymine nucleotides MeSH D13.695.740.706.788 - thymidine monophosphate MeSH D13.695.740.850 - uracil nucleotides MeSH D13.695. ... deoxyguanine nucleotides MeSH D13.695.201.200 - deoxyuracil nucleotides MeSH D13.695.201.200.270 - fluorodeoxyuridylate MeSH ... deoxyadenine nucleotides MeSH D13.695.201.150 - deoxycytosine nucleotides MeSH D13.695.201.150.200 - deoxycytidine ...
Several nucleotide positions are highly conserved, with many around the terminal loops involved in the pseudoknot interaction. ... a mechanism commonly used in engineered aptamers but not previously observed in nature. Cyclic di-GMP-II riboswitches are a ...
Allows construction of Cas9 complexes with protein binding cassettes, artificial aptamers, pools of random sequences as well as ... 80-250 nucleotides) to overcome this limitation. CRISPR-Display can therefore add larger RNA domains, like natural and lncRNA ... artificial aptamers and small molecules with varying size. While all the complexes were functional and viable, and successfully ... insert sequence was also determined through a set of unique sgRNA variants displaying cassettes of 25 random nucleotides. ...
The function of the FMN riboswitch is twofold; first, riboswitches contain an aptamer component, which allows this RNA molecule ... FMN riboswitches also have various magnesium and potassium ions dispersed throughout the nucleotide structure, some of which ... and forms several water-mediated contacts with neighboring nucleotides. ... also suggest that these conformational changes in the structure of the FMN riboswitch are localized to specific nucleotide ...
... is an anticoagulation system cosisting of two drugs: pegnivacogin, a single-stranded 31-nucleotide aptamer that binds and ... Sinha, Gunjan (2013-12-01). "Regado's aptamer lines up against anticoagulants". Nature Biotechnology. 31 (12): 1060. doi: ... a novel actively controlled factor IX inhibitor using RNA aptamer technology for treatment of acute coronary syndrome". Future ... inhibits Factor IXa, and anivamersen, a complementary sequence reversal 15-nucleotide control agent. REG1 mechanism of action ...
... can also be altered by having its nucleotides modified to nucleotides other than A, C, G and U. In eukaryotes, ... structure RNA virus DNA History of RNA Biology List of RNA Biologists RNA Society Macromolecule RNA-based evolution Aptamer RNA ... Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in ... Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto ...
... in position 74 of the aptamer domain, it has been found that conversion of a cytosine to a uracil changes an aptamer from being ... Such a conversion is owed to the ability of a nucleotide in position 74 to Watson-Crick base pair with the ligand in the ... The xpt guanine riboswitch aptamer is stabilized by guanine in a way that allows the riboswitch to more easily bind magnesium, ... In the absence of adenine, the aptamer domain of the riboswitch instead associates with the riboswitch expression platform, ...
... alongside the four naturally occurring nucleotides, and by including individual artificial nucleotides in the culture media, ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... 2006). "An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA". Nat. ... In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, ...
... and aptamer (nucleotide) complex among many other interesting studies. Molecular dynamics is used in many fields of science. ... and a 1063 nucleotide single stranded RNA genome. One key finding is that the capsid is very unstable when there is no RNA ... RNA structure in the ribosome and other large systems has been modeled with one pseudo-atom per nucleotide. Virtual cell ... "Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex". Scientific Reports. 6 (1): 37449. Bibcode: ...
Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of ... One experiment conducted at the University of Florida led to the production of an XNA aptamer by the AEGIS-SELEX (artificially ... Using a genetic code of six XNAs rather than the four naturally occurring DNA nucleotide bases yields endless opportunities for ... in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA have been replaced with other chemical structures. ...
... lacking the first and the last nucleotides of 29-mer form) nucleotides. This aptamer recognizes the exosite II of thrombin, ... Despite that this aptamer only shows moderate effect on fibrinogen regulation, the affinity of this aptamer is slightly higher ... The aptamer HD22 (also known as HTDQ) is an optimized aptamer with 29 (5'-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3') or 27 ( ... These two aptamers have high affinity and good specificity and have been widely studied and used for the development of aptamer ...
Each three-nucleotide codon is translated into one of twenty naturally occurring amino acids. There is at least one tRNA for ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... The 3'-end of the tRNA is mutated from CCA to CGA, while two cytidine nucleotides in the ribosomes A- and P-sites are mutated ... However, by co-mutating the binding nucleotides in such a way, that they can still base pair, the translational fidelity can be ...
AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Chemical analogs of nucleotides can take the place of proper nucleotides and establish ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non- ... The nucleotides, which encoded RNA and proteins, were successfully replicated in vitro. Since then, Benner's team has been ...
Spinach is an 84-nucleotide-long structure with two helical strands and an internal bulge with a G-quadruplex motif. It is at ... The aptamer was designed to be an RNA mimic of green fluorescent protein (GFP); similar to GFP for proteins, Spinach can be ... This aptamer was created using Systematic Evolution for Ligands by EXponential enrichment, or SELEX, which is also known as in ... Spinach is a synthetically derived RNA aptamer born out of the need for a way of studying the role of RNAs at the cellular ...
The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of ... The hachimoji DNA system produced one type of catalytic RNA (ribozyme or aptamer) in vitro. Natural DNA is a molecule carrying ... DNA and RNA are naturally composed of four nucleotide bases that form hydrogen bonds in order to pair. Hachimoji DNA uses an ... In natural DNA, each nucleotide is composed of one of four nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T ...
SELEX is a well known selection method for fabrication and selection of nucleotide aptamers. SELEX is relatively limited by the ... When the probe surface neighboring an aptamer is blocked by an adjacent aptamer, the redox tag on the target-bound aptamer will ... The concentration of aptamer in solution that incubates a clean probe is found to be proportional to the density of aptamers ... In this method, libraries of aptamers are separated into aptamer particles and separated by FACS based on affinity. Only the ...
L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. L-RNA ... L-RNA aptamers themselves have low antigenicity. In contrast to other aptamers, L-RNA aptamers have high stability in blood ... such as PEGylated L-RNA aptamers, show a prolonged plasma half-life. Unlike other aptamers, L-RNA aptamers are not directly ... This information is used for the synthesis of the oligonucleotide's enantiomer, the L-RNA aptamer, using L-nucleotides. L-RNA ...
He isolated the first aptamer (term he used for the first time). He isolated RNA enzymes with RNA ligase activity directly from ... Phosphorimidazolides were first proposed to be critical for early-earth nucleotide polymerization by Leslie E. Orgel and ... "The Mechanism of Nonenzymatic Template Copying with Imidazole-Activated Nucleotides". Angewandte Chemie International Edition. ...
"Optimers as next-generation aptamers". YouTube. Aptamer Group. Retrieved 2021-08-09. "Optimer platform". Aptamer Group. ... The Optimer is trimmed to contain only this sequence, removing additional free non-target binding nucleotide bases. This ... "Aptamer Group, Mologic Ink Deal to Develop Coronavirus Antigen Test". 360Dx. Retrieved 2020-12-02. "APTAMER GROUP AND CYTIVA TO ... Aptamer Group. Retrieved 2021-08-09. "Rapid identification and development of SARS-CoV-2 selective Optimers". Aptamer Group. ...
