Any technique by which an unknown color is evaluated in terms of standard colors. The technique may be visual, photoelectric, or indirect by means of spectrophotometry. It is used in chemistry and physics. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
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.
Inorganic compounds that contain uranium as an integral part of the molecule.
A method of generating a large library of randomized nucleotides and selecting NUCLEOTIDE APTAMERS by iterative rounds of in vitro selection. A modified procedure substitutes AMINO ACIDS in place of NUCLEOTIDES to make PEPTIDE APTAMERS.
Peptide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.
Observation and acquisition of physical data from a distance by viewing and making measurements from a distance or receiving transmitted data from observations made at distant location.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
A signal transducing adaptor protein and tumor suppressor protein. It forms a complex with activated RECEPTOR-REGULATED SMAD PROTEINS. The complex then translocates to the CELL NUCLEUS and regulates GENETIC TRANSCRIPTION of target GENES.
A receptor-regulated smad protein that undergoes PHOSPHORYLATION by ACTIVIN RECEPTORS, TYPE I. Activated Smad3 can bind directly to DNA, and it regulates TRANSFORMING GROWTH FACTOR BETA and ACTIVIN signaling.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The branch of chemistry dealing with detection (qualitative) and determination (quantitative) of substances. (Grant & Hackh's Chemical Dictionary, 5th ed)
Methodologies used for the isolation, identification, detection, and quantitation of chemical substances.
Materials that have a limited and usually variable electrical conductivity. They are particularly useful for the production of solid-state electronic devices.
The technology of transmitting light over long distances through strands of glass or other transparent material.
Shortened forms of written words or phrases used for brevity.
A CXC chemokine that is found in the alpha granules of PLATELETS. The protein has a molecular size of 7800 kDa and can occur as a monomer, a dimer or a tetramer depending upon its concentration in solution. Platelet factor 4 has a high affinity for HEPARIN and is often found complexed with GLYCOPROTEINS such as PROTEIN C.
Non-nucleated disk-shaped cells formed in the megakaryocyte and found in the blood of all mammals. They are mainly involved in blood coagulation.
A series of progressive, overlapping events, triggered by exposure of the PLATELETS to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
The attachment of PLATELETS to one another. This clumping together can be induced by a number of agents (e.g., THROMBIN; COLLAGEN) and is part of the mechanism leading to the formation of a THROMBUS.
A subnormal level of BLOOD PLATELETS.
A highly acidic mucopolysaccharide formed of equal parts of sulfated D-glucosamine and D-glucuronic acid with sulfaminic bridges. The molecular weight ranges from six to twenty thousand. Heparin occurs in and is obtained from liver, lung, mast cells, etc., of vertebrates. Its function is unknown, but it is used to prevent blood clotting in vivo and vitro, in the form of many different salts.
Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
The act of ligating UBIQUITINS to PROTEINS to form ubiquitin-protein ligase complexes to label proteins for transport to the PROTEASOME ENDOPEPTIDASE COMPLEX where proteolysis occurs.
The process by which a DNA molecule is duplicated.
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.
Human alloantigens expressed only on platelets, specifically on platelet membrane glycoproteins. These platelet-specific antigens are immunogenic and can result in pathological reactions to transfusion therapy.
A condition in newborns caused by immunity of the mother to PLATELET ALLOANTIGENS on the fetal platelets. The PLATELETS, coated with maternal ANTIBODIES, are destroyed and removed by the fetal MONONUCLEAR PHAGOCYTE SYSTEM. Affected infants may have INTRACRANIAL HEMORRHAGES.
Antibodies that are chemically bound to a substrate material which renders their location fixed.
The process of the interaction of BLOOD COAGULATION FACTORS that results in an insoluble FIBRIN clot.
Compounds that interact with ESTROGEN RECEPTORS in target tissues to bring about the effects similar to those of ESTRADIOL. Estrogens stimulate the female reproductive organs, and the development of secondary female SEX CHARACTERISTICS. Estrogenic chemicals include natural, synthetic, steroidal, or non-steroidal compounds.
A space in which the pressure is far below atmospheric pressure so that the remaining gases do not affect processes being carried on in the space.
A group of islands in the southwest Pacific. Its capital is Wellington. It was discovered by the Dutch explorer Abel Tasman in 1642 and circumnavigated by Cook in 1769. Colonized in 1840 by the New Zealand Company, it became a British crown colony in 1840 until 1907 when colonial status was terminated. New Zealand is a partly anglicized form of the original Dutch name Nieuw Zeeland, new sea land, possibly with reference to the Dutch province of Zeeland. (From Webster's New Geographical Dictionary, 1988, p842 & Room, Brewer's Dictionary of Names, 1992, p378)
The study of natural phenomena by observation, measurement, and experimentation.
Cytoplasmic proteins that bind estrogens and migrate to the nucleus where they regulate DNA transcription. Evaluation of the state of estrogen receptors in breast cancer patients has become clinically important.
One of the ESTROGEN RECEPTORS that has marked affinity for ESTRADIOL. Its expression and function differs from, and in some ways opposes, ESTROGEN RECEPTOR BETA.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Nucleic acid aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with very high affinity and specificity, and are generally selected by a process referred to as systematic evolution of ligands by exponential enrichment. Conventional antibody-based therapeutic and diagnostic approach currently employed against biotoxins pose major limitations such as the requirement of a live animal for the in vivo enrichment of the antibody species, decreased stability, high production cost, and side effects. Aptamer technology is a viable alternative that can be used to combat these problems. Fully sequestered in vitro, aptamers eliminate the need for a living host. Furthermore, one of the key advantages of using aptamers instead of antibodies is that they can be selected against very weakly immunogenic and cytotoxic substances. In this review, we focus on nucleic acid aptamers developed against various biotoxins of plant, microorganism, or animal origin and show how ...
TY - JOUR. T1 - BODIPY-labeled fluorescent aptamer sensors for turn-on sensing of interferon-gamma and adenine compounds on cells. AU - Tsuchiya, Akira. AU - Hashim, Siti N.. AU - Ise, Shoko. AU - Furuhata, Takafumi. AU - Kawai, Kiyohiko. AU - Wakabayashi, Rie. AU - Goto, Masahiro. AU - Kamiya, Noriho. AU - Sando, Shinsuke. PY - 2016/1/1. Y1 - 2016/1/1. N2 - An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-? and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a turn-on detection of the target molecule with improved off/on efficiency.. AB - An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-? and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a ...
TY - JOUR. T1 - Nucleic Acid Aptamers as a Potential Nucleus Targeted Drug Delivery System. AU - Shrivastava, Garima. AU - Bakshi, Hamid A.. AU - Aljabali, Alaa A.. AU - Mishra, Vijay. AU - Faruck, Lukmanul Hakkim. AU - Charbe, Nitin B.. AU - Kesharwani, Prashant. AU - Chellappan, Dinesh Kumar. AU - Dua, Kamal. AU - Tambuwala, Murtaza M.. N1 - Email sent to journal requesting confirmation of publication date - awaiting reply (27/4/20). PY - 2020/1/31. Y1 - 2020/1/31. N2 - Background: Nucleus targeted drug delivery provides several opportunities for the treatment of fatal diseases such as cancer. However, the complex nucleocytoplasmic barriers pose significant challenges for delivering a drug directly and efficiently into the nucleus. Aptamers representing single-stranded DNA and RNA qualify as next-generation highly advanced and personalized medicinal agents that successfully inhibit the expression of certain proteins; possess extraordinary gene-expression for manoeuvring the diseased cells ...
