Aptamers, Nucleotide: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.Aptamers, Peptide: Peptide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.Nucleotides: 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)Molecular Sequence Data: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Adenine NucleotidesRNA: 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)Amino Acid Sequence: 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.Guanine NucleotidesOligonucleotides: 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)Oligoribonucleotides: 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.Cloning, Molecular: 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.Purine Nucleotides: Purines attached to a RIBOSE and a phosphate that can polymerize to form DNA and RNA.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.DNA: 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).Sequence Homology, Nucleic Acid: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Directed Molecular Evolution: 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.Protein Binding: 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.Biosensing Techniques: 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.Nucleotides, CyclicDNA, Catalytic: Molecules of DNA that possess enzymatic activity.Guanine Nucleotide Exchange Factors: Protein factors that promote the exchange of GTP for GDP bound to GTP-BINDING PROTEINS.Escherichia coli: 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.Surface Plasmon Resonance: 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.Pyrimidine Nucleotides: Pyrimidines with a RIBOSE and phosphate attached that can polymerize to form DNA and RNA.Gene Library: 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.Kinetics: The rate dynamics in chemical or physical systems.Adenosine Triphosphate: 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.Mutation: 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.Protein Footprinting: 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.DNA Primers: 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.Streptavidin: 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.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Ligands: 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)Polymerase Chain Reaction: 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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.G-Quadruplexes: 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)Nucleic Acids: High molecular weight polymers containing a mixture of purine and pyrimidine nucleotides chained together by ribose or deoxyribose linkages.Combinatorial Chemistry Techniques: 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, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.RNA, Messenger: 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.Plasmids: 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.Genes: 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.Sequence Alignment: 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.Genes, Bacterial: The functional hereditary units of BACTERIA.Fluorine Compounds: Inorganic compounds that contain fluorine as an integral part of the molecule.Adenosine Diphosphate: Adenosine 5'-(trihydrogen diphosphate). An adenine nucleotide containing two phosphate groups esterified to the sugar moiety at the 5'-position.DNA Restriction Enzymes: 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.Genetic Variation: Genotypic differences observed among individuals in a population.Codon: 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).Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Riboswitch: 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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Guanosine Triphosphate: Guanosine 5'-(tetrahydrogen triphosphate). A guanine nucleotide containing three phosphate groups esterified to the sugar moiety.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Open Reading Frames: 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).DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Molecular Probe Techniques: The use of devices which use detector molecules to detect, investigate, or analyze other molecules, macromolecules, molecular aggregates, or organisms.RNA, Catalytic: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Oligodeoxyribonucleotides: 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.Bacterial Proteins: Proteins found in any species of bacterium.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Binding, Competitive: 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.Peptide Library: 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.Thrombin: An enzyme formed from PROTHROMBIN that converts FIBRINOGEN to FIBRIN.Protein Structure, Tertiary: 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.Guanosine Monophosphate: A guanine nucleotide containing one phosphate group esterified to the sugar moiety and found widely in nature.Molecular Probes: 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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.RNA Folding: The processes of RNA tertiary structure formation.Guanosine Diphosphate: A guanine nucleotide containing two phosphate groups esterified to the sugar moiety.Adenosine Monophosphate: Adenine nucleotide containing one phosphate group esterified to the sugar moiety in the 2'-, 3'-, or 5'-position.Thymine Nucleotides: Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)Cytosine NucleotidesNucleic Acid Hybridization: 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)Flexiviridae: 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.Species Specificity: 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.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Consensus Sequence: 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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Genes, Viral: The functional hereditary units of VIRUSES.High-Throughput Nucleotide Sequencing: 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.Promoter Regions, Genetic: 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.Nanotechnology: The development and use of techniques to study physical phenomena and construct structures in the nanoscale size range or smaller.Protein Conformation: 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).Recombinant Proteins: Proteins prepared by recombinant DNA technology.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Microfluidics: 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.Conserved Sequence: 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.Proteins: 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.Cattle: 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.Models, Genetic: 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.Drug Delivery Systems: 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.Electrophoresis, Capillary: 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)Viral Proteins: Proteins found in any species of virus.Haplotypes: 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.Deoxyadenine Nucleotides: Adenine nucleotides which contain deoxyribose as the sugar moiety.Uridine Triphosphate: Uridine 5'-(tetrahydrogen triphosphate). A uracil nucleotide containing three phosphate groups esterified to the sugar moiety.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.DNA-Binding Proteins: 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.DNA Repair: 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.Saccharomyces cerevisiae: 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.Microfluidic Analytical Techniques: Methods utilizing the principles of MICROFLUIDICS for sample handling, reagent mixing, and separation and detection of specific components in fluids.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Templates, Genetic: 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.Introns: 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.Fluorescent Dyes: 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.Deoxyguanine Nucleotides: Guanine nucleotides which contain deoxyribose as the sugar moiety.5' Untranslated Regions: 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.Exons: 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 ...
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 ...
... 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. ...
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 ...
... ,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 ...
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 ...
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
RNA interference (RNAi) is an important biological process that ultimately leads to suppression of gene expression. Activators of RNAi are typically s..
antibody-antibodies.com 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 ...
This will be a randomized, double-masked, controlled, dose-ranging, multi-center comparative trial, in parallel groups. Patients will be stratified by clinical center and foveal thickness to be treated either Macugen or a sham injection. After 24 weeks, all patients will treated with Macugen until the end of the study at 54 weeks ...
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This work demonstrates an aptasensor for ultrasensitive electrochemiluminescence (ECL) detection of thrombin based on an "off-on-off" approach. The system is composed of an Eu3+-doped CdS nanocrystals (CdS:Eu NCs) film on glassy carbon electrode (GCE) as ECL emitter. Then gold nanoparticles (AuNPs) labeled hairpin-DNA probe (ssDNA1) containing thrombin-binding aptamer (TBA) sequence was linked on the NCs film, which led to ECL quenching (off) as a result of Förster-resonance energy transfer (FRET) between the CdS:Eu NC film and the proximal AuNPs. Upon the occurrence of hybridization with its complementary DNA (ssDNA2), an ECL enhancement (on) occurred owing to the interactions of the excited CdS:Eu NCs with ECL-induced surface plasmon resonance (SPR) in AuNPs at large separation. Thrombin could induce ssDNA1 forming a G-quadruplex and cause the AuNPs to be close to CdS:Eu NCs film again, which resulted in an enhanced ECL quenching (off). This "off-on-off" system showed a maximum 7.4-fold ...