The main difficulty in using aptamer-based drug delivery is sourcing unique aptamers and other multimers for specific ... Φ29 forms a replication complex involving the p3 terminal protein, the dAMP nucleotide, and its own DNA polymerase to ... incorporates a motor for the delivery of therapeutic molecules like ribozymes and aptamers. The small size of pRNA-derived ...
Yao F, An Y, Li X, Li Z, Duan J, Yang XD (2020-03-27). "Targeted Therapy of Colon Cancer by Aptamer-Guided Holliday Junctions ... Cruciform DNA structures require at least a six nucleotide sequence of inverted repeats to form a structure consisting of a ... This opening has several adenine and thymine nucleotides distal to the inverted repeat. As the unwound section gets larger, ... "Targeted delivery of doxorubicin to cancer cells by a cruciform DNA nanostructure composed of AS1411 and FOXM1 aptamers". ...
... es are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds ... but have more significant differences than a single nucleotide mutation. SAH riboswitches bind S-adenosylhomocysteine to ... as it contains contiguous dual aptamers. Though no longer shown to be cooperative, the cause of dual aptamers still remains ... of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. In 2002, ...
Oki, T.; Yoshimoto, A.; Sato, S.; Takamatsu, A. (1975-12-18). "Purine nucleotide pyrophosphotransferase from Streptomyces ... "Self-Assembled Signaling Aptamer DNA Arrays for Protein Detection". Angewandte Chemie International Edition. 45 (32): 5296-5301 ...
... s are typically 21 nucleotides in length with a 2 nucleotide overhang at the 3' end of each strand, the same structure as ... saRNA by Pancreatic Ductal Adenocarcinoma-specific RNA Aptamers Inhibits Tumor Growth In Vivo". Molecular Therapy. 24 (6): 1106 ...
Ouellet E, Foley JH, Conway EM, Haynes C (August 2015). "Hi-Fi SELEX: A High-Fidelity Digital-PCR Based Therapeutic Aptamer ... Wood-Bouwens CM, Ji HP (2018). "Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant ... Partitioning in digital PCR increases sensitivity and allows for detection of rare events, especially single nucleotide ... occurs when a biomarker exists within a background of a highly abundant counterpart that differs by only a single nucleotide ...
The structure of a nucleic acid molecule consists of a sequence of nucleotides distinguished by which nucleobase they contain. ... and aptamers, which can bind to specific proteins or small molecules. Structural DNA nanotechnology, sometimes abbreviated as ... an actual sequence of nucleotides that will form into the desired structure must be devised. Nucleic acid design is the process ... and the limited chemical diversity of the four nucleotides as compared to the twenty proteinogenic amino acids. The sequences ...
Aptamer - Oligonucleotide or peptide molecules that bind specific targets Ribozyme - Type of RNA molecules Systematic evolution ... The 10-23 DNAzyme contains a 15-nucleotide catalytic core that is flanked by two substrate recognition domains. This DNAzyme ... Spill F, Weinstein ZB, Irani Shemirani A, Ho N, Desai D, Zaman MH (October 2016). "Controlling uncertainty in aptamer selection ... Travascio P, Li Y, Sen D (September 1998). "DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex". Chemistry & ...
March 2008). "Single-nucleotide-specific siRNA targeting in a dominant-negative skin model". The Journal of Investigative ... However recently a large Phase III trial of PEGylated RNA aptamer against factor IX had to be discontinued by Regado ... The mRNA molecule is then cut precisely by cleaving the phosphodiester bond between the target nucleotides which are paired to ... Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (May 2001). "Duplexes of 21-nucleotide RNAs mediate RNA ...
These structures include riboswitches, ribozymes, interaction sites, and aptamers. Aptamer structures allow the binding of ... This is largely a result of four different nucleotides: adenine (A), cytosine (C), guanine (G) and uracil (U), and ability to ...
They consist of artificial peptides or proteins, or aptamer-based nucleic acid molecules with a molar mass of about 3 to 20 kDa ... SHM results in approximately one nucleotide change per variable gene, per cell division. As a consequence, any daughter B cells ... Affimer Anti-mitochondrial antibodies Anti-nuclear antibodies Antibody mimetic Aptamer Colostrum ELISA Humoral immunity ... This mechanism relies on conserved nucleotide motifs, called switch (S) regions, found in DNA upstream of each constant region ...
The type of RNA editing that is most prevalent in higher eukaryotes converts adenosine nucleotides into inosine in dsRNAs via ... Kruspe, S; Giangrande, P (2017). "Aptamer-siRNA Chimeras: Discovery, Progress, and Future Prospects". Biomedicines. 5 (4): 45. ... RNAi has an important role in defending cells against parasitic nucleotide sequences (e.g., viruses or transposons) and also ... 2001). "Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells". Nature. 411 (6836): 494-498. ...
... and one nucleotide unit measured 3.3 Å (0.33 nm) long. Although each individual nucleotide is very small, a DNA polymer can be ... DNA and other nucleic acids are the basis of aptamers, synthetic oligonucleotide ligands for specific target molecules used in ... and T to call the four DNA nucleotides Nucleic acid sequence - Succession of nucleotides in a nucleic acid Ribosomal DNA ... The nucleotides are joined to one another in a chain by covalent bonds (known as the phospho-diester linkage) between the sugar ...
... the second and third nucleotides form a turn in the RNA strand and a base-pair between the first and fourth nucleotides ... The core of malachite green aptamer is also a kind of base quadruplex with a different hydrogen bonding pattern (See Figure). ... Stem-loops can vary greatly in size and sequence, but tetraloops of four nucleotides are very common and they usually belong to ... For example, in GNRA-tetraloop interactions, the second nucleotide of the tetraloop stacks directly on an A-platform motif (see ...
The drug filled DNA tube is held shut by a DNA aptamer, configured to identify and seek certain diseased related protein. Once ... "Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution". Nature Communications. 11 (1): 6229. ... the origami nanobots get to the infected cells, the aptamers break apart and release the drug. The first disease model the ...
Hairpin aptamers are attached to the tetra loop and the stem loop 2 of the sgRNA to become binding sites for dimerized MS2 ... See: Guide RNA, CRISPR A small guide RNA (sgRNA), or gRNA is an RNA with around 20 nucleotides used to direct Cas9 or dCas9 to ... The spacer region has nucleotides that are complementary to those found on the target genes, often in the promoter region. The ... Similar to its unmutated form, dCas9 is used in CRISPR systems along with gRNAs to target specific genes or nucleotides ...
Likewise, the spinach aptamer is an engineered RNA sequence which can bind GFP chromophore chemical mimics, thereby conferring ... Kricka LJ, Fortina P (April 2009). "Analytical ancestry: "firsts" in fluorescent labeling of nucleosides, nucleotides, and ...
Downstream-peptide RNAs overlap a predicted non-coding RNA called yfr6 that is over 200 nucleotides in length, but it was ... Ames TD, Breaker RR (January 2011). "Bacterial aptamers that selectively bind glutamine". RNA Biol. 8 (1): 82-89. doi:10.4161/ ... The most striking similarity is the nucleotide conservation within the P1 stem of both motifs, and this and other similarities ...