TY - JOUR. T1 - Programmable hydrogels for the controlled release of therapeutic nucleic acid aptamers via reversible DNA hybridization. AU - Zhang, Xiaolong. AU - Battig, Mark R.. AU - Wang, Yong. N1 - Copyright: Copyright 2013 Elsevier B.V., All rights reserved.. PY - 2013/10/25. Y1 - 2013/10/25. N2 - Reversible DNA hybridization can be used as a new mechanism to control the sustained and triggered release of therapeutic oligonucleotides from hydrogels.. AB - Reversible DNA hybridization can be used as a new mechanism to control the sustained and triggered release of therapeutic oligonucleotides from hydrogels.. UR - UR - U2 - 10.1039/c3cc45594g. DO - 10.1039/c3cc45594g. M3 - Article. C2 - 24018965. AN - SCOPUS:84884614812. VL - 49. SP - 9600. EP - 9602. JO - Chemical Communications. JF - Chemical Communications. SN - 1359-7345. IS - 83. ER - ...
Human Immunodeficiency Virus (HIV) reverse transcriptase (RT) is the most common molecular target of current HIV treatments. Oligonucleotide aptamers bind and inhibit the RNA- and DNA-dependent polymerization activities of HIV RT. Libraries consisting of aptamers including 32, 70 or 80 nucleotide variable regions were previously screened by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) against RT. Roughly half of the resulting aptamers were represented by pseudoknots with well defined signature sequences (the Family I), but also additional pseudoknots with little sequence convergence (Family II), and non-pseudoknot aptamers (Family III). Nucleic acid aptamers bind RT in the primer/template binding site. Aptamers are generally non-toxic and non-immunogenic molecules making them enticing drug prospects. Many aptamers inhibit DNA dependent DNA polymerization by RT from several phenotypically different recombinant viruses, but inhibition depends on a single amino acid mutation at ...
RNA APTAMERS AGAINST BAFF-R AS CELL-TYPE SPECIFIC DELIVERY AGENTS AND METHODS FOR THEIR USE - In one embodiment, a B cell specific aptamer-siRNA chimera is provided. The B cell specific aptamer-siRNa chimera may include an RNA aptamer that binds BAFF-R and an siRNA molecule conjugated to the RNA aptamer via a nucleotide linker. In another embodiment, a B cell specific RNA aptamer is provided. The RNA aptamer may be a molecule that binds to BAFF-R that has the sequence SEQ ID NO:37, SEQ ID NO:38 or SEQ ID NO:39. In some embodiments, the RNA aptamer is conjugated, via a nucleotide linker, to an siRNA molecule that suppresses expression of one or more target oncogenes in one or more B cells. In one aspect, the one or more target oncogenes are selected from Bcl6, Bcl2, STAT3, Cyclin D1, Cyclin E2 and c-myc. In another embodiment, methods for treating a B cell malignancy in a cancer patient are provided. Such methods may include administering a therapeutically effective amount of a therapeutic ...
Aptamer Solutions Ltd is a York based Biotechnology Company specialising in the custom selection of high-affinity and highly specific nucleic acid aptamers for use in the life sciences sector. Our proprietary automated high-throughput aptamer selection processes allow us to offer a flexible and competitive pricing structure for the development of RNA and DNA aptamers. In addition, we are about to launch a new complementary technology in the area of biomarker discovery.. Our proprietary aptamer based biomarker discovery platform and proprietary combinatorial libraries contain up to and over 1018 different molecules, this diversity and bespoke library design is fundamental to the success of the screening process. This technology enables us to greatly speed up the identification of novel biomarkers as well as diagnostics and/or therapeutic candidate molecules. This technology builds on one of the most powerful uses of aptamer technology, which is the ability for aptamers to be isolated against ...
Macugen (pegaptanib sodium injection) is a sterile, aqueous solution containing pegaptanib sodium for intravitreous injection. Macugen is supplied in a single-dose, pre-filled syringe.
Anti-thrombin aptamers are G-quadruplex-bearing oligonucleotides, which recognizes the exosites of human thrombin. The first anti-thrombin aptamer, TBA, was generated through via SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology in 1992 by L.C. Bock, J.J. Toole and colleagues. A second thrombin-binding aptamer, HD22, recognizes thrombin exosite II and was discovered in 1997 by NeXstar (now Gilead Sciences). These two aptamers have high affinity and good specificity and have been widely studied and used for the development of aptamer-based therapeutics and diagnostics. The aptamer TBA (also known as G15D, HTQ, HD1 or ARC183) is a 15-mer single-stranded DNA with the sequence 5-GGTTGGTGTGGTTGG-3. It interacts with the exosite I of human alpha-thrombin, which is the binding site of fibrinogen, so this aptamer acts as an anti-coagulant agent inhibiting the activation of fibrinogen as well as platelet aggregation. In addition, TBA shows good affinity and specificity ...
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents.
An L-ribonucleic acid aptamer (L-RNA aptamer, trade name Spiegelmer - from German Spiegel mirror - by Noxxon Pharma) is an RNA-like molecule built from L-ribose units. It is an artificial oligonucleotide named for being a mirror image of natural oligonucleotides. L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. Spiegelmers are considered potential drugs and are currently being tested in clinical trials. Spiegelmers, built using L-ribose, are the enantiomers of natural oligonucleotides, which are made with D-ribose. Nucleic acid aptamers, including L-RNA aptamers, contain adenosine monophosphate, guanosine monophosphate, cytidine monophosphate, uridine monophosphate, a phosphate group, a nucleobase and a ribose sugar. Like other aptamers, L-RNA aptamers are able to bind molecules such as peptides, proteins, and substances of low molecular weight. The affinity of L-RNA aptamers to their target molecules often lies in the ...
70846 Oilseed contains sterols and related compounds with economic potential. The extraction and analysis of these compounds would be aided by the availability of highly selective aptamers with high affinities for their particular sterol ligands. This project will develop aptamers for use in microarrays to analyze and extract sterol contents of oil and other biological extracts. Bacterial expression vectors will be prepared from which the aptamers can be expressed in large quantities. In Phase I, one or more DNA aptamers for sitosterol will be selected. The aptamers will be evaluated for their specificity and affinity for sitosterol and related compounds. A bacterial expression vector will be developed from which aptamers can be prepared. Commercial Applications and Other Benefits as described by the awardee: Commercial applications include (1) the use of aptamers in the analysis and extraction of sitosterol and related compounds, and (2) a general method for economically mass-producing DNA ...
Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B
Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B Apple Stem Pitting Virus of PSAH PearIsolate, DNA Aptamer, Biotinylated DNA Aptamers AD-107-B
Human Neutrophil Elastase (DNA I) , DNA Aptamer, Biotinylated DNA Aptamers AD-155-B Human Neutrophil Elastase (DNA I) , DNA Aptamer, Biotinylated DNA Aptamers AD-155-B
After three decades, the human immunodeficiency virus type 1 (HIV-1) remains a global pandemic. It has been difficult to develop therapeutic agents and vaccines against HIV due partly to the virus s ability to mutate rapidly. As a result, there is a constant need to develop new therapeutic agents that target HIV-1. This research seeks to develop an RNA aptamer that would bind tightly to the Pre-Hairpin Intermediate state of the HIV-1 envelope glycoprotein gp41 to inhibit viral fusion. The project targets the envelope glycoprotein of HIV-1, gp41, with nucleic acid aptamers. Aptamers are selected from random pools (libraries) by an in vitro selection called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). The aptamers go through rounds of selection, where the weak binders will be washed off in each round. Once these aptamers are developed, they will be tested for their ability to prevent viral membrane fusion, and their potential use in HIV therapeutics. ...
However, even among aptamers, those nucleic acid aptamers that are polynucleotides (i.e. high-molecular-weight compounds with nucleic acid bases and sugars bound together) are biological high-molecular-weight compounds that offer the below advantages not shown by peptides, proteins or antibodies, and it is hoped that they will be new molecular-targeted agents and molecular-recognition elements.. Advantages of nucleic acid aptamers ...
4DII: High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment). During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometry or microscopy. Some have also been used as drugs by inhibiting or activating functions of their targets in a manner similar to neutralizing or agonistic antibodies. Additionally, it is straightforward to conjugate aptamers to other agents without losing their affinity and they have successfully been used in vitro and in vivo to deliver drugs, siRNA, nanoparticles or contrast agents to target cells. Hence, aptamers identified against cell surface biomarkers represent a promising class of ligands. This review
Aptamers are single-stranded oligonucleotides isolated via in vitro systematic evolution of ligands by exponential enrichment (SELEX),1,2 which can specifically bind to a wide range of targets including proteins, small molecules and metal ions.3 Aptamers offer several advantages as recognition elements for biosensor applications relative to antibodies. First, aptamers can be chemically synthesized with high reproducibility at relatively low cost.4,5 Second, the high chemical stability of DNA aptamers means that they can be used under harsher conditions and stored with a longer shelf life.6 Finally, it is possible to generate unstructured aptamers that form specific secondary structures such as three-way junctions7,8 or tertiary folds such as G-quadruplex structures9,10 upon target binding. Such target-induced conformational changes can be readily exploited for specific target detection in a variety of applications, including medical diagnostics, environmental monitoring and drug screening.11-13 ...
Standard DNA Aptamer Microarray from LC Sciences,Microarrays designed for DNA aptamer screening and binding optimization and built on the flexible and powerful Paraflo microfluidic on-chip synthesis platform. These microarrays are available as part of our comprehensive DNA/RNA Aptamer Microarray Service. Our Standar,biological,biology supply,biology supplies,biology product
ELRIG are busily preparing for the 8th Annual Drug Discovery conference which will be held at Manchester Convention Centre on 2nd & 3rd September 2014. The programme contain presentations from leading scientists across Europe and beyond, covering exciting advances in basic and translational aspects of drug discovery and brings together Academia, Biotech, Vendors and Pharma into a single community.. Aptamer Group are delighted to be invited back to the Innovation Zone (stand IZ12) for the second year running, where we will be exhibiting our new and exciting technologies. We have over 20 years combined expertise in the development of nucleic acid aptamers to peptides, proteins, cells, tissue samples, micro-organisms and small molecules.. Dr David Bunka, CTO, world leading high-throughput aptamer selection expert will be addressing the Target Validation audience on 3 September at 12.00 in Charter 1. Dr Bunka will be discussing how our technology enables us to greatly speed up the identification of ...
Background: RNA aptamers are small RNA molecules that bind antigens like antibodies and are currently being explored as alternatives to antibodies for diagnosis and therapy. A potential merit of aptamers is that they can be generated against native cellular antigens, such as those with unique post-translational modifications or receptor-ligand complexes, for which antibody generation can be difficult. Here, we report the use of a cell-based systematic enrichment approach (SELEX) to develop a novel Treg-binding RNA aptamer specific to IL2Rα-IL2 receptor-ligand complex.. Methods and Results:. A. Generation of Treg-binding aptamers:. We designed a cell-based SELEX strategy to generate RNA aptamers specific to human T regulatory (Treg) cells. The starting library consisted of random RNA aptamers with a structural diversity of ~1012. Aptamers against common T cell antigens were pre-cleared using CD4+CD25- Teff cells. Treg-binding aptamers were then positively selected using CD4+CD25+ Tregs from the ...
Multitasking by Multivalent Circular DNA Aptamers | Daniel A. Di Giusto; Sarah M. Knox; Yuching Lai; Gregory D. Tyrelle; May T. Aung; Garry C. King | download | BookSC. Download books for free. Find books
and / or polyclonal antibodies specific to a particular target for capture and / or quantitative detection. Most ELISAs employ a 96-well plate-based format. ELISAs are currently used in a wide range of industries, with wide-spread application for the detection of protein biomarkers in research, diagnostics and therapeutics. While antibody-based immunoassays have proven to be very sensitive and specific, there are some limitations which can be overcome with the ELASA, or Enzyme-Linked Aptamer Sorbent Assay. Unlike antibodies, aptamers can be selected for specific binding to poorly immunogenic and toxic compounds. Aptamers can also distinguish between highly conserved molecules. Chemical aptamer synthesis enables rapid, low-cost production of new batches with low lot-to-lot variability. As with traditional ELISAs, ELASAs can be direct, indirect, and sandwich assays. Several sandwich ELASA assays have been developed at Base Pair Biotechnologies. Biotinylated capture aptamers are typically bound to ...
Shigdar, Sarah, Lv, Li, Wang, Lifen and Duan, Wei 2016, Application of aptamers in histopathology. In Mayer, Gunter (ed), Nucleic acid aptamers : selection, characterization and application, Humana Press, New York, N.Y., pp.191-196, doi: 10.1007/978-1-4939-3197-2_16. ...
TY - JOUR. T1 - Oligonucleotide-based systems. T2 - DNA, microRNAs, DNA/RNA aptamers. AU - Jolly, Pawan. AU - Estrela, Pedro. AU - Ladomery, Michael. N1 - Special volume Biosensor technologies for detection of biomolecules (Ed: P. Estrela) PY - 2016/6/30. Y1 - 2016/6/30. N2 - There is an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of DNA, RNA or a synthetic analogue to naturally occurring nucleic acids. This chapter will draw light upon various types of nucleic acids such as DNA, RNA (particularly microRNAs), their role and their application in biosensing. Also, it will cover DNA/RNA aptamers, which can be used as bioreceptors to a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides like PNA or LNA has pushed the ...
endothelial progenitor cells in a porcine myocardial infarction model. Nucleic Acid Therapeutics, 25: 20-26.. Ireson, C. and Kelland, L. (2006): Discovery and development of anticancer aptamers. Molecular Cancer Therapeuics, 5: 2957-2962.. Kaittanis, C., Santra, S. and Perez, J. (2010): Emerging nanotechnologybased strategies for the identification of microbial pathogenesis. Advanced Drug Delivery Reviews, 62: 408-442.Kanamori, H., Yuhashi, K., Uchiyama, Y., Kodama, T., and Ohnishi, S. (2009). In vitro selection of RNA aptamers that bind the RNAdependent RNA polymerase of hepatitis C virus: a possible role of GC-rich RNA motifs in NS5B binding. Virology, 388: 91-102.. Keefe, A., Pai, S. and Ellington, A. (2010). Aptamers as therapeutics. Nature Reviews Drug Discovery, 9: 537-550.. Kikuchi, K., Umehara, T., Fukuda, K., Hwang, J., Kuno, A., Hasegawa, T. and Nishikawa, S. (2003): RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region. Journal of ...