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.
DNA and RNA aptamers interact with their target proteins with high selectivity, specificity and affinity. The SELEX method consists of iterative cycles of in vitro screening of a combinatorial oligonucleotide library containing to 1016 different molecules and possible secondary and tertiary structures for target binding followed by PCR amplification of selected sequences. Aptamer ligands can be developed against almost any target protein. Due to the wide spectrum of applications, these novel molecules are used in numerous pharmacological, clinical and industrial processes. In the beginning, RNA and DNA aptamers were identified which bind to proteins that naturally interact with nucleic acids or small molecules such as ATP. In the following years, the use of the SELEX technique was extended in order to isolate oligonucleotide ligands for a wide range of proteins of importance for therapy and diagnostics, such as growth factors (3), cell surface antigens, entire cells and even whole organisms. ...
Patients undergoing pars plana vitrectomy for active PDR with TRD will receive a single intravitreal pre-operative 0.3mg Macugen™ prior to surgery versus sham injection.. Specific timing of the injection will be at no sooner than 7 days and no longer than 14 days prior to surgery.. Patients will receive a preinjection fundus photo and another post injection photo the day of surgery as dictated by the operative schedule.. Some photos may be limited secondary to vitreous hemorrhage. Follow up visits after surgery will be one day, one week, one month, and three months. ...
Aptamers are oligonucleotides that bind ligands-sometimes strongly and sometimes very specifically. They are, or will be, the basis of therapeutics, assays, and sensors. We consider how these molecules are designed and selected, and to what extent computational methods have helped or might help. ...
The Systematic Evolution of Ligands by EXponential enrichment (SELEX) process has allowed the discovery of aptamers with the ability to bind target molecules with high affinity and specificity. This opens up avenues to develop easy, selective and cost-effective methods to monitor aptamer-target interactions. Conventional optical assays involve the functionalization of the termini of an oligonucleotide with a fluorophore and a quencher for detecting analytes. In this work, i utilized nucleic acid staining reagents as chromophores to develop a signaling strategy that avoids synthetic modification of aptamers. Three different aptamers (thrombin-, theophylline-, and ATP-binding aptamers) that span a range of sizes, secondary structures and affinities were employed for this work. I monitored the formation of the fluorescent complex by nucleic acid and chromophore in the presence and absence of a cognate target. My study reveals that the chromophores SYBR Green I and thiazole orange (TO) can be used across
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... DUBLIN November 8 2013 /- ...Research and Markets ( a href http://www.researchandmarkets.com... (Logo: http://photos.prnewswire.com/prnh/2013...Aptamers Market - Technology Trend Analysis By Applications - Therapeu...,Global,Aptamers,Market,Technology,Trend,Analysis,Market,Report,2013-2018:,Therapeutics,,Diagnostics,,Biosensors,,Biomarker/Drug,Discovery,&,Applications,biological,advanced biology technology,biology laboratory technology,biology device technology,latest biology technology
(EMAILWIRE.COM, March 20, 2017 ) According to the report Middle-East and Africa Aptamers Market published by Market Data Forecast, the Middle-East and African market was worth $9.53 million in 2016 and is projected to reach $11.82 million with CAGR of 15.0% by 2021 For full report refer to http://www.marketdataforecast.com/market-reports/middle-east-and-africa-aptamers-market-1139/ Aptamers...
Aptamers are dedicated oligonucleotides that bind in the active center of the polymerase and prevent attachment to nucleic acid targets at temperatures below the optimal reaction temperature of the Tth enzyme. Therefore, no primer elongation occurs during setup of the reaction and the following heating phase prior to the RT step. At higher temperatures, the Aptamers are released from the enzyme, and RT or DNA polymerization can be initiated. In addition, the recommended incubation temperature for RT with Tth (+61°C) is helpful to overcome secondary structures of RNA. This results in highly specific and efficient cDNA synthesis, which leads to highly specific and sensitive PCR ...
This thesis includes the synthesis, conjugation and applications of nano and microparticles for the detection and diagnosis of clinically important units such as cell lysates or proteins. Chapter one presents details of the synthesis and characterization of aptamer-AuNP conjugates for the detection of proteins based on dynamic light scattering. Addition of proteins to aptamer-conjugated gold nanoparticles (AuNPs) induced the formation of dimers, trimers, oligomers or aggregates. The average hydrodynamic diameter of the aggregates as measured by DLS, increased with the corresponding increase in protein concentration. This correlation formed the analytical basis of the assay. A linear dynamic range of up to 300 nM (1800 nm) and Limit of detection of 2.67 was realized using thrombin as the model analyte. This thesis also discusses a novel surface-based method to detect cancer cell membrane using lateral flow technology. This is conceptualized based on familiar streptavidin-biotin and lectin-glycan
Biomarkers are clinical, molecular, or image-based measurable parameters that can characterize an individuals specific biological state, whether normal, pathological or in response to treatment. A biomarker is considered of clinically valuable if: (i) it can be measured repeatedly with accuracy and relatively rapid clinical turnaround, (ii) it provides unique, superior information on patient status, and (iii) it aids in clinical decision-making with high precision1. High-quality biomarkers can critically inform clinical diagnosis (e.g. high-sensitivity troponin for acute myocardial infarction), and guide therapy (e.g. CYP2C19 status for clopidogrel therapy). The ideal biomarkers can further reveal underlying biological processes, inform therapeutic deployment, and pave the way for true personalized precision medicine. In this issue of Circulation, Ngo et al. demonstrates the use of a developing proteomics technology to rapidly screen for protein biomarkers in patients with planned and ...