L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. L-RNA ... L-RNA aptamers themselves have low antigenicity. In contrast to other aptamers, L-RNA aptamers have high stability in blood ... such as PEGylated L-RNA aptamers, show a prolonged plasma half-life. Unlike other aptamers, L-RNA aptamers are not directly ... This information is used for the synthesis of the oligonucleotides enantiomer, the L-RNA aptamer, using L-nucleotides. L-RNA ...
Split aptamers which are inactive until the halves are brought within close proximity can become useful for visualizing the ... Here, we design and test several sets of F30 Broccoli aptamer splits, that we call fluorets, to compare their relative ... RNA aptamers selected to bind fluorophores and activate their fluorescence offer a simple and modular way to visualize native ... Broccoli Aptamer and Fluoret Assembly. F30-Broccoli RNA or Broc and Coli RNA strands composed of unmodified nucleotides were ...
Nucleotide Biochemistry, Genetics and Molecular Biology 46% * Mutant Medicine and Dentistry 41% ... A synthetic biology approach to fighting Francisella tularensis: Development of aptamer presenting DNA-nanorings. *Brady, R L ( ...
Aptamers are synthetic oligonucleotides selected from a random nucleotide library by the combination of combinatorial chemistry ... Aptamers are immobilized at the gold layer sputtered on a glass prism. The binding of the analyte with aptamers resulted in the ... High efficiency of aptamer selection and the specificity of target interactions make it possible to avoid labor- and time- ... Meanwhile, aptamers are more stable toward oxidation and hydrolysis than antibodies and can be easily modified by the ...
R06, an RNA aptamer, was previously shown to form a kissing complex with the TAR (trans-activating responsive) hairpin of HIV-1 ... the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in ... Aptamers interacting with RNA hairpins through loop-loop (so-called kissing) interactions have been described as an alternative ... Aptamers Targeted to an RNA Hairpin Show Improved Specificity Compared to that of Complementary Oligonucleotides † ...
Base-modified nucleotides are better substrates for DNA polymerases than sugar-modified nucleotides due to the steric gate of ... By providing the additional interactions that are not available in a canonical nucleic acid aptamer, next-generation aptamers ... Aptamers are short nucleic acids that can bind with high affinity to a variety of biological targets through shape ... This aptamer shows 6.5-fold and 9-fold higher binding affinities than the appropriate control sequences which contain non- ...
Aptamer-Assisted Delivery of Nucleotides with Tumor-Suppressing Properties for Targeted Cancer Therapies ...
Also provided herein are pharmaceutical compositions comprising such anti-TNF aptamers and methods for the using the same for ... Nucleic acid aptamers that bind to tumor necrosis factor alpha (TNF). ... Either one or both of the two aptamers in a dimer may comprise a nucleotide sequence of SEQ ID NO: 1. The two anti-TNF aptamers ... 5. The nucleic acid aptamer of claim 1, wherein the aptamer consists of 40-100 nucleotides. ...
In the absence of DA, FAM-aptamer was adsorbed on the surface of GO through π-π stacking interactions between nucleotide bases ... Consequently, the aptamer remains adsorbed on the GO surface inducing the fluorescence quenching. In particular, the aptamer ... FAM-modified aptamer is adsorbed onto the surface of GO via hydrophobic and π-π stacking interaction between the nucleotide ... any known aptamer can be engineered into a molecular aptamer beacon (MBA) that shows a FRET in response to a specific biomarker ...
Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a ... aptamer / protonated adenine / GTP. Function / homology. GUANOSINE-5-TRIPHOSPHATE / RNA / RNA (> 10). Function and homology ... Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.. ... PDB-5lwj: Solution NMR structure of the GTP binding Class II RNA aptamer-li... - ...
Nucleotide Aptamers Medicine & Life Sciences 22% * Microfluidics Engineering & Materials Science 16% * Molecules Engineering & ... A sequence of electrode deprotection and aptamer incubation steps were used to assemble anti-IFN-γ DNA aptamers and anti-TNF-α ... A sequence of electrode deprotection and aptamer incubation steps were used to assemble anti-IFN-γ DNA aptamers and anti-TNF-α ... A sequence of electrode deprotection and aptamer incubation steps were used to assemble anti-IFN-γ DNA aptamers and anti-TNF-α ...
... cholerae GEMM RNAs to determine whether they function as aptamers for cyclic di-GMP. A 110-nucleotide Vc2 RNA construct (110 ...
A library template was synthesized as ssDNA containing a central random region of 40 nucleotides (DNA library: 5-CAC CTA ATA ... The suspensions were washed twice to remove unbound aptamers, then the EN2-aptamer complexes were obtained using binding buffer ... 5- FAM modified aptamers were heated at 95 °C for 5 min then cooled on ice for 1 h in binding buffer prior to use. First, 100 ... Home›Coefficient of Variation›Aptamer-antibody hybrid ELONA that uses hybridization chain reaction to detect a urinary ...
... ribozymes and aptamers. Here, critical advancements have come through the advancement of nucleotide analogues with improved ... Substitution of C for G on the last 3-end nucleotide placement in the MG led to nondetection of RNA transcription or ... Deletions and nucleotide substitutions within the MG 5 end that disrupted terminal complementarity abolished chloramphenicol ... properties over organic nucleotides and lately a number of these such as for example phosphorothioates (8,9), 2-O-Me (10,11), 2 ...
Conversion of RNA Aptamer into Modified DNA Aptamers Provides for Prolonged Stability and Enhanced Antitumor Activity. Amero, P ...
Nucleotide Aptamers 100% * Fibroblast Growth Factor Receptors 58% * SELEX Aptamer Technique 37% ... Development of a Monomeric Inhibitory RNA Aptamer Specific for FGFR3 that Acts as an Activator When Dimerized. Kamatkar, N., ...
An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Kiga, D., Futamura, Y., Sakamoto, K. ... Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA ... In vitro selection of a photoresponsive peptide aptamer to glutathione-immobilized microbeads. Tada, S., Zang, Q., Wang, W., ...
Nucleotide Aptamers 9% * Effects of Fish Oil on Alcoholic Liver Disease in Rats Based on Pathological Mechanisms. Yang, S. ... The Build of Functional Protein Molecular Shuttles by Using a Genetically Engineered Kinesin and Nucleic Acid Aptamers - with ...
... by diminishing the aptamer density and by introducing PR-104 a spacer molecule which consists of 14 additional nucleotides. The ... The aptamer V7t1 was covalently immobilized on polystyrene magnetic beads in a controlled orientation resulting in a ... Conclusions A new aptamer-based affinity purification platform for the Vascular Endothelial Growth Factor was developed and ... this work demonstrates that the aptamer V7t1 is a promising alternative to heparin for VEGF affinity purification. ...
Design of nucleotide aptamers Global Experts from Bangladesh. Global Experts in Subject. ...
This study uses an RNA aptamer i.e. a nucleotide sequence with a unique 3D structure, that is bound by a bacterial ... Finally, by constructing an shRNA-aptamer fusion molecule against cyclin B1 and CDK-1 they were able to show light-dependent ... These findings were extended to an shRNA-aptamer targeting an eGFP reporter. Here they also optimise the hinge region present ... between the aptamer hairpin and dsRNA targeting sequence to find marked differences based on the nucleotides chosen. For ...