The functionality of aptamers is similar to that of antibodies. Aptamer are selected for specific target molecules by an in vitro selection and amplification method called SELEX. They can recognise and bind their targets with high affinity and specificity. As single-stranded oligonucleotides, aptamers are able to fold into complex and stable three-dimensional structures, which allow them to specifically interact with their targets. Aptamers are receiving increasing attention as alternative affinity reagents and represent essential tools in both basic and applied research. Aptamers can be used to detect and characterise their targets but also to modify the activity of their targets. Therefore, they provide a broad range of applications, e.g., affinity enrichment, analytics, medical diagnostics, or therapy.. Research focuses ...
Aptamers are typically selected from libraries of random DNA (or RNA) sequences through systematic evolution of ligands by exponential enrichment (SELEX), which involves several rounds of alternating steps of partitioning of candidate oligonucleotides and their PCR amplification. Here we describe a protocol for non-SELEX selection of aptamers - a process that involves repetitive steps of partitioning with no amplification between them. Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), which is a highly efficient affinity method, is used for partitioning. NECEEM also facilitates monitoring of bulk affinity of enriched libraries at every step of partitioning and screening of individual clones for their affinity to the target. NECEEM allows all clones to be screened prior to sequencing, so that only clones with suitable binding parameters are sequenced. The entire protocol can be completed in 1 wk, whereas conventional SELEX protocols take several weeks even in a specialized
Infectious diseases are a subject of public health safety. In case of events such as bioterrorism or food samples tainted with a disease causing bacteria or virus the standard traditional methods of detection of viral or bacterial detection are too slow. We have developed molecular probes known as ?aptamers? to detect infection with high specificity and sensitivity. Aptamer, a word derived from Latin ?aptus? meaning ?to fit?; are molecular probes which are generated using nucleic acids which recognize and bind their target with a very high affinity and specificity. Aptamers are evolved in vitro in a test tube for its target. Aptamers are generated using a screening process known an SELEX, which stands for Systematic Evolution of Ligands by Exponential Enrichment. A library of 10 14 to 10 16 unique sequences is synthesized. These sequences are fractionated based on interactions with the target for which the aptamer is generated. The weaker binding sequences are weeded out after each successive ... 0 0 Prabodhika Mallikaratchy Prabodhika Mallikaratchy2009-07-30 07:30:062019-05-22 19:52:41Cell-specific aptamer probes for membrane protein elucidation in cancer cells ...
The adenosine aptamer was split into two halves and linked to a fluid liposome surface; addition of adenosine resulted in aptamer assembly, which did not occur if the split aptamer was attached to silica nanoparticles, demonstrating the feasibility of using aptamer probes to study diffusion within lipid membranes ...
Aptamers are an interesting class of molecules that have potential in many facets of human health. They are characterized by high affinity and specificity to their targets, are small in size, have similar properties to antibodies, but are made synthetically. All of these properties, among others, give aptamers the potential to diagnose, image and treat like no other molecules. By combining the unique properties of aptamers with the ever expanding field of nanotechnology and all it has to offer, we are entering a very promising new area of targeted nanodelivery treatments. These treatments have found success in the complex disease processes of cancer, eye and inflammatory diseases ...
LC Sciences provides unique aptamer microarray services using a novel µParaflo technology, a list of aptamer sequences, and sequence design software. The
We have recently described the isolation of 2-fluoropyrimidine-substituted RNA aptamers that bind selectively to disease-associated beta-sheet-rich forms of the prion protein, PrP, from a number of mammalian species. These aptamers inhibit the accumulation of protease-resistant forms of PrP in a prion-seeded, in vitro conversion assay. Here we identify the minimal portions of two of these aptamers that retain binding specificity. We determine their secondary structures by a combination of modeling and solution probing. Finally, we identify an internal site for biotinylation of a minimized, synthetic aptamer and use the resultant reagent in the detection of abnormal forms of PrP in vitro.
Aptamers, synthetic oligonucleotide‐based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets
Membrane Accelerator and Membrane Rudder are both post-translational controlling device to regulate metabolic flux of the host cell. To connect this relatively isolated post-translational control system to genetic circuits, we employed RNA signal, which is present in cytoplasm. Rationally designed RNA D0 with MS2 and PP7 aptamer domain is recruited. When RNA molecule with this two aptamer domains is present in cells, their cognate aptamer binding proteins can thus aggregate together. Furthermore, if we place RNA D0 (with PP7 and MS2 aptamer domains) under various promoters regulated by different signals, approaches to induce dimerization would be expanded sharply. Thus, Membrane Rudder could sense much more signals. We constructed our device as demonstrated in Fig.3. In RNA-sensing Membrane Rudder, VioA, VioB, VioE and VioC with interacting Membrane Anchors constitutively aggregate. RNA D0, can aggregate with RNA aptamer binding protein MS2 and PP7. So when RNA D0 is present, VioD with ...
RNA interference (RNAi) is an important biological process that ultimately leads to suppression of gene expression. Activators of RNAi are typically s.. is the marketplace for research antibodies. Find the right antibody for your research needs. Enzymatic conjugation of multiple proteins on a DNA aptamer in a tail-specific manner.
An Aptamer-siRNA Chimera Suppresses HIV-1 Viral Loads and Protects from Helper CD4+ T Cell Decline in Humanized Mice. C. Preston Neff, Jiehua Zhou, Leila Remling, Jes Kuruvilla, Jane Zhang, Haitang Li, David Smith, Piotr Swiderski, John Rossi and Ramesh Akkina. Science Translational Medicine Vol 3: 66ra6. Yes faithful readers of the MIPnews, for the first time in history we have an MIP laboratory who has garnered back-to-back MIPublication of the Month honors! Ramesh Akkina and his collaborators at the City of Hope have come out with a very exciting approach to harness the awesome power of in vitro-evolved RNA aptamers and RNA interference. In this paper in the Science spin off Science Translational Medicine journal, they report on a form of superdrug that not only effectively targets HIV in cells but appears to overcome one of the main hurdles for these RNA-based technologies - effective in vivo delivery.. Ramesh et al make their superdrug in a very straightforward fashion on a ribonucleic ...
Aptamers are single-stranded RNA or DNA oligonucleotides, which could be screened and synthesized for specific target (including any cell type), using systematic evolution of ligands by exponential enrichment (SELEX) technology..... Read More ...
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 ...