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Antibodies have now been widely used for clinical treatment of a number of tumors. However, there are serious problems associated with antibody therapy, such as potential interactions of antibodies with the immune system as well as long production cycles. Recently, aptamers have been found to function similar to an
Aptamers Market was valued at USD 2142.8 Million in 2018 and is projected to reach around USD 7456.8 Million by 2025, at a CAGR...
Macugen is injected into the vitreous of the eye using a scleral approach. Once in the vitreous, it is absorbed into the retina and binds with VEGF 165, preventing the VEGF 165 from stimulating new growth of friable, or leaky, blood vessels. These fragile blood vessels are called choroidal neovascularizations. As they leak serum and blood, they damage the macula, resulting in the loss of central vision. This leakage occurs within a short period of time after these blood vessels start to form. It is important to understand that this form of VEGF is not a normal product in a healthy eye.. Macugen needs to be injected every six weeks - not an appealing thought - and patient compliance could be an issue. But the company has two years of data that demonstrate that the procedure is well tolerated with 92 percent of the patients completing the trials. It is unknown at this time how long the therapy will need to be continued. There is a hope that the disease may not need therapy for life, but this is ...
This medication is given by injection into the eye by your doctor (usually an eye doctor) under a local anesthetic.. The usual dose of pegaptanib is 0.3 mg injected into the eye once every 6 weeks. Your doctor may ask you to use antibiotic eye drops for a few days before and after each injection to prevent infection.. Many things can affect the dose of a medication that a person needs, such as body weight, other medical conditions, and other medications. If your doctor has recommended a dose different from the ones listed here, do not change the way that you are taking the medication without consulting your doctor.. It is important this medication be given exactly as recommended by your doctor. If you miss an appointment to receive pegaptanib, contact your doctor as soon as possible to reschedule your appointment.. Store this medication in the refrigerator and do not allow it to freeze. It should be protected from light and kept out of the reach of children.. Do not dispose of medications in ...
SelectScience visited the EDM Millipore booth at Neuroscience 2012 to find out more about the SNAP i.d.® 2.0 Protein Detection System. The new and improved SNAP i.d.® 2.0 Protein Detection System is the second generation of the SNAP i.d.® method for detecting immunoreactive proteins on western blots. With this unique vacuum-driven system, the length of time required for immunodetection is greatly reduced.
Recently, they have improved the sensors reliability and sought new applications for the technology. To sense biological agents, the device takes rapid, direct measurements of the binding of an antigen to a chemical receptor on the waveguide surface. Researchers previously used antibodies as receptors. But they are more expensive and less reliable than aptamers, the synthetic, nucleic-acid-based receptors used in the sensor now, Campbell says. GTRI research scientist Jie Xu has been assisting Campbell with the aptamer work. ...
The regulation of food safety has drastically changed over the past two decades. Today, public and private actors share the responsibility of ensuring safe food. Private standards play a significant role in managing and controlling food safety risks in supply chains as major food retailers and producers increasingly require suppliers to meet these private standards or obtain certification for them. This chapter outlines the architecture of the private regulation of food safety and demonstrates that multiple national and international private actors are involved in the development and implementation of private food safety standards.. ...
In Arabidopsis thaliana, lateral roots (LRs) initiate from anticlinal cell divisions of pericycle founder cells. The formation of LR primordia is regulated antagonistically by the phytohormones cytokinin and auxin. It has previously been shown that cytokinin has an inhibitory effect on the patterning events occurring during LR formation. However, the molecular players involved in cytokinin repression are still unknown. In a similar manner to protoxylem formation in Arabidopsis roots, in which AHP6 (ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6) acts as a cytokinin inhibitor, we reveal that AHP6 also functions as a cytokinin repressor during early stages of LR development. We show that AHP6 is expressed at different developmental stages during LR formation and is required for the correct orientation of cell divisions at the onset of LR development. Moreover, we demonstrate that AHP6 influences the localization of the auxin efflux carrier PIN1, which is necessary for patterning the LR primordia. ...
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 - 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 ...
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...
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. http://www3.interscience.wiley.com.ezp1.harvard.edu/cgi-bin/fulltext/110526995/PDFSTART 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.. ...
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 ...
Press release - Transparency Market Research - Aptamer Market to Reflect Impressive Growth Rate by 2025 - published on openPR.com
Clontech offers three different his tag antibodies and an HA tag antibody for highly sensitive and specific protein detection in Westerns, ELISA and IHC assays.
Clontech offers three different his tag antibodies and an HA tag antibody for highly sensitive and specific protein detection in Westerns, ELISA and IHC assays.
Please join EMD Millipore for a highly technical seminar describing two novel approaches for protein detection, the Direct Detect FTIR system and Multiplexing assays on the Luminex platform. The presentation is suitable for every level of scientist involved in protein research. Both of these technologies enable researchers to more fully understand the complexities of their cell/tissue samples by more accurately quantifying proteins and lipids, saving precious sample volume, and generating dozens of data points from a single biological sample.. Lunch will be provided. Registration is not required for this event.. ...
For the development of specific and effective basic genetic materials to inhibit replication of hepatitis C virus (HCV), HCV genome-targeting trans-splicing aptazyme, which activity is allosterically regulated by a specific ligand, was developed. The aptazyme was designed to be comprised of sequence of RNA aptamer to the ligand, communication module sequence which can transfer structural transition for inducing ribozyme activity upon binding the ligand to the aptamer, and trans-splicing ribozyme targeting +199 nt of HCV IRES. Especially, when the aptamer and the communication module was inserted at both P6 and P8 catalytic domain of the specific ribozyme, allosteric activity of the aptazyme was the most induced. The aptazyme was shown to induce activity of trans-splicing reaction specifically and efficiently only in the presence of the specific ligand, but neither in the absence of any ligand nor in the presence of control ligand. This aptazyme can be used as a specific and effective genetic ...