Aptamers, NucleotideBiosensing TechniquesElectrochemical TechniquesEuropiumHumansLimit of DetectionLinear ModelsLuminescent ... In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. Extended dsDNA ... In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. Extended dsDNA ... Subsequently, the hybrid between the capture probe and the complementary thrombin binding aptamer (TBA) was aimed at obtaining ...
Nucleotide Aptamers 10% * Capsid Proteins 8% * Biotin 7% * Ligases 7% * Protein Domains 7% ...
Development of RNA aptamers targeting Ebola virus VP35. Binning, J. M., Wang, T., Luthra, P., Shabman, R. S., Borek, D. M., Liu ... Aptamers in virology: Recent advances and challenges. Binning, J. M., Leung, D. W. & Amarasinghe, G. K., 2012, In: Frontiers in ...
Wachowius, F.; Höbartner, C.: Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide ... Wachowius, F.; Javadi Zarnaghi, F.; Höbartner, C.: Combinatorial mutation interference analysis reveals functional nucleotides ...
c) fluorescence images of aptamer-based nanosensors in the. Pas cher commander stéroïdes en ligne expédition dans le monde ... Structural symmetry of dna nucleotides and steroid hormones. Thumbnail image of schaper charles dna steroid symmetry 20200316 ... E1: estrone; e2: estradiol; er: estrogen receptor; t: testosterone;. (c) fluorescence images of aptamer-based nanosensors in ... Structural symmetry of dna nucleotides and steroid hormones. Thumbnail image of schaper charles dna steroid symmetry 20200316. ...
Multiple aptamer-based assay formats including a single and multiplex aptamer-based assay, an aptamer sandwich assay and a " ... process and oligonucleotides having one or more base modified nucleotides (single type or dual type base modified nucleotides) ... Specific nucleic acid aptamer sequence motifs ("sequence families"). *Methods for treating a condition or disease with a ... Methods for detecting and quantifying a single target or multiple targets in a biological sample with an aptamer (SomaScan ...
Nucleosides and nucleotides remain one of the most fruitful drug classes, providing about 50% of antiviral drugs and 20% of ... Nucleosides and Nucleotides: synthetic and biological chemistry 17 April 2015, London, United Kingdom ... Nucleoside and nucleotide chemistry constitute a vibrant field of research for both synthetic and biological chemists. This ... ProTides and phosphorodiamidates as nucleotide pro-drug forms: from the lab to clinical use ...
... and RNA-like systems built from eight nucleotide ... We report DNA- and RNA-like systems built from eight nucleotide ... Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These ...
  • By providing the additional interactions that are not available in a canonical nucleic acid aptamer, next-generation aptamers with high target binding affinity and kinetic are anticipated. (
  • Accordingly, one aspect of the present disclosure features a nucleic acid aptamer that binds TNF and neutralizes the activity of TNF (anti-TNF aptamer). (
  • For example, an anti-TNF nucleic acid aptamer may consist of 40-100 nts. (
  • In some embodiments, the nucleic acid aptamer comprises a nucleic acid motif having the nucleotide sequence of 5′-GCGCCACTACAGGGGAGCTGCCATTCGAATAGGTGGGCCGC-3′ (SEQ ID NO: 1). (
  • In one example, the nucleic acid aptamer comprises the nucleic acid sequence of SEQ ID NO: 1. (
  • In another example, the nucleic acid aptamer consists of the nucleic acid sequence of SEQ ID NO: 1. (
  • In some embodiments, the nucleic acid aptamer is conjugated to a polyethylene (PEG) moiety (e.g., a PEG moiety with a molecular weight of about 15-40 kDa). (
  • In some embodiments, the nucleic acid aptamer is in a dimeric format containing two copies of the nucleic acid aptamer. (
  • In some embodiments, a PEG moiety links the two copies of the nucleic acid aptamer. (
  • In some embodiments, the nucleic acid aptamer is conjugated to a detectable label. (
  • Unlike other aptamers, L-RNA aptamers are not directly made using systematic evolution of ligands by exponential enrichment (SELEX), as L-nucleic acids are not amenable to enzymatic methods, such as polymerase chain reaction (PCR), used in SELEX. (
  • For their uses in SELEX to discover next-generation aptamer, the acceptance of chemically functionalised triphosphates by DNA polymerase is firstly examined. (
  • Especially, 5-propargylamino-iodotriazole-dUTP (5-ITZ-dUTP), a monomer which can potentially allow aptamers to form halogen bonding interaction is used in SELEX. (
  • Aptamers are developed through the SELEX process and over the years these have become primary tools for aptamer synthesis. (
  • Over the past three decades, since the invention of SELEX by Larry Gold and Jack William in the 1990, the technology has seen several modifications to streamline and standardized aptamer-isolation process. (
  • Herein, we apply rG4-SELEX to develop a novel L-RNA aptamer, L-Apt.8f, which binds to APP 3′UTR D-rG4 strongly with subnanomolar affinity. (
  • Nucleic acid aptamers, with a length in the range of 10-100 nucleotides (nt), are identified from an in vitro selection process, systemic evolution of ligands by exponential enrichment (SELEX). (
  • A typical SELEX process flow for aptamer screening includes repetition selection cycle and amplification. (
  • Cell-SELEX identifies aptamers that specifically bind to a certain cell type based on unique cell membrane extracellular characteristics. (
  • They are usually selected from vast oligonucleotide-libraries in an in vitro process termed SELEX (systematic evolution of ligands by exponential enrichment), wherein the oligonucleotides that bind most readily to the target are amplified and their nucleotide sequence is finally identified. (
  • Aside from this immediate software in protein purification, identification of this DNA aptamer demonstrates the feasibility of using SELEX to develop aptamers that block specific antibodies. (
  • Despite being simple, this method may contribute to the process of aptamer design in the future to reduce the number of sequences in the initial SELEX pool, by generating more sequences with similar nucleotides distribution or introducing minor mutations, or through coupling with other more sophisticated approaches. (
  • Aptamers are created via an selection technique called Systematic Progression of Ligands by EXponential enrichment (SELEX) with the recurring partitioning of binders from a big collection of oligonucleotides having a short variety of 1013C1015 arbitrary sequences30,31. (
  • Each circular of aptamer selection in SELEX is conducted by eluting and binding aptamers from focus on substances or cells, leading to selecting aptamers in the collection with high specificity and affinity because of their goals32,33. (
  • Aptamers derive from the combinatorial approach to selection, or SELEX (for Selective Development of Ligands by EXponential enrichment). (
  • Traditional SELEX-based aptamer development requires multiple rounds of amplification that result in PCR bias. (
  • Like its fellow aptamer company Archemix , NOXXON, a Berlin-based, VC-backed private company holds a license to SELEX (Systematic Evolution of Ligands by EXponential Enrichment), a patented method for generating potent aptamer binders. (
  • Like other aptamers, L-RNA aptamers are able to bind molecules such as peptides, proteins, and substances of low molecular weight. (
  • Here we have utilised an aptamer-based proteomics approach to profile 1,129 proteins in the serum of wild-type and mdx (dystrophin deficient) mice. (
  • The DNA aptamer and Flag peptide competed for binding to the M2 antibody, thereby permitting the aptamer to elute Flag-tagged proteins from an immobilized M2 antibody, a generally used process in protein purification. (
  • The outcomes obtained with this research indicate the fantastic potential for the usage of aptamers to identify MGB1 and MGB2 proteins biomarkers, indicated on the top of breasts CTCs. (
  • Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. (
  • Caught in action: selecting Peptide aptamers against intrinsically disordered proteins in live cells. (
  • The lead aptamer demonstrates pM level affinity, high specificity against homolog proteins, and high potency in blocking target signaling. (