Kit 30500-050 Kit 30500-096 DNA marker 81-0020 DNA marker 81-0100 DNA marker 82-0100 DNA marker 82-0200 DNA marker 82-0500 DNA marker 82-1000 DNA marker 83-2500 DNA marker 83-5000 DNA Aptamers AD-155-B DNA Aptamers AD-155-F DNA Aptamers AD-155-U Peptide Aptamers AP-302-B Peptide Aptamers AP-302-F Peptide Aptamers AP-302-U Peptide Aptamers AP-304-B Peptide Aptamers AP-304-F Peptide Aptamers AP-304-U Peptide Aptamers AP-306-B Peptide Aptamers AP-306-F Peptide Aptamers AP-306-U Peptide Aptamers AP-308-B Peptide Aptamers AP-308-F Peptide Aptamers AP-308-U Peptide Aptamers AP-309-B Peptide Aptamers AP-309-F Peptide Aptamers AP-309-U Peptide Aptamers AP-310-B Peptide Aptamers AP-310-F Peptide Aptamers AP-310-U Peptide Aptamers AP-312-B Peptide Aptamers AP-312-F Peptide Aptamers AP-312-U Peptide Aptamers AP-315-B Peptide Aptamers AP-315-F Peptide Aptamers AP-315-U Peptide Aptamers AP-318-B Peptide Aptamers AP-318-F Peptide Aptamers AP-318-U Peptide Aptamers AP-319-B Peptide Aptamers AP-319-F Peptide Aptamers
TY - JOUR. T1 - Cancer-targeted Nucleic Acid Delivery and Quantum Dot Imaging Using EGF Receptor Aptamer-conjugated Lipid Nanoparticles. AU - Kim, Min Woo. AU - Jeong, Hwa Yeon. AU - Kang, Seong Jae. AU - Choi, Moon Jung. AU - You, Young Myoung. AU - Im, Chan Su. AU - Lee, Tae Sup. AU - Song, In Ho. AU - Lee, Chang Gun. AU - Rhee, Ki Jong. AU - Lee, Yeon Kyung. AU - Park, Yong Serk. PY - 2017/12/1. Y1 - 2017/12/1. N2 - Co-application of fluorescent quantum dot nanocrystals and therapeutics has recently become a promising theranostic methodology for cancer treatment. We developed a tumor-targeted lipid nanocarrier that demonstrates notable efficacy in gene delivery as well as tumor bio-imaging. Coupling of aptamer molecules against the EGF receptor (EGFR) to the distal termini of lipid nanoparticles provided the carrier with tumor-specific recognition capability. The cationic lipid component, referred to as O,O-dimyristyl-N-lysyl glutamate (DMKE), was able to effectively complex with anionic ...
TY - JOUR. T1 - A novel RNA aptamer identifies plasma membrane ATP synthase beta subunit as an early marker and therapeutic target in aggressive cancer. AU - Speransky, S.. AU - Serafini, Paolo. AU - Caroli, J.. AU - Bicciato, S.. AU - Lippman, M. E.. AU - Bishopric, N. H.. PY - 2019/1/1. Y1 - 2019/1/1. N2 - Purpose: Primary breast and prostate cancers can be cured, but metastatic disease cannot. Identifying cell factors that predict metastatic potential could guide both prognosis and treatment. Methods: We used Cell-SELEX to screen an RNA aptamer library for differential binding to prostate cancer cell lines with high vs. low metastatic potential. Mass spectroscopy, immunoblot, and immunohistochemistry were used to identify and validate aptamer targets. Aptamer properties were tested in vitro, in xenograft models, and in clinical biopsies. Gene expression datasets were queried for target associations in cancer. Results: We identified a novel aptamer (Apt63) that binds to the beta subunit of F 1 ...
TY - JOUR. T1 - DNA aptamer-based sandwich microfluidic assays for dual quantification and multi-glycan profiling of cancer biomarkers. AU - Jolly, Pawan. AU - Damborsky, P.. AU - Madaboosi, N.. AU - Soares, R.R.G.. AU - Chu, V.. AU - Conde, J.P.. AU - Katrlik, J.. AU - Estrela, Pedro. PY - 2016/5/16. Y1 - 2016/5/16. N2 - Two novel sandwich-based immunoassays for prostate cancer (PCa) diagnosis are reported, in which the primary antibody for capture is replaced by a DNA aptamer. The assays, which can be performed in parallel, were developed in a microfluidic device and tested for the detection of free Prostate Specific Antigen (fPSA). A secondary antibody (Aptamer-Antibody Assay) or a lectin (Aptamer-Lectin Assay) is used to quantify, by chemiluminescence, both the amount of fPSA and its glycosylation levels. The use of aptamers enables a more reliable, selective and controlled sensing of the analyte. The dual approach provides sensitive detection of fPSA along with selective fPSA ...
TY - JOUR. T1 - A sensitive method to detect Escherichia coli based on immunomagnetic separation and real-time PCR amplification of aptamers. AU - Lee, Hye Jin. AU - Kim, Byoung Chan. AU - Kim, Kyung Woo. AU - Kim, Young Keun. AU - Kim, Jungbae. AU - Oh, Min Kyu. PY - 2009/8/15. Y1 - 2009/8/15. N2 - Aptamers, single-stranded nucleic acids, provide a unique opportunity as amplifiable molecules using polymerase chain reaction (PCR) as well as recognition molecules like antibodies. We report a highly sensitive detection of Escherichia coli by taking advantage of the aptamer amplification as well as the specific binding of aptamers onto E. coli. This unique approach consists of three steps. First, the target E. coli was captured by antibody-conjugated magnetic beads. Second, the RNA aptamers were bound onto the surface of captured E. coli in a sandwich way. Finally, the heat-released aptamers were amplified by using real-time reverse-transcriptase-PCR (RT-PCR). The aptamer amplification in this ...
Easy capture and easy release! The cover illustrates a nanostructured platform that combines silicon nanowire arrays and targeted DNA aptamers, realizing significant capture and efficient release of T lymphocytes. This method of capture and release provides an artful strategy to fulfill the demands of cell isolation and diagnostics, as reported by Dong Han, Shutao Wang, and co-workers on page 4376.. ...
Article Aptamer-based and DNAzyme-based biosensors for environmental monitoring. Aptamers and DNAzymes are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure with high specificity to various ligands, such as...
Thrombin is an important serine protease in blood and a therapeutic biomarker. The aptamer-based assays for thrombin take advantage of unique features of nucleic acid aptamers in selection, preparation, stability, and modification of functional groups. Aptamer affinity capillary electrophoresis coupled with
Aptamer selection protocols, named cell-SELEX, have been developed to target trans-membrane proteins using whole living cells as target. This technique presents several advantages. (1) It does not...
摘要:A simple approach based on exfoliating and disintegrating treatments for graphite oxide, followed by hydrothermal synthesis, was developed to prepare water-soluble graphene quantum dots (GQDs). The as-prepared GQDs exhibited bright blue emission under ultraviolet irradiation (similar to 365 nm), and showed an excitation-independent photoluminescence feature. More importantly, a newly anodic electrochemiluminescence (ECL) was observed from the water-soluble GQDs with H2O2 as coreactant for the first time, and the ECL induced a strong light emission at a low potential (ca. 0.4 V vs. Ag/AgCl). The ECL mechanism is investigated in detail. Employing SiO2 nanospheres as signal carrier, a novel SiO2/GQDs ECL signal amplification labels were synthesized based on which a ultrasensitive ECL aptamer sensor was proposed. Under the optimized experimental conditions, the proposed ECL aptamer sensor exhibited excellent analytical performance for adenosine triphosphate (ATP) determination, ranging from ...