Identifying targets that are exposed on the plasma membrane of tumor cells, but expressed internally in normal cells, is a fundamental issue for improving the specificity and efficacy of anticancer therpeutics. Using blind cell SELEX (Systemic Evolution of Ligands by EXponetial enrichment) which is untargeted SELEX, we have identified an aptamer, P15, which specifically bound to the human pancreatic adenocarcinoma cells. To identify the aptamer binding plasma membrane protein, liquid chromatography tandem mass spectrometry (LC-MS/MS) was used. The results of this unbiased proteomic mass spectrometry approach identified the target of P15 as the intermediate filament vimentin, biomarker of epithelial mesenchymal transition (EMT), which is an intracellular protein but is specifically expressed on the plasma membrane of cancer cells. As EMT plays a pivotal role to transit cancer cells to invasive cells, tumor cell metastasis assays were performed in vitro. P15 treated pancreatic cancer cells showed ...
The lowly jellyfish, a gelatinous, free-swimming Cnidarian, is an unlikely source of scientific inspiration. Yet, in an article published in this weeks issue of Proceedings of the National Academy of Science, researchers from Harvard, MIT, and the Xian Jiaotong University of China reported an innovative method, inspired by jellyfish tentacles, of isolating and removing tumor cells from blood samples.. This novel technology has the potential to transform cancer diagnostis by facilitating efficient retrieval and analysis of cancer cells from the bloodstream. The study developed microfluidic devices coated in a network of dangling DNA aptamers, or stable strands of synthetic DNA, that can identify and capture particles and cells. Like the tentacles of a jellyfish, which extend into water surrounding the animal to capture food particles, the protruding DNA aptamers were designed to extend into blood samples and bind to a surface protein called tyrosine kinase-7 (PTK-7). Because PTK-7 is ...
This thesis is embedded in the CATAMARAN research project, which is aimed at developing aptamer-based radiopharmaceuticals for targeted radiotherapy and molecular diagnosis of cancers. In this thesis, we attempted to characterize in vitro the binding properties of the DNA aptamer HB5. This aptamer is already described in literature and targets the protein HER2, which is overexpressed in several cancer cells including breast cancer. The first step is the production of HB5 in sufficient quantities. Herefore, we performed asymmetric PCR or PCR with a subsequent separation of the double-stranded PCR product. We can conclude that both techniques are not ideal in the production of HB5, especially regarding the production of pure aptamers. Next, flow cytometry is used to study the binding properties to HER2. We can conclude that a subtile binding can be detected, although it was difficult to confirm. Finally, the chemical toxicity of gallium3+, suitable for molecular imaging, and its decay product of ...
Video articles in JoVE about mercuric chloride include Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques, Chick Heart Invasion Assay for Testing the Invasiveness of Cancer Cells and the Activity of Potentially Anti-invasive Compounds, Production of Germ-Free Fast-Growing Broilers from a Commercial Line for Microbiota Studies, Assessment of Hippocampal Dendritic Complexity in Aged Mice Using the Golgi-Cox Method.
Orit Jacobson1+, Ido D. Weiss2+, Lu Wang3, Zhe Wang1, Xiangyu Yang1, Andrew Dewhurst1, Ying Ma1, Guizhi Zhu1, Gang Niu1, Dale O. Kiesewetter1, Neil Vasdev3, Steven H. Liang3* and Xiaoyuan Chen1* 1Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering; and 2Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD, USA. 3Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital & Department of Radiology, Harvard Medical School, Boston, MA, USA
The detection of biomarkers is of great significance in the diagnosis of numerous diseases, especially cancer. Herein, we developed a sensitive and universal fluorescent aptasensor strategy based on magnetic beads, DNA G-quadruplex, and exonuclease Ⅲ (Exo Ⅲ). In the presence of a target protein, a label-free single strand DNA (ssDNA) hybridized with the aptamer was released as a trigger DNA due to specific recognition between the aptamer and target. Subsequently, ssDNA initiates the Exo Ⅲ-aided recycling to amplify the fluorescence signal, which was caused by N-methylmesoporphyrin Ⅸ (NMM) insertion into the G-quadruplex structure. This proposed strategy combines the excellent specificity between the aptamer and target, high sensitivity of the fluorescence signal by G-quadruplex and Exo Ⅲaided recycling amplification. We selected (50-1200 nmol/L) MUC1, a common tumor biomarker, as the proof-of-concept target to test the specificity of our aptasensor. Results reveal that the sensor ...
Evidence-based recommendations on ranibizumab (Lucentis) and pegaptanib (Macugen) for the treatment of age-related macular degeneration (AMD)
These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride. Upon binding ...
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. ...
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 ...
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 ...
... 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 ... deoxyadenine nucleotides MeSH D13.695.201.150 --- deoxycytosine nucleotides MeSH D13.695.201.150.200 --- deoxycytidine ... monophosphate MeSH D13.695.201.175 --- deoxyguanine nucleotides MeSH D13.695.201.200 --- deoxyuracil nucleotides MeSH D13.695. ...
... 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, ...
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. Some of these replacement ...
... 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, ...
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 ...
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 ...
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to ... 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 ...
... 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 ...
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to ... Kimoto M, Yamashige R, Matsunaga K, Yokoyama S, Hirao I (May 2013). "Generation of high-affinity DNA aptamers using an expanded ... Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non- ... For single-stranded DNA/RNA, units of nucleotides are used-abbreviated nt (or knt, Mnt, Gnt)-as they are not paired. To ...
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 ...
L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. ... 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. ... Like other aptamers, L-RNA aptamers are able to bind molecules such as peptides, proteins, and substances of low molecular ...
A DNA aptamer inhibitor of Autotaxin has also been described. The crystal structures rat and mouse autotaxin have been solved. ... Autotaxin is able to cleave the phosphodiester bond between the α and the β position of triphosphate nucleotides, acting as an ... Gijsbers R, Aoki J, Arai H, Bollen M (March 2003). "The hydrolysis of lysophospholipids and nucleotides by autotaxin (NPP2) ... Clair T, Lee HY, Liotta LA, Stracke ML (January 1997). "Autotaxin is an exoenzyme possessing 5'-nucleotide phosphodiesterase/ ...