  • That's no small feat. The ribosome is a molecular behemoth, made up of three large RNA fragments, consisting of approximately 2900 nucleotide building blocks in total, along with 54 proteins. (
  • Small peptides, especially those derived from natural proteins as inhibitory peptide aptamers (iPAs), can produce highly effective and selective blockade of specific nociceptive molecular pathways to reduce pain with minimal off-target effects. (
  • Aptamers are short nucleic acids that can bind with high affinity to a variety of biological targets through shape complementary. (
  • However, by adding the target, the aptamer undergoes a conformational change to bind to DA with high affinity, resulting in a fluorescence recovery. (
  • Nucleic acid aptamers that bind to tumor necrosis factor alpha (TNF). (
  • Target molecule is incubated along with the oligonucleotide library allowing for nucleic acids to bind to them resulting in the formation of aptamers. (
  • However, selected aptamers cannot bind the same protein expressed from eukaryotic cells because glycosylation, a post-translational modification present only in eukaryotic systems, significantly alters the structure of the target protein. (
  • Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences of approximately 20 - 100 nucleotides that bind specific target molecules with high affinity 1,2 . (
  • As biotechnology is rapidly developing, a plethora of generated aptamers now can bind many kinds of targets, ranging from simple inorganic molecules to large protein complexes, and even entire cells. (
  • Aptamers are short single-stranded DNA- or RNA-based oligonucleotides that can selectively bind to small molecular ligands or protein targets with high affinity and specificity. (
  • Aptamers are short, single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) oligonucleotides, which can take on certain three-dimensional conformations that allow them to bind to a specific target. (
  • In total, six aptamers were found to reliably bind to rituximab within a robust experimental setup. (
  • One of the aptamers was found to also bind to the IgG1 monoclonal antibodies adalimumab and bevacizumab, as well as to the glycosylated Fc fragment of rituximab, suggesting that this aptamer binds to antibody constant regions. (
  • Nucleotide polymers are also able to bind to each other, through hydrogen bonds between the nitrogenous bases. (
  • Aptamers are single-stranded oligonucleotide sequences that specifically bind to target molecules. (
  • In Burke's lab, she works with ribonucleic acid (RNA) aptamers - artificial RNA molecules that bind a particular target. (
  • Its specificity towards various types of the i-motif was confirmed via ELISA and bio-layer interferometry (BLI) which showed that iMab did not bind to any similar structures and molecules (most importantly, it did not bind to various DNA G4 quadruplex forms, such as promoter G4s c-MYC44, BCL245, VEGF, telomeric 2JSM47, 2GKU and aptamer G4 TBA) (Zeraati et al. (
  • Specifically, we are combining data from single nucleotide polymorphisms (SNP), multilocus sequence typing (MLST) and copy number variations (CNVs) to cluster different samples of a pathogen in order to understand their relatedness. (
  • The Eclipse Quencher is a new non-fluorescent quencher that allows DNA detection probes to be used for real time PCR applications such as measuring gene expression or detecting single nucleotide polymorphisms (SNPs). (
  • Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. (
  • This indicates a high unmet need of patients thus, paving a way for aptamer - based solutions due to their advantages over traditional antibody-based therapies. (
  • Flexibility of aptamers offer wider applications as they can be developed against molecules as small as 60 Daltons this means aptamers can target molecules that are ten times smaller than antibody targets. (
  • On one hand, in the clinic of cancer therapy, aptamer-based therapeutics is gaining momentum, which can be used as conventional therapeutic drugs in the same way as monoclonal antibody. (
  • was to assess whether aptamers can be used to evaluate potential structural differences of the therapeutic IgG1 antibody rituximab [2]. (
  • In some full cases, the peptide aptamer from the antinuclear autoantibodies competitively, stopping antibody-mediated injury [10 thus, 11]. (
  • In comparison to their NAV3 broadly-used antibody Fucoxanthin counterparts, aptamers have exclusive properties for the reason that they could be synthesized and also have the capability to end up being chemically improved conveniently, making aptamers far more convenient to make use of as molecular probes for several applications34C36. (
  • In contrast to chemically modified or antibody-based hot start polymerases, NEB's One Taq Hot Start utilizes aptamer technology. (
  • Aptitude scientists published a paper in Angewandte Chemie, reporting unprecedented aptamer specificity and superior performance to commercial antibody product, enabled by our proprietary Multi-Parameter Particle Display technology. (
  • Nucleotide aptamer binds to polymerase through non-covalent bond to inhibit polymerase activity. (
  • E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs. (
  • Moreover, the hOX40 aptamer-streptavidin complex has an apparent binding affinity of ~50 nM for hOX40 on activated T cells as determined by flow cytometry and specifically binds activated human T cells. (
  • The aptamer binds to Taq DNA Polymerase and inhibits the enzyme activity at temperatures below 45°C. This ensures full hot-start functionality. (
  • The affinity of L-RNA aptamers to their target molecules often lies in the pico to nanomolar range and is thus comparable to antibodies. (
  • Aptamer molecules were thiolated for assembly on gold and were functionalized with methylene blue redox reporter for electrochemical signal transduction. (
  • Additionally, aptamers do not require immune response and binding of tertiary aptamer structures to target molecules. (
  • Nucleic acid aptamers have low immunogenicity and can be synthesized chemically in large quantities (mg up to kg) at very high purity and much lower cost than antibodies or other biologically derived therapeutic molecules. (
  • Because of their high affinity for targeted molecules, nucleic acid aptamers have fewer off-target effects than antibodies 1,2 . (
  • With distinctive advantages, aptamers become ideal candidates for diagnostic and therapeutic applications, purification of target molecules from complex mixtures, biosensor design, etc . (
  • In theory, aptamers can be generated for virtually any target molecule irrespective of size or immunogenicity, and they can distinguish between molecules that differ by as little as one methyl group. (
  • Aptamers, the single-stranded nucleic acid analogs of antibodies, hold a great promise in molecular diagnostics, therapeutics, and drug targeting, due to their sensitivity and high selectivity toward target molecules. (
  • When a cell repli- Nucleic acids are nucleotide polymers (from cates itself, identical copies of DNA molecules the Greek word poly, meaning "several", and are produced, therefore the hereditary line of mer, meaning "unit"), that store and transmit descent is conserved, and the genetic informa- genetic information. (
  • L-RNA aptamers, built using L-ribose, are the enantiomers of natural oligonucleotides, which are made with D-ribose. (
  • Oligonucleotides having a single type or dual type base modified nucleotides (e.g. (
  • We offer the Nap-dU CE-Phosphoramidite (NACN5-001) which can be used to incorporate functional diversity into oligonucleotides for aptamer research. (
  • these include antibodies (SERS-CoV- or MERS-CoV-specific), cytokines (cytokines, interferons, interleukins and lymphokines) and RNA therapies (siRNAs, RNA aptamers, ribozymes and antisense oligonucleotides). (
  • These are synthetic, brief (15C100 nucleotides long) one stranded DNA or RNA oligonucleotides that recognize molecular goals, such as for example biomarkers, through a distinctive three-dimensional interaction with the mark with high specificity30 and affinity. (