The present invention provides an aptamer-based calorimetric sensor system for determining the presence and optionally the concentration of an analyte in a sample. Methods of utilizing the sensor syst
There is currently an urgent need for biomarkers that can be used to monitor the efficacy of experimental therapies for Duchenne Muscular Dystrophy (DMD) in clinical trials. Identification of novel protein biomarkers has been limited due to the massive complexity of the serum proteome and the presence of a small number of very highly abundant proteins. Here we have utilised an aptamer-based proteomics approach to profile 1,129 proteins in the serum of wild-type and mdx (dystrophin deficient) mice. The serum levels of 96 proteins were found to be significantly altered (P | 0.001, q | 0.01) in mdx mice. Additionally, systemic treatment with a peptide-antisense oligonucleotide conjugate designed to induce Dmd exon skipping and recover dystrophin protein expression caused many of the differentially abundant serum proteins to be restored towards wild-type levels. Results for five leading candidate protein biomarkers (Pgam1, Tnni3, Camk2b, Cycs and Adamts5) were validated by ELISA in the mouse samples.
Some bioterrorism agents cause disease at very low infective doses and their presence can be masked by the environment. Therefore, ultrasensitive detection is required for homeland defense applications. In this Phase I research project, Operational Technologies Corporation (OpTech) proposes to couple DNA aptamers made by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process to commercially available fluorescent nanoparticles (NPs, composed of chelated europium in polystyrene). OpTech will demonstrate aptamer-NP-mediated detection of a bacterial, viral, and toxin simulant at low levels. Fluorescent NPs are nanometer-sized plastic and metallic ¿beads¿ that endow superior sensitivity in clinical assays (up to zeptomolar [10-21] detection limits). OpTech also will couple the DNA aptamers to magnetic microbeads and demonstrate magnetic separation and purification of the bioterrorism agent simulants from natural water samples in conjunction with aptamer-fluorescent NP ...
For the development of K(+)-responsive RNA aptamers, we proposed a new general strategy that makes use of a G-quadruplex formation in response to K(+). This is the first report of developing an RNA aptamer that demonstrates ON/OFF switching of its target-binding activity by sensing the addition/removal of K(+).. ...
Molecular and Functional Characterization of ssDNA Aptamers that Specifically Bind Leishmania infantum PABP. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Trying to incorporate quantum dots into biological systems has proven difficult due to their lack of biocompatibility and the toxicity of heavy metals inside cells. Recently developed carbon nanodots retain the advantages of quantum dots, but can function in biological media. Xianogang Qu and researchers at the Chinese Academy of Sciences incorporated carbon nanodots in a thrombin detection assay using DNA aptamers. Thrombin contains two binding sites that are recognized by different aptamers on both a silica nanoparticle and carbon nanodot. The multi-binding site capabilities of aptamers allow for greater sensitivity when compared to single site antibodies, and the fluorescent signal of the carbon nanodot is only detected when bound to thrombin on the silica nanoparticle. Click on the paper below to read more, it will be free to read until November 16th.. Aptamer carbon nanodot sandwich used for fluorescent detection of protein ...
Data accumulated over the latest two decades have established that the serine protease urokinase-type plasminogen activator (uPA) is a potential therapeutic target in cancer. When designing inhibitors of the proteolytic activity of serine proteases, obtaining sufficient specificity is problematic, because the topology of the proteases active sites are highly similar. In an effort to generate highly specific uPA inhibitors with new inhibitory modalities, we isolated uPA-binding RNA aptamers by screening a library of 35 nucleotides long 2′-fluoro-pyrimidine RNA molecules using a version of human pro-uPA lacking the epidermal growth factor-like and kringle domains as bait. One pro-uPA-binding aptamer sequence, referred to as upanap-126, proved to be highly specific for human uPA. Upanap-126 delayed the proteolytic conversion of human pro-uPA to active uPA, but did not inhibit plasminogen activation catalyzed by two-chain uPA. The aptamer also inhibited the binding of pro-uPA to uPAR and the ...
Disclosed are single-stranded DNA molecules which bind adenosine or an adenosine-5-phosphate and methods for their production and isolation. Also disclosed are methods for producing and isolating related catalytic DNA molecules.
Pivotal Scientific Ltd and Base Pair Biotechnologies Partner to Expand Access to Novel Aptamer Technologies to Global Markets. Oxfordshire, UK and Texas, US, June 3, 2013 - Pivotal Scientific Ltd, a consultancy company specialising in developing the international growth of biotech SMEs, and Base Pair Biotechnologies, a specialist developer of novel aptamer based technologies for research and diagnostics, are pleased to announce their collaboration to expand the reach of Base Pair Biotechnologies products and services.. A mainstay of bioscience research is the antibody. Yet standard antibody technologies can take months to produce an antibody against a new target; a long time in the fast paced and global arena of the biosciences. Base Pair Biotechnologies patented development process can turn around aptamers - short strands of DNA or RNA that specifically bind a target with equal specificity and affinity to antibodies - in weeks instead of months, getting researchers the reagents they need ...
2. This paper is also talking about how protein arrays can be self-assembled using DNA nanostructures in the shape of a lattice. The biotin-streptavidin interaction provides only one type of protein-ligand interaction; while it is possible to fuse other proteins with streptavidin, this process is both complicated and may affect the functionality of the proteins themselves during the process. They then introduce aptamers, which are DNA or RNA molecules that have the ability to bind to other molecules such as proteins, nucleic acids, organic compounds, and organisms. There are a wide range of aptamers suited to a variety of proteins that guarantee specificity and high affinity. This method has three components: the DNA lattice nanostructure, a DNA-docking site with the aptamer sequence that will bind the protein of interest to the nanostructure, and the protein itself. In the paper, they use the ...
Systemic administration of the noncompetitive NMDA-receptor antagonist, MK-801, has been proposed to model cognitive deficits similar to those seen in patients with schizophrenia. The present work investigated the ability of a dopamine-binding DNA aptamer to regulate these MK-801-induced cognitive deficits when injected into the nucleus accumbens. Rats were trained to bar press for chocolate pellet rewards then randomly assigned to receive an intra-accumbens injection of a DNA aptamer (200 nM; n = 7), tris buffer (n = 6) or a randomized DNA oligonucleotide (n = 7). Animals were then treated systemically with MK-801 (0.1 mg/kg) and tested for their ability to extinguish their bar pressing response. Two control groups were also included that did not receive MK-801. Data revealed that injection of Tris buffer or the random oligonucleotide sequence into the nucleus accumbens prior to treatment with MK-801 did not reduce the MK-801-induced extinction deficit. Animals continued to press at a high rate over
Background SELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection. Methodology/Principal Findings To evaluate SELEX and assess the extent of these effects, we designed and performed a Neutral SELEX experiment omitting the selection step, such that the sequences are under the sole selective pressure of SELEXs amplification steps. Using high-throughput sequencing, we obtained thousands of full-length sequences from the initial genomic library and the pools after each of the 10 rounds of Neutral SELEX. We compared these to sequences obtained from a Genomic SELEX experiment deriving from the same initial library, but screening for RNAs binding with high affinity to the E.