The SAM-II riboswitch is short with less than 70 nucleotides and is structurally relatively simple being composed of a single ... Poiata E, Meyer MM, Ames TD, Breaker RR (November 2009). "A variant riboswitch aptamer class for S-adenosylmethionine common in ...
Thus it is possible to change up to about a third of the nucleotides in an open reading frame and still produce the same ... 2013). "Generation of high-affinity DNA aptamers using an expanded genetic alphabet". Nat. Biotechnol. 31: 453-457. doi:10.1038 ... This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which ... They usually employ oligonucleotides of 40-50 nucleotides long that overlap each other. These oligonucleotides are designed to ...
... they did not create mRNA or proteins able to use the artificial nucleotides. The artificial nucleotides featured 2 fused ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... When a nucleotide containing 5-bromouracil is incorporated into the DNA, it is most likely to pair with adenine; however, it ... Artificial nucleotides (Unnatural Base Pairs (UBPs) named d5SICS UBP and dNaM UBP) have been inserted into bacterial DNA but ...
Nanopore and Aptamer Biosensor group{NAB group} G-Quadruplex World - a website to discuss publications and other information of ... QGRS Mapper: a web-based application for predicting G-quadruplexes in nucleotide sequences and NCBI genes from Bagga's group. ... 2011). Potent and selective antisense oligonucleotides targeting single nucleotide polymorphisms in the Huntington disease gene ... where N is any nucleotide base (including guanine). This rule has been widely used in on-line algorithms. Although the rule ...
Gilbert W, Maxam A (1973). "The nucleotide sequence of the lac operator". Proceedings of the National Academy of Sciences of ... Baaske P, Wienken CJ, Reineck P, Duhr S, Braun D (Feb 2010). "Optical Thermophoresis quantifies Buffer dependence of Aptamer ... Bulyk M.L; Johnson P.L; Church G.M (2002). "Nucleotides of transcription factor binding sites exert interdependent effects on ... Schneider TD, Stormo GD, Gold L, Ehrenfeucht A (1986). "Information content of binding sites on nucleotide sequences". Journal ...
... 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, ...
Nucleotide sugars [54]. Monosaccharides. Bacteria, archaea and eukaryotes 3'-Phosphoadenosine-5'-phosphosulfate [55]. Sulfate ... "The tyranny of adenosine recognition among RNA aptamers to coenzyme A". BMC Evol. Biol. 3: 26. doi:10.1186/1471-2148-3-26. PMC ... Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. ... Organic cofactors may have been present even earlier in the history of life on Earth.[65] The nucleotide adenosine is present ...
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 ...
HANDS (Homo-Tag Assisted Non-Dimer System): a nucleotide tail, complementary to the 3' end of the primer is added to the 5' end ... antibody or aptamer are non-covalently bound to the enzyme at low temperature and inhibit its activity. After an incubation of ... nucleotides, ionic strength and temperature of the reaction. This method is somewhat limited by the physical-chemical ... improved specificity and single nucleotide polymorphism detection using blocked cleavable primers". BMC Biotechnology. 11: 80. ...
BDNF has several known single nucleotide polymorphisms (SNP), including, but not limited to, rs6265, C270T, rs7103411, ... Aptamers: Against NGF: RBM-004. *Decoy receptors: LEVI-04 (p75NTR-Fc) ...
By their targeting of short, linear motif type of interactions, peptide aptamers have joined nucleic acid aptamers for use in ... Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, ... We then discuss the opportunities for using aptamers in other complex pathways, including Wnt/β-catenin, and focus on ... We propose that peptide aptamers can provide a very useful and new alternative for interfering with protein-protein ...
These genetic switches are composed of two modular domains consisting of an aptamer and an expression platform. The aptamer is ... A) Predicted secondary structure of the lysC riboswitch in the presence of lysine (OFF state). Nucleotides shared by the ... 2007) A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene ... The region shared by the antisequestering stem (ON state) and the aptamer (OFF state) is represented in red. (B) β- ...
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 ...
In this study, we use corneal model of HSV infection to report the high antiviral activity of a 45 nucleotide DNA aptamer ... Antiviral activity of a 45 nucleotide DNA aptamer during HSV-1 infection of the cornea. ... Antiviral activity of a 45 nucleotide DNA aptamer during HSV-1 infection of the cornea. ... Antiviral activity of a 45 nucleotide DNA aptamer during HSV-1 infection of the cornea.. Invest. Ophthalmol. Vis. Sci. 2017;58( ...
A) Aptamers predicted secondary structure and location of AEGIS nucleotides (in red, P, and green, Z). (B) Binding plots for ... A) Aptamers predicted secondary structure and location of AEGIS nucleotides (in red, P, and green, Z). (B) Binding plots for ... Indeed, the aptamers with the lowest kd contained Z and/or P residues, and were as low as 14 nM, while ACTG-only aptamers had k ... Several aptamers were obtained from deep sequencing, and a quantitative improvement in DNA performance with added nucleotides ...
The present invention provides an aptamer-based calorimetric sensor system for determining the presence and optionally the ... Preferable biomolecules also may include small biomolecules, such as amino acids (e.g. arginine), nucleotides (e.g. ATP, GTP), ... After selecting an appropriate aptamer or aptamers in 120, a linker 128 is formed that includes the aptamer 124. In one aspect ... The aptamer selection 120 may provide one or more aptamers that demonstrate enhanced folding in the presence of the selected ...
Amino acid based antibodies Affinity reagents Aptamers Nucleotides Moleculary imprinted polymers Immunoglobulin Scaffold ... An Enzyme-Linked Aptamer Sorbent Assay to Evaluate Aptamer Binding Matthew D. Moore, Blanca I. Escudero-Abarca, Lee-Ann Jaykus ... Selection of Aptamers Against Whole Living Cells: From Cell-SELEX to Identification of Biomarkers ... Incorporating Aptamers in the Multiple Analyte Profiling Assays (xMAP): Detection of C-Reactive Protein ...