  • RNA oligonucleotides synthesized using 2′-MOE modifications phosphoramidites have shown to be more nuclease resistant, with lower toxicity, and slightly increased hybridization affinities, making them well suited for therapeutic in vivo applications, such as ASO, siRNA, and aptamers. (
  • Promisingly, a G-quadruplex streptavidin aptamer containing nine 5-ITZ-dUTPs which has a high affinity to the target is discovered. (
  • 4.?Conclusions A new aptamer-based affinity purification platform for the Vascular Endothelial Growth Factor was developed and optimized in a small scale by utilizing magnetic beads. (
  • The aptamer V7t1 was covalently immobilized on polystyrene magnetic beads in a controlled orientation resulting in a functionally active stationary affinity matrix which concomitantly exhibits low unspecific binding. (
  • In summary, this work demonstrates that the aptamer V7t1 is a promising alternative to heparin for VEGF affinity purification. (
  • The interaction between TB and its aptamer led to the dissociation of dsDNA because TB has a higher affinity to TBA than the complementary strands. (
  • Representative aptamer E21 has a dissociation constant (Kd) of 33x10(-9) m, and exhibits high affinity and specificity for EGFRvIII in ELISA and surface plasmon resonance assays. (
  • The project will involve in vitro selection of aptamers with modified nucleotides towards various protein targets, affinity screening of the best aptamer candidates and further developments. (
  • Aptamers as nucleic acid based affinity ligands are more promising than monoclonal antibodies. (
  • Results: Results showed that the binding affinity of the 44 nucleotide aptamer was more than 81 nucleotide aptamer sequence. (
  • As a result, this aptamer could be optimized in order to develop aptamer based affinity chromatography process for this form of recombinant coagulation factor VIIa. (
  • Discussion: Aptamers with shorter length of sequence could show higher affinity in target binding, as they could adapt more easily to suitable conformation according to target interaction. (
  • Another practical method of stop antinuclear antibodies could be to make use of DNA aptamers, provided the high-affinity of the antibodies for proof and DNA of nucleotide bottom specificity. (
  • By combining Partile Display with non-natural nucleotides, Aptitude can harness greatly expanded chemical diversity to enable improved affinity, specificity and success rate. (
  • Aptitude has developed Multi-Parameter Particle Display, enabling simultaneous quantitative measurement of the affinity, specificity, and other desired properties of each aptamer candidate. (
  • In mouse types of systemic lupus erythematosus, tries were designed to stop the function of the cross-reacting antibodies using peptide aptamers, produced either off their cognate peptide self-antigens or from phage screen libraries [10, 11]. (
  • biotechrabbit ApStarTaq™ DNA Polymerase is an aptamer based hot-start enzyme and the first-choice for fast PCR reactions. (
  • An aptamer-based hot-start formulation of the included blood-resistant DNA polymerase prevents false amplification. (
  • LAROVA provides the pivotal ingredients nucleotides, enzymes and additives for diagnostic and research Polymerase Chain Reactions (PCR) and related applications. (
  • Subsequently, the hybrid between the capture probe and the complementary thrombin binding aptamer (TBA) was aimed at obtaining double-stranded DNA (dsDNA). (
  • On the other hand, since the first DNA thrombin aptamer was isolated in 1992, recent research has found that the rapid onset of action and short half-life in vivo suggest that the thrombin aptamer may be useful in anticoagulation with extracorporeal circuits and acute clinical settings like surgical interventions. (
  • Aptamers could also successfully differentiate between native and heat-treated thrombin, whereas antibodies could not [1]. (
  • Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer. (
  • The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer. (
  • Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. (
  • Such an anti-TNF aptamer may comprise a nucleic acid sequence that is at least 85% (e.g., at least 90%, at least 95% or above) identical to SEQ ID NO: 1. (
  • A sequence of electrode deprotection and aptamer incubation steps were used to assemble anti-IFN-γ DNA aptamers and anti-TNF-α RNA aptamers on individually addressable half-ring electrodes. (
  • This study uses an RNA aptamer i.e. a nucleotide sequence with a unique 3D structure, that is bound by a bacterial photoreceptor PAL in the presence of blue light (1). (
  • This aptamer can, in principle, be incorporated into the sequence of any shRNA or miR that targets a gene of interest. (
  • In HEK293 cells stably expressing mCherry-PAL, they co-express these targetable reporters along with a plasmid expressing the miR-21-aptamer sequence. (
  • Here they also optimise the hinge region present between the aptamer hairpin and dsRNA targeting sequence to find marked differences based on the nucleotides chosen. (
  • Aptamers can target cells through the exponential enrichment process, which generates a highly specific DNA sequence by multiple rounds of selection. (
  • Molecular modeling involves the prediction of the secondary structure of RNA from its primary nucleotides sequence, then, building a 3D tertiary structure based on this secondary structure. (
  • In the study, the tyrosine kinase domain of the NT-3 growth factor receptor was used as a target to demonstrate the potential of the bioinformatics methods as promising tools in the area of aptamer design and selection, by employing a complete set of in silico strategies for the development of aptamers, using a simple sequence-based procedure. (
  • 1. A nucleic acid regulatory element for enhancing muscle-specific gene expression comprising at least two diaphragm-specific regulatory elements selected from a diaphragm-specific regulatory element consisting of the nucleotide sequence set forth in SEQ ID NO:2 (e.g. (
  • Dph-CRE02) or a functional fragment thereof, a diaphragm-specific regulatory element consisting of the nucleotide sequence set forth in SEQ ID NO:3 (e.g. (
  • Dph-CRE04) or a functional fragment thereof, and a diaphragm-specific regulatory consisting of the nucleotide sequence set forth in SEQ ID NO:4 (e.g. (
  • and a heart- and skeletal muscle-specific regulatory element consisting of the nucleotide sequence set forth in SEQ ID NO:l (e.g. (
  • 2. The nucleic acid regulatory element according to claim 1 comprising at least: a) the diaphragm-specific regulatory consisting of the nucleotide sequence set forth in SEQ ID NO:4 (e.g. (
  • The consensus is a representation of conserved sequence and secondary-structure features, the degree of conservation of nucleotides and a summary of covarying positions that retain base-pair complementarity. (
  • The nucleotide sequence analysis can be provided in cooperation with external partners, either as a standard service, or in compliance with Good Laboratory Practice (GLP) regulations. (
  • This aptamer shows 6.5-fold and 9-fold higher binding affinities than the appropriate control sequences which contain non-halogen bearing nucleotides (5-propargylamino-prototriazole-dU or canonical dT). (
  • RET, VEGF) located in different regions of DNA (telomeres, centromeres, promoters of proto-oncogenes) which might have distinc nucleotide sequences. (
  • Base-modified nucleotides are better substrates for DNA polymerases than sugar-modified nucleotides due to the steric gate of the enzyme. (
  • Figure 1: Chemical structures of sugar modified nucleotides used in the aptamer generation resulting in increased nuclease resistance : 2'-fluorouridine-5'-triphosphate, 2'-aminouridine-5'-triphosphate, 2'-methoxyuridine-5'-triphosphate and 4'-thiouridine-5'-triphosphate, These are currently not available from Biosearch Technologies as stock items. (
  • An L-ribonucleic acid aptamer (L-RNA aptamer, trade name Spiegelmer) is an RNA-like molecule built from L-ribose units. (
  • The aptamers binding activity was optimized by diminishing the aptamer density and by introducing PR-104 a spacer molecule which consists of 14 additional nucleotides. (