Dynamical systems are often used to model biochemical and biological processes. In Seo et al. (2010, 2014) we studied two mathematical models of the iterative biochemical procedure known as SELEX (Systematic Evolution of Ligands by EXponential Enrichment): multiple target SELEX and alternate SELEX. It is the purpose of this paper to revisit the mathematics of these processes in the language of dynamical systems on compact manifolds but for a dynamical system on a manifold with compact closure. From the experimentalists point of view, multiple target SELEX provides a way of obtaining the best binding ligands to a pool of several fixed targets, whereas alternate SELEX provides a way to specify which of the best binding ligands also bind best to a specified subtarget. Because these procedures are iterative, it is natural to investigate them in the context of the theory of discrete dynamical systems. Although the iterative schemes are nonautonomous, they have the same limiting properties as two closely
CURRENT STEM CELL NEWS. 1. Bioengineered protein -The latest Therapeutic Invention to fight Leukemia. In a fascinating discovery US scientists have reported a bioengineered protein CD19-L, that can target the CD19-positive leukemic stem cells and destroy them Click to read more... 2. Worlds First RNA Aptamer -The chemical Guided missile against cancer. Deakin University medical scientists along with scientists in India and Australia have created the worlds first RNA aptamer which can act as a cell target missile against cancer cells that in future can help in designing Cell Therapy Bombs against Cancer cells Click to read more... 3. Reprogramming Cells may result in Genomic Aberrations, reveal studies. Recent studies have reported that reprogrammed stem cells exhibit a genomic instability that results in genetic mutations akin to mutations found in cancer cells which has lead to the conclusion that reprogrammed stem cells need to be extensively investigated before applied clinically Click to ...
A new Transparency Market Research report states that the global aptamers market stood at US$0.93 bn in 2012 and is predicted to reach US$4.3 bn by 2019. It...
FNAs), as described by Dr. S.K. Silverman, are DNA and RNA aptamers that bind targets, or they are deoxyribozymes (single stranded DNA) and ribozymes (RNA) that have catalytic activity.,cite,Silverman2012,/cite, Aptamers, Ribozymes, and Deoxyribozymes are grouped into three main categories that are further classified into either natural or artificial depending on their origin. The exception being Deoxyribozymes as they have yet to be discovered in a living organism. Although the first ribozyme was discovered only in the 1980s, the search for new and better FNAs continues. This has led the development of new methodologies, such as the SELEX ,cite,Stozack1990, Gold1990 ,/cite, or In vitro selection, as we strive to expand their potential both as tools for exploring biology and solving real world problem solving ...
AgNCs are complexes between few Ag atoms and a specific DNA sequence template to stabilize the clusters. In most cases, AgNCs are synthesized either at the 3 or 5 end of the template. Our results show that AgNCs can successfully be generated from a template embedded in the middle of a hybridization probe, used for the isothermal amplification of aptamers, called rolling circle amplification (RCA). RCA uses circular oligonucleotide probes to generate long, ssDNA molecules containing periodic repeats of the circular probe.[4][5] Previous works show that overexpression of aptamers by RCA increases target binding efficiency compared to monovalent aptamers.[6] The RCA concatemer combines both the aptamer and the fluorescent AgNC template. Subsequently synthetized AgNCs exhibit strong, robust and tunable fluorescence, eliminating the need for labeling.[7] Importantly, it has been shown that aptamer-AgNCs retain the same specificity and affinity for the cognate protein and that target binding results ...
View PROTEIN DETECTION for MB.BS.pptx from AA 1PROTEIN DETECTION Dr.Sajida Parveen Shaikh OBJECTIVES Define proteins List major body proteins in various body fluids. Proteinuria State Principle of
Flow cytometry has gained popularity and demand in the field of biology because of its accurate analysis and high throughput. The use of multiple lasers, affinity ligands and attached fluorophores allows simultaneous analysis of several markers expressed on thousands of cells per second (Figure 1). Some of the most widely used applications include drug testing, microbiological analysis of bacteria and viruses, cell phenotyping, stem cell research and most importantly detecting cancer cells. Aptamers compete with antibodies in many such applications, in which high-affinity and specificity ligands are needed. Moreover, low specificity and inconsistent labelling of antibodies may lead to significant loss of function and reliability in detecting the target of interest. In this regard, fluorescence-tagged aptamers have shown increased use in flow and imaging cytometry for detecting cells expressing distinct antigens.. ...
Riboswitches are defined as RNA domains at the 5-ends of mRNA that recognize small molecules and respond by changing their three-dimensional structure. This change in turn affects the translation of the mRNA or, sometimes, its premature termination, especially during protein synthesis in the cell, including microbial cells. A riboswitch can be defined as an RNA domain, usually in an mRNA molecule, that can bind a specific small molecule and alter its secondary structure. And this alteration in turn controls translation of the mRNA in the affected cell. Riboswitching as explained above is an important process in molecular biology because it helps to control biosynthetic pathways for amino acids and other metabolites in the cell of an organism. Riboswitches are mostly used to control biosynthetic pathways for amino acids, purines, and other metabolites produced in the cells of microbes.. One of the most interesting findings in molecular biology has been the discovery that RNA molecules can carry ...
The integration of anatomic, molecular, and genomic pathology into surgical pathology practice is conspicuous in oncology, where definition of molecular pathways important for specific tumors has enabled development of new biomarkers and innovative approaches to the detection of cancer and metastases. The so-called liquid biopsy includes a wide array of new technologies, including tumor-derived tumor vesicles and aptamer probes. The surgical pathologist will need to understand these new technologies and be aware of their advantages and pitfalls as they are applied into practice. Upon completion of this educational activity, participants should be able to:. ...
In this study, we investigated the efficacy of an LNA (locked nucleic acid)-modified DNA aptamer named RNV66 targeting VEGF against various breast cancer cell lines. Our results demonstrate that RNV66 efficiently inhibits breast cancer cell proliferation both in vitro and in vivo. Introduction of LNA nucleotides were crucial for higher efficacy. Furthermore, the binding interaction of RNV66 with VEGF was investigated using molecular dynamic simulations leading to the first computational model of the LNA aptamer-VEGF complex blocking its interaction with VEGF-receptor.. ...
My research interests lie in the interface of engineering, nanotechnology and biology towards the utilization of the fundamentals of biomolecular recognition in the development of ultra sensitive diagnostic assays to meet the urgent and critical need for the early diagnosis of disease. My research includes the use of standard biophysical techniques such as, fluorescence anisotropy and SPR to acquire a mechanistic understanding of the details of antibody-antigen and DNA aptamer -protein recognition. It extends to the development of nanoparticle-based assays with main focus on optimizing surface chemistry for controlling specificity and fine tuning of the ligand-analyte detection schemes.. ...