Schematic view of the aptamer molecular recognition principle (Graphic: Regina Stoltenburg, UFZ). nt = nucleotide; RNA = ... The selected aptamer pool is cloned to obtain individual aptamers and the individual aptamers are sequenced. Sequences are ... aptamers can direct the transport of aptamer-nanoparticle conjugates. The binding of the aptamers to the target "anchors" the ... aptamers can direct the transport of the aptamer-nanoparticle conjugate to this target. The subsequent aptamer binding to the ...
7.3.2 Recognition of Non-Nucleotide Compounds 123. 7.3.3 Recognition by Aptamers 124 ... 16.2.8 Nucleic Acids as Recognition Materials for Non-Nucleotide Compounds 361 ...
... an aptamer which specifically bind to EpCAM and which demonstrates superior tumor penetrating ability. ... The present disclosure relates to an RNA aptamer and uses thereof, in particular, ... Aptamer DT3 and control aptamer were described previously (Shigdar S et al, supra), while aptamer 23 is a 19 base nucleotide ... Thus, aptamers are the oligonucleotide analogy to antibodies. In general, aptamers comprise about 15 to about 100 nucleotides, ...
Via hybridization, we detect and differentiate single-nucleotide polymorphisms sans amplification. Paths to temporally resolved ... Rare aptamer sequences are identified via solution-phase SELEX, thereby circumventing target tethering and epitope masking. ... We developed field-effect transistors (FETs) coupled with nucleic-acid receptors (i.e., aptamers), for sensing in situ. ... Target-induced conformational rearrangements of stem-loop aptamers are transduced into conductance changes at nanometer-thin In ...
0 (Aptamers, Nucleotide); 0 (DNA Probes); 0 (Thiazoles); 145563-68-4 (thrombin aptamer); 2390-54-7 (thioflavin T); EC 2.7.7.- ( ... We have developed a label-free assay for the detection of DNA polymerase activity based on a thrombin-binding aptamer (TBA) G- ... In order to achieve a better affinity, this compound has been linked with natural nucleotide at different positions. The ... Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by ...
Nucleotides are color-coded as indicated, here and throughout. (C) Example smFCS assays. Hydrodynamic radius (Rh) values for CP ... 2013) Satellite tobacco necrosis virus (STNV) virus like particle in complex with the B3 aptamer. J Mol Biol 425:1050-1064. ... The inner nucleotide variants form T = 1 capsids with roughly similar efficiency as PS3, confirming that their identities are ... Previously, we identified the highest-affinity STNV PS using RNA SELEX against the cognate CP (31). One aptamer, B3 (Fig. 1B), ...
SELEX with modified nucleotides. Curr Opin Chem Biol 2008;12:448-56. ... Anti-IL4Rα aptamer, irrelevant aptamer, or no aptamer were added to the cultures. PhosphoSTAT6 was evaluated by FACS 2 hours ... plated with or without IL-13 in the presence of anti-IL4Rα aptamer, an irrelevant aptamer or no aptamer. PhosphoSTAT6 was ... Whereas the irrelevant aptamer failed to recognize any beads, the cl.42 aptamer successfully bound to the IL4Rα epoxy beads but ...
... - Xiaoyan Yu, Yimin Gao, Binbin Xue, Xiaohong Wang, Darong ... Aptamers, Nucleotide (isolation & purification, pharmacology) *Cell Line. *Hepacivirus (drug effects, physiology) *Hepatocytes ... NS5A aptamer disrupts the interaction of NS5A with core protein. The data suggest that the aptamers against NS5A protein may ... The mechanisms through which the aptamers exert their antiviral activity were explored. The aptamers NS5A-4 and NS5A-5 inhibit ...
Aptatope mapping of the binding site of a progesterone aptamer on the steroid ring structure. Vasso Skouridou, Thomas Schubert ... In this work we report the mapping of the binding site of the only progesterone aptamer published to date, in an approach ... Aptatope mapping of the binding site of a progesterone aptamer on the steroid ring structure. Analytical biochemistry. 2017 Aug ... This approach can be further exploited for the characterization of aptamer specificity and ultimately facilitate the ...
Aptamer. Telomerase RNA. Small nucleotide fragments. Double Helices. Triple Helices. Quadruple Helices. Protein Function ... Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.. Nat Commun 9 pp.4542 - ... Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.. Nat Commun 9 pp.4542 - ... Structure of HIV-1 Reverse Transcriptase Bound to a 38-mer Hairpin Template-Primer RNA-DNA Aptamer. To Be Published pp. - 0. ...
Therefore, aptamers that bind cell surface receptors have been exploited for the delivery of a variety of cargoes into cells. ... Therefore, relatively few aptamers have been generated that bind cell surface receptors. However, improvements in recombinant ... Several studies have demonstrated that aptamers that bind cell surface receptors may have functions other than just blocking ... This review focuses on recent progress and current challenges in the field of aptamer-mediated delivery. ...
Yeast tRNA and salmon sperm DNA were denatured and sonicated to ≈200 nucleotides before use. Body-labeled DNA library (50-100 ... To monitor aptamer pool binding at various rounds, 32P-labeled DNA was incubated with 2e5 U251 cells per well for 1 h, washing ... ELISA of the Aptamer-Tenascin Interaction. In ELISA format A, wells of the ELISA plate (Corning) were coated overnight at 37°C ... A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment. Dion A. Daniels ...
... riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers ... Aptamers, Nucleotide / chemistry* * Aptamers, Nucleotide / metabolism * Binding Sites * Gene Expression Regulation * Glycine / ... that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the ... riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers ...
Nucleotide Aptamers Related Therapies and Procedures. 1. Quantum Dots (Quantum Dot) 2. Drug Therapy (Chemotherapy) ... 08/08/2006 - "The cell-based aptamer selection holds a great promise in developing specific molecular probes for cancer ... cell-based aptamer selection holds great promise for the development of specific molecular probes for cancer diagnosis and ...