  • Finally, by constructing an shRNA-aptamer fusion molecule against cyclin B1 and CDK-1 they were able to show light-dependent changes in cell-cycle arrest, suggesting that their tool is compatible with biologically relevant functional assays. (
  • Currently, aptamers for small molecule drugs, peptides, dyes and viral particles have been developed successfully. (
  • The Spinach aptamer was featured as the Molecule of the Month on the Protein Data Bank website. (
  • Mass spectrometry-based analyses of these products revealed only minor differences between Reditux and the originator molecule MabThera, suggesting potential fold differences at the respective aptamer binding site. (
  • It's unprecedented that we found an aptamer that can do that, because it's such a minor change to the molecule," Willis said. (
  • The method of synthesis and purification of a nucleoside and/or a nucleotide, a modified nucleoside and/or nucleotide, a DNA molecule and an oligonucleotide library comprising said modified nucleoside and/or nucleotide, and the use of said oligonucleotide library"), zgłoszony pod numerem US 15/760,915 w dniu 16 marca 2018 r. (
  • The principle of this aptasensor is based on fluorescence resonance energy transfer (FRET), where GO was used as energy donor, and a carboxyfluorescein (FAM)-labeled aptamer as acceptor. (
  • In the absence of DA, FAM-aptamer was adsorbed on the surface of GO through π-π stacking interactions between nucleotide bases and the carbon network, leading to a weak FRET and a quenching of the FAM fluorescence. (
  • c) fluorescence images of aptamer-based nanosensors in the. (
  • Spectral tuning by a single nucleotide controls the fluorescence properties of a fluorogenic aptamer. (
  • Several aptamer-based molecular beacons have been designed, such as structure-switching signaling aptamer applied for real-time activation and amplification for fluorescence imaging and targeting therapy. (
  • The dissociation constant of aptamers was calculated using according to the fluorescence index Prism5 software. (
  • Sullenger, B. Nucleic Acid Aptamers as Antithrombotic Agents: Opportunities in Extracellular Therapeutics. (
  • Aptamer-functionalized hydrogels can be programmed to release various and multiple therapeutics when needed through specific nucleic acid recognition and complementary hybridization process, as well as to control cell capture and release. (
  • Who are the key players engaged in the development of aptamer-based therapeutics and technologies? (
  • What is the evolving trend of publications focused on aptamer-based therapeutics and technologies? (
  • Further studies to demonstrate halogen bonding in aptamer-target interaction are required to confirm this as the first example of halogen bonding in aptamer-protein interactions. (
  • To develop targeted therapies for brain tumors, we selected RNA aptamers against the histidine-tagged EGFRvIII ectodomain, using an Escherichia coli system for protein expression and purification. (
  • Our work establishes the feasibility of disrupting protein post-translational modifications in situ with aptamers. (
  • In this study, the authors were able to show for the first time that aptamers are suitable for comparison of an originator biopharmaceutical and its biosimilar(s) when analysed in the native protein conformation. (
  • Identification of novel, therapy-responsive protein biomarkers in a mouse model of Duchenne muscular dystrophy by aptamer-based serum proteomics. (
  • The chimeric structure proposed here consists of an aptamer against the SARS-Cov-2 spike protein (S) and an siRNA against the virus genome. (
  • In all three cases, the selected RNA aptamers interacted selectively with their NBI-74330 related protein focuses on and, in the process, inhibited their blood coagulation activities. (
  • Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. (
  • Saporin is a plant enzyme with N-glycosidase activity that depurinates a specific nucleotide in the ribosomal RNA 28S, thus irreversibly blocking protein synthesis. (
  • Recently, several research groups have reported aptamer-based tumor marker discovery platforms with versatile development potential or multiplexing capabilities. (
  • However, aptamers composed of natural bases are susceptible to nuclease degradation and have a limited range of intermolecular interactions with their targets. (
  • Due to their small size (30-80 nucleotides), they have enhanced ability to penetrate tissues thus, allowing them to reach specific targets efficiently. (
  • In this study, we describe the development of an agonistic aptamer that targets human OX40 (hOX40). (
  • For example, adenine and uridine upstream of the aptamer domain were more effective in blocking shRNA activity. (
  • A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. (
  • The selection of aptamers involves two steps: upstream screening and downstream truncation. (
  • Optical molecular imaging with aptamer-based probes are also a hot topic, which has already been used to image disease associated biomarkers. (
  • Aptamers are effective molecular identification probes30. (
  • Aptamers can be used for synthetic biology applications, molecular therapies and to investigate origin of life questions. (
  • Nevertheless, both RNA and DNA aptamers are important research equipment for dissecting the molecular systems PFI-1 IC50 of viral replication and pathogenesis. (
  • An alternative antiviral approach we propose here relies on an aptamer-siRNA-based system for the treatment of COVID-19. (
  • Therefore, the proposed chimeric aptamer-siRNA-based system might be auspicious in the treatment of COVID-19. (
  • Also provided herein are pharmaceutical compositions comprising such anti-TNF aptamers and methods for the using the same for therapeutic and diagnostic applications, for example, alleviating liver injury and monitoring presence of TNF in vivo or in vitro. (
  • The present disclosure is based on the development of anti-TNFα (i.e.: anti-TNF) nucleic acid aptamers, which suppressed TNF signaling in vitro and attenuated TNF-mediated acute liver injury in vivo. (
  • A fluorescent split aptamer for visualizing RNA-RNA assembly in vivo. (
  • PEGylation protects nucleic acid aptamers from enzymatic degradation in vivo and can extend in vivo serum half-life of these aptamers by increasing the hydrodynamic volume 1-4 . (
  • Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy. (
  • Aptitude has successfully demonstrated the in vivo efficacy of the second aptamer program in preclinical animal models, in collaboration with researchers from Bascom Palmer Eye Institute. (
  • Aptitude has successfully demonstrated the in vivo efficacy and safety of our first therapeutic aptamer program in two different preclinical animal models. (
  • Aptitude has further expanded the capability of Particle Display to uniquely develop fully modified aptamers, which possess optimal in vivo stability for therapeutic applications. (
  • Aptamer development process does not involve animals or living cells thus, making it possible to select aptamers for toxic compounds such as zootoxins and pathogenic bacteria. (
  • Nucleoside and nucleotide chemistry constitute a vibrant field of research for both synthetic and biological chemists. (
  • In this context, fluorescently-labeled aptamers can be used as bioreceptors to develop several aptasensors using FRET as a detection method. (
  • In this paper, we describe the development of micropatterned electrodes functionalized with electroactive aptamers for multiplexed detection of immune-cell-produced cytokines. (
  • Programmable RNA detection with a fluorescent RNA aptamer using optimized three-way junction formation. (
  • Novel technologies using aptamers continue to evolve in precision medicine, providing enormous opportunities for tumor-related biomarker discovery and detection. (
  • Hemin-graphene hybrid nanosheets with intrinsic peroxidase-like activity for label-free colorimetric detection of single-nucleotide polymorphism. (
  • The phosphate and sugar groups are involved in connecting nucleotides with each other, forming a phosphodiester bond. (
  • Single stranded dinucleotides consist of two nucleotides that are linked by a 3'-5' phosphodiester bond via the 3' hydroxyl group of one nucleotide and the 5' hydroxyl group of the other one, just a as bonding occurs in native RNA. (
  • They are abbreviated as pNpN where N stands for any nucleotide and p indicates the phosphodiester bond and remaining 5' phosphate group, respectively. (
  • Biochemical and genetic analyses were carried out with both V. cholerae GEMM RNAs to determine whether they function as aptamers for cyclic di-GMP. (
  • Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. (
  • Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. (
  • Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage. (
  • Zhang, G. Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes. (
  • Aptitude has launched a bispecific therapeutic program which leverages the unique physicochemical properties of aptamers to achieve the effect of combination therapy with a single agent. (
  • Aptitude has completed the in vitro discovery of our first fully-modified therapeutic aptamer. (
  • Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. (
  • RNA structures and cellular applications of fluorescent light-up aptamer. (
  • Development of genetically encodable FRET system using fluorescent RNA aptamers. (
  • Fluorescent RNA aptamers as a tool to study RNA-modifying enzymes. (
  • Today's study builds from your aptamer set chosen by Schneider with half-maximal inhibitory ideals (IC50) of 500 nM. (
  • In contrast to other aptamers, L-RNA aptamers have high stability in blood serum, since they are less susceptible to be cleaved hydrolytically by enzymes. (
  • A 110-nucleotide Vc2 RNA construct (110 Vc2) (Fig. 1A) was subjected to in-line probing (17) in the absence or presence of 100mM cyclic di-GMP (Fig.1B). (
  • Phosphodiesterase 1 bridges glutamate inputs with NO- and dopamine-induced cyclic nucleotide signals in the striatum. (
  • Muhammad is focused on employing computational techniques to design and screen for new types of drugs and targeted therapies such as natural extracts from plants and microbes, RNA aptamers, and short peptides instead of conventional chemotherapies. (
  • Aptamers are an emerging class of highly specific targeting ligands. (
  • Aptamers are highly specific and demonstrate high reproducibility due to the fact that they are chemically synthesized. (
  • In principle we demonstrate reversibility using luciferase as reporter gene and, thus, do believe that this feature might also apply to other shRNA-PAL aptamer constructs. (
  • Our work introduces a novel strategy and reports a new L-aptamer candidate to target APP 3′UTR rG4 structure, which laid the foundation for further applying L-RNA as an important class of biomolecule for practical L-aptamer-based targeting and controlling of gene expression in cells. (
  • Clinical software of RNA aptamers may ultimately take the proper execution of gene therapy, wherein genes that immediate the expression from the restorative aptamer are sent to focus on cells (e.g. (
  • It is my belief that nucleic acids, especially aptamers and RNAi but also some other categories, hold huge promise for drug development , a belief that has been validated by pharma interest in some areas (think RNAi) more than in others (gene therapy). (
  • Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. (
  • And several methods have been developed for aptamer truncation, such as the "rational truncation" approach and the hybridization inhibition approach. (
  • These data offer insight in to the requirements for broad-spectrum RT inhibition by nucleic acidity aptamers. (
  • Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of DNA. (
  • Combinatorial mutation interference analysis reveals functional nucleotides required for DNA catalysis. (
  • Other noteworthy developments in modifications of aptamers, include the addition of functional units of non-nucleic origin and nucleotide modifications, which further improves aptamer performance. (
  • Due to their L-nucleotides, they are highly resistant to degradation by nucleases. (
  • Studies have shown that 3′ end capping (including PEGylation) helps the oligonucleotide chain resist nuclease degradation, while 5′ end PEGylation reduces renal clearance of the aptamer 3 . (
  • To ensure the development of more effective aptamer-based therapies candidates, several players have developed novel aptamer technologies that can be used for research, drug delivery and diagnostic applications. (
  • iii) Chemical substance derivatization could be readily achieved by existing COG3 artificial solutions to adapt confirmed aptamer to a number of delivery and diagnostic systems. (
  • Aptitude has initiated a collaboration with a top diagnostic company to exploit the unique properties of aptamers for applications at the point of care. (
  • Each nucleotide consists of 3 main components: A pentose (containing 5 carbons) sugar group, a phosphate group, and a nitrogenous base. (
  • In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. (
  • We structurally characterize the aptamer and find that it contains a thermostable and parallel G4 motif, and mutagenesis analysis identifies the key nucleotides that are involved in the target recognition. (
  • A strategy for overcoming the delivery challenge of siRNAs is combining them with aptamers, which have achieved success in cell-specific delivery of siRNAs and subsequent target RNA cleavage (7,8). (
  • As a result, a 69-nt aptamer was optimized to have a relatively stable structure and acceptable binding score to the target domain. (
  • These companies have reduced to practice the ability to quickly generate aptamers to almost any target. (
  • As those stress conditions led to different recognition patterns, the involvement of distinct aptamer-rituximab binding epitopes can be anticipated. (
  • L-RNA aptamers are considered potential drugs and are currently being tested in clinical trials. (
  • With great biocompatibility, the use of aptamer-polymer hybrid delivery system is considered as attractive materials for clinical application, which have shown promise in clinical applications for drug delivery. (
  • A second generation Rabbit Polyclonal to ARSI of aptamers was developed, and, among these, some have NBI-74330 entered clinical tests in individuals with blood coagulation disorders [15]. (
  • Direct clinical software of DNA aptamer inhibitors of RT will PFI-1 IC50 demand additional improvements in delivery to the correct focus on cells. (
  • Spiegelmers, the new drug class consisting of mirror-image aptamers created by Germany's NOXXON Pharma , achieved an important clinical milestone this week. (
  • Aptitude has entered into a collaboration with a global leader in clinical diagnostics, who is interested in leveraging aptamers' unique properties to address unmet needs in diagnostics. (
  • While antibodies are highly effective for a wide range of applications, there are unique aptamer advantages that can overcome some difficult scientific challenges. (
  • While both RNA and DNA aptamers to RT have already been explained, DNA aptamers present several exclusive advantages and possibilities. (
  • Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa. (
  • A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer. (
  • Willis works on the latter of the three questions and is characterizing features of an RNA aptamer that can discriminate between the two redox states of Flavin adenine dinucleotide (FAD) - a nucleotide cofactor that appears along with many others in modern metabolism. (
  • Owing to their smaller size than antibodies, aptamers have high biocompatibility, low immunogenicity and toxicity, and better transport and tissue penetration properties. (
  • Nucleosides and nucleotides remain one of the most fruitful drug classes, providing about 50% of antiviral drugs and 20% of cancer drugs used in the UK. (
  • In addition, aptamers could also be used for targeted delivery of drugs and other genetic elements, such as siRNAs, to the cells. (
  • Generally, aptamers and other nucleic-acid-based drugs have not yet fulfilled their initial promise. (
  • If the aptamer can change the redox potential of bound FAD, it could potentially enable redox chemistry, which is essential for life. (