Once the appropriate sequence of nucleotides is known, the aptamers can be easily generated. ... The beauty of the aptamer plus CNT FET sensors is that the aptamers can be easily replaced with new ones that target a ... They found that in the presence of estrogen the short aptamer device produced an electrical signal, while the long aptamer ... "Aptamers are a potentially powerful tool for sensors because they are so versatile and selective," said Natalie Plank, a ...
A highly nuclease-resistant aptamer, Spiegelmer, a mirror-image aptamer built from nucleotides of the nonnatural L-chirality, ... aptamers have also been the subject in the aptamer-based capture assay. In the capture assay applications, aptamers are applied ... As these L-aptamers are mirror images of the natural D-aptamer counterpart of the same sequence, the former is unrecognized by ... One example of aptamer used in the apta-decontaminant assay is the DNA aptamer against arsenite [As(III)] and arsenate [As(V ...
Structural optimization and anti-allergic activity of nucleotide aptamers target to Cε3-Cε4. ...
... nucleotides and their complementary nucleotides; aptamers (nucleotides which bind to a target analyte molecule) and their ... nucleotides, or other active binding substances whose complement, or binding partners, (which are designated herein as "target ... complementary nucleotide sequences; effector/receptor molecules; enzyme cofactors/enzymes; enzyme inhibitors/enzymes; a peptide ...
  • The aptamer is involved in the specific recognition of the metabolite, and the expression platform is used to control gene expression by altering the structure of the mRNA. (pnas.org)
  • The riboswitching action of preQ1 riboswitches in bacteria is regulated by binding of metabolite preQ1 to the aptamer region leading to structural changes in the messenger RNA (mRNA) that governs the downstream genetic regulation. (wikipedia.org)
  • In the native mRNA structure, binding of preQ1 to the aptamer region in the riboswitch leads to the formation of a terminator hairpin which causes RNA polymerase to stop transcription, a process which is commonly known as OFF- regulation of genetic expression or transcription termination. (wikipedia.org)
  • Although PreQ1-II riboswitch also works as queuosine biosynthetic intermediate, the structural and molecular recognition characteristics are distinct from preQ1-I riboswitch, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. (wikipedia.org)
  • In this organism, PreQ1 binding to the riboswitch aptamer is thought to induce premature transcription termination within the leader to down-regulate expression of these genes. (wikipedia.org)
  • Specifically, the colour change caused by their aggregation or disaggregation and connected to the aptamer-target binding reaction has been used in the development of assays and tests. (smw.ch)
  • They are particular suitable for quantum dot-stimulated FRET-based (beacon) aptamer assays . (smw.ch)
  • Reusability of the aptamer and the development of point-of-care apta-decontamination assays are explored before envisaging the potential future trend of the apta-decontamination assay. (hindawi.com)
  • In addition, single-round in vitro transcription assays confirmed that transcription downstream of the predicted transcription terminator was dose dependent and specific to c-di-GMP binding to the riboswitch aptamer. (asm.org)
  • Malachite green binding aptamers were already for screening assays and aptamers in general were lately tested in mammalian cells in vivo (F. Simmel, personal communication). (igem.org)
  • Six rounds of in vitro selection were performed, enriching for xPSM binding as monitored by aptamer inhibition of xPSM N -acetyl-α-linked acid dipeptidase (NAALADase) enzymatic activity. (aacrjournals.org)
  • Employing in vitro selection techniques, we identified an L-aptamer (Spiegelmer®) to S1P designated NOX-S93. (nih.gov)
  • In this study, we use corneal model of HSV infection to report the high antiviral activity of a 45 nucleotide DNA aptamer directed against HSV-1 gD protein. (arvojournals.org)
  • We propose that peptide aptamers can provide a very useful and new alternative for interfering with protein-protein interactions in intracellular signal transduction cascades, including those emanating from activated receptors for growth factors. (mdpi.com)
  • NS5A aptamer disrupts the interaction of NS5A with core protein. (curehunter.com)
  • The data suggest that the aptamers against NS5A protein may exert antiviral effects through inhibiting viral RNA replication, preventing the interaction of NS5A with core protein. (curehunter.com)
  • With cell-based selection, a specific protein target is not always chosen, but selection is performed against a target cell type with the goal of letting the aptamer choose the target. (mdpi.com)
  • Here we characterize the interaction of the DNA aptamer, GBI-10, with tenascin-C, an extracellular protein found in the tumor matrix. (pnas.org)
  • An adapted structure, which includes two binding sites, limits fluorescence of the aptamer to (1) the fluorophore and (2) the protein or small molecule. (wikipedia.org)
  • Thus it is possible to change up to about a third of the nucleotides in an open reading frame and still produce the same protein. (wikipedia.org)
  • This aptamer selectively targets MDSCs and TAM in vivo , blocks IL4Rα signaling, induces MDSCs apoptosis, and significantly delays tumor progression in 4T1-bearing mice. (aacrjournals.org)
  • Here, we show that aptamer-siRNA chimeras (AsiC, an EpCAM aptamer linked to an siRNA sense strand and annealed to the siRNA antisense strand) are selectively taken up and knock down gene expression in EpCAM + cancer cells in vitro and in human cancer biopsy tissues. (aacrjournals.org)
  • The Adenine Riboswitch selectively recognizes adenine, and contains a uracil ribonucleotide in position 74 of the adenine-binding aptamer domain. (wikipedia.org)
  • In this report, the United States Single Nucleotide Polymorphism (SNP) Genotyping market is valued at USD XX million in 2016 and is expected to reach USD XX million by the end of 2022, growing at a CAGR of XX% between 2016 and 2022. (rnrmarketresearch.com)
  • The laboratory specializes in generating modified nucleoside triphosphate analogs used to isolate DNA and RNA aptamers and catalysts. (mt.com)
  • in contrast, the effects of chemical modifications on biostability are well studied using various nucleotide analogs. (hindawi.com)
  • Owing to the limited tolerance for modified substrates of the RNA polymerase (T7 RNA polymerase) used for SELEX, the 2′-methoxy (-OMe) groups need to be replaced with 2′-hydroxy (-OH) groups of natural purine nucleotides after obtaining the precursor from a modified RNA library involving 2′-fluoro (-F) analogs of uridine and cytidine and natural adenosine and guanosine (Figure 1 ). (hindawi.com)
  • A base-paired DNA sequence: ATCGATTGAGCTCTAGCG TAGCTAACTCGAGATCGC The corresponding RNA sequence, in which uracil is substituted for thymine where uracil takes its place in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly point mutations) in DNA replication and DNA transcription. (wikipedia.org)
  • You will learn about the different composition and roles of nucleic acids in the cell, their interactions with each other and the use of ribozymes, aptamers, antisense and hybridization as tools in molecular research. (nottingham.ac.uk)
  • Aptamers can be used for a broad range of applications: While in our case the malachitegreen-binding aptamer is only used for detection of RNA synthesis in response to an antitermination signal, other approaches use aptamers for regulating gene expression and - together with ribozymes - to design logical gates. (igem.org)
  • The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. (biomedcentral.com)
  • They also show that natural cells use allosteric ribozymes to regulate gene expression, a mechanism commonly used in engineered aptamers but not previously observed in nature. (wikipedia.org)
  • Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. (pnas.org)
  • We developed a simple aptamer fluorescence assay for aflatoxin B1 (AFB1) detection by using an array of capillaries. (rsc.org)
  • The 34-nt aptamer having a single fluorescein (FAM) label on the 24th T nucleotide generated a remarkable fluorescence increase upon AFB1 binding. (rsc.org)
  • 1 nm in physiological fluids) to enable direct target quantification over 5 - 6 orders of magnitude and at concentrations well below aptamer-target dissociation constants. (anl.gov)
  • However, target-induced conformational change is hard to control, especially for small-molecule-binding aptamers that have relatively high dissociation constants (∼μM K D ). 14 For example, the well-characterized cocaine-binding aptamer MNS-4.1 ( K D ∼ 5 μM) is structurally stable and forms a three-way junction even before binding cocaine. (rsc.org)
  • Ex-vivo studies on pig corneal models showed therapeutic efficacy of the aptamer in reducing productive infection over a period of 168 hours. (arvojournals.org)
  • In-vivo experiments on mice models exhibited significant decrease in ocular infection through prophylactic, therapeutic and neutralization treatment of corneal tissue with the DNA aptamer. (arvojournals.org)
  • The huge potential of aptamer-nanoparticle-based detection of cancer cells and biomedical in - vivo imaging has been shown, with some examples. (smw.ch)
  • Aptamer-modified nanoparticles for medical applications are developed mostly for the detection of analytes, for biomedical in-vivo imaging and for in-vivo drug delivering. (smw.ch)
  • 11. The aptamer according to claim 9 or 10, wherein the cell is in vivo or in vitro. (freepatentsonline.com)
  • Several aspects of the apta-decontamination assay will be deliberated, which encompasses the functionalization of the aptamer to the usage of the aptamer in decontaminating environment, food sample, and in in vivo application. (hindawi.com)
  • The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs. (nih.gov)
  • This elegant study demonstrates how nucleotide modifications can mitigate against nuclease degradation of aptamers, as vital a concern as is delivery for successful in vivo therapeutic or diagnostic applications,' says Executive Editor Graham C. Parker, PhD, The Carman and Ann Adams Department of Pediatrics, Wayne State University School of Medicine, Children's Hospital of Michigan, Detroit, MI. (news-medical.net)
  • These findings demonstrate the feasibility of using SELEX to develop ssDNA aptamers that block the function of a specific antibody, a capability that could lead to the development of novel therapeutic modalities for patients with systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. (hindawi.com)
  • The bimodular ssDNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC(50) values. (nih.gov)
  • Improving the pharmacokinetic properties of therapeutic aptamers is an important aspect of optimizing their drug-like properties, as discussed in the study published in Nucleic Acid Therapeutics , a peer-reviewed journal from Mary Ann Liebert, Inc. publishers. (news-medical.net)
  • Interferon beta (IFN-β) and interferon -stimulated genes (ISGs) are not induced by the aptamers in HCV-infected hepatocytes. (curehunter.com)
  • A) Effect of aptamer monomer (M) on the level of HS genes measured by conventional RT-PCR. (nih.gov)
  • HS (20 min at 39°C). (B) Effect of both aptamer monomer (M) and dimer (D) on the level of HS genes measured by RT-qPCR. (nih.gov)
  • These genes were not induced by HS and were not inhibited by the aptamer.Figure 4. (nih.gov)
  • citation needed] Because of the large numbers of nucleotide changes made to the original DNA sequence, the only practical way to create the newly designed genes is to use gene synthesis. (wikipedia.org)
  • The spacer region has nucleotides that are complimentary to those found on the target genes, often in the promoter region. (wikipedia.org)
  • In tumor-bearing mice, this anti-IL4Rα aptamer preferentially targeted MDSCs and TAM and unexpectedly promoted their elimination, an effect that was associated with an increased number of tumor-infiltrating T cells and a reduction in tumor growth. (aacrjournals.org)
  • We have probed antigens presented by a monolayer of tumor cells for their ability to interact with a pool of aptamers. (pnas.org)
  • Aptamer-linked siRNAs, known as aptamer-siRNA chimeras (AsiC), have been used in small animal models to treat prostate cancer and prevent HIV infection ( 10-18 ). (aacrjournals.org)
  • siRNAs have a well-defined structure: a short (usually 20 to 24-bp) double-stranded RNA (dsRNA) with phosphorylated 5' ends and hydroxylated 3' ends with two overhanging nucleotides. (wikipedia.org)
  • The conserved sites G 133 K 134 and D 138 K 139 R 140 of C-terminal SmpB were identified by interacting with N-terminal SN, and concurrently the residue K 62 of ArfA was recognized by interacting with the surface loop of the specific peptide aptamer PA-2. (frontiersin.org)