There is growing appreciation that small, non-coding RNAs can participate in gene regulation. Can small RNAs inhibit DNA-binding proteins? We have developed an artificial example by performing in vitro genetic selection experiments identifying a small RNA aptamer that competitively inhibits human transcription factor NF-kappaB binding to DNA in vitro. Optimization by yeast in vivo genetic selections resulted in an RNA that inhibits NF-kappaB in living yeast cells. We have solved the X-ray co-crystal structure of this unusual RNA/NF-I ...
The design and implementation of synthetic biological systems often require information on transcription and translation rates and on the impact of both RNA and protein levels on metabolic activities of host cells. Such information is needed when both strong and low levels of expression are desired, depending on the biologists goal, e.g. high production or cell localization of a protein, respectively. To date, however, quantitative information about the expression strength of a promoter is difficult to obtain due to the lack of noninvasive and quick approaches to measure the levels of RNA and protein in cells. Here, we engineer a fluorescence-based sensor that can provide information on both transcription strength and translation efficiency that is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies. The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating ...
There are surprisingly few ways to directly observe how cells and proteins work inside living creatures. Weian Zhao devised simple sensors that let scientists do exactly that.. Zhao starts by identifying a short, single-stranded piece of DNA called an aptamer that selectively binds with a protein or other biomolecule researchers are interested in. He attaches a fluorescent dye to the aptamer and then attaches the aptamer-dye combination to the surface of a type of stem cell, found in bone marrow and fat tissue, that homes in on inflamed tissue and tumors.. When the combination of dye, aptamer, and stem cell is injected into a living organism, the stem cell seeks out the targeted biomolecules. For example, if researchers want to look at unhealthy tissue, the aptamer latches onto the biomolecule suspected of being at the root of the problem, and the dye lights up or changes color.. By putting mice that have been injected with these sensors under a special microscope designed to hold a living ...
Press release - Transparency Market Research - Aptamer Market to Reflect Impressive Growth Rate by 2025 - published on
SPR imaging platform would be a good choice to characterize aptamer -protein interactions. To study the aptamer-protein ... Thiol groups are introduced on DNA nucleotides by N-hydroxysuccinimide (NHS). Target oligonucleotides having a primary amine ... The interaction of thrombin and the aptamer can be monitored on microarray in real-time during injections of thrombin at ... Daniel, C; Roupioz, Y; Gasparutti, D; Livache, T; Buhot, A (2013). "Solution-Phase vs Surface-Phase Aptamer-Protein Affinity ...
These modified nucleotides allow for the selection of aptamers with novel binding properties and potentially improved stability ... Aptamer Deoxyribozyme Anti-thrombin aptamers Bacterial one-hybrid system Hak-Hagir A (September 1978). "[The Hak-Hagir skin ... Aptamers have emerged as a novel category in the field of bioreceptors due to their wide applications ranging from biosensing ... If a good binding affinity for the selected aptamer is not a concern, then an excess of target can be used to increase the ...
These nucleotide regions in the crcB RNA motif play important roles in the aptamer binding region for fluoride. Upon binding ...
BNA nucleotides can be incorporated into DNA or RNA oligonucleotides at any desired position. Such oligomers are synthesized ... design and synthesis of RNA aptamers; siRNA; antisense probes; diagnostics; isolation; microarray analysis; Northern blotting; ... A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible ... BNAs are structurally rigid oligo-nucleotides with increased binding affinities and stability. Chemical structures of BNA ...
incorporated modified nucleotides in aptamers to introduce new confrontational features and high affinity interactions from the ... uses ACE to investigate protein-protein interactions using aptamers. A α-thrombin binding aptamer was labeled with 6- ... Aptamer-based affinity capillary electrophoresis is utilized for the analysis and modifications of specific affinity reagents. ... Modified aptamers ideally exhibit and high binding affinity, specificity, and nuclease resistance. Ren et al. ...
Another example of an RNA aptamer therapeutic is NOX-A12, a 45 nucleotide RNA aptamer that is in clinical trials for chronic ... Broadly, aptamers are small molecules composed of either single-stranded DNA or RNA and are typically 20-100 nucleotides in ... In order to combat some of the in vivo limitations of RNA aptamers, various modifications can be added to the nucleotides to ... Originally approved in 2004 to treat age-related macular degeneration, Pegaptanib is a 28 nucleotide RNA aptamer that acts as a ...
PreQ1-I has a distinctly small aptamer, ranging from 25 to 45 nucleotides long, compared to the structures of PreQ1-II ... with an average of 58 nucleotides composing its aptamer, which forms as many as five base-paired substructures. PreQ1-III ... Binding of preQ1 to the aptamer domain promotes the sequestration of a part of SD sequence at the 5' end to the P2 stem of the ... In the native mRNA structure, binding of preQ1 to the aptamer region in the riboswitch leads to the formation of a terminator ...
... but lacks most of the highly-conserved nucleotides of SAM-III class. SAM-VI aptamers bind the cofactor S-adenosylmethinine SAM ...
This would include the evolution of TNA aptamers that can bind to specific small molecule and protein targets, as well as the ... These structures demonstrate imperfect recognition of the incoming TNA nucleotide triphosphate and support the need for further ... 140, 5706-5713, (2018). Rangel, A. E., Chen, Z., Ayele, T. M. & Heemstra, J. M. In vitro selection of an XNA aptamer capable of ... The availability of TNA polymerases have enabled the in vitro selection of biologically stable TNA aptamers to both small ...
Mutagenesis confirmed that changing nucleotides within the loop regions of this riboswitch altered the specificity for ligand ... classed as novel riboswitches as they deviate in sequence and structure within the loops regions that are required in aptamer ...
... aptamers, nucleotide MeSH D13.695.578.424.450 - oligodeoxyribonucleotides MeSH D13.695.578.424.450.275 - dna primers MeSH ... thymine nucleotides MeSH D13.695.740.706.788 - thymidine monophosphate MeSH D13.695.740.850 - uracil nucleotides MeSH D13.695. ... deoxyguanine nucleotides MeSH D13.695.201.200 - deoxyuracil nucleotides MeSH D13.695.201.200.270 - fluorodeoxyuridylate MeSH ... deoxyadenine nucleotides MeSH D13.695.201.150 - deoxycytosine nucleotides MeSH D13.695.201.150.200 - deoxycytidine ...
Several nucleotide positions are highly conserved, with many around the terminal loops involved in the pseudoknot interaction. ... a mechanism commonly used in engineered aptamers but not previously observed in nature. Cyclic di-GMP-II riboswitches are a ...
He isolated the first aptamer (term he used for the first time). He isolated RNA enzymes with RNA ligase activity directly from ... Phosphorimidazolides were first proposed to be critical for early-earth nucleotide polymerization by Leslie E. Orgel and ... "The Mechanism of Nonenzymatic Template Copying with Imidazole-Activated Nucleotides". Angewandte Chemie International Edition ...
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. ...
Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of ... One experiment conducted at the University of Florida led to the production of an XNA aptamer by the AEGIS-SELEX (artificially ... Using a genetic code of six XNAs rather than the four naturally occurring DNA nucleotide bases yields endless opportunities for ... in XNA nucleotides, the deoxyribose and ribose sugar groups of DNA and RNA have been replaced with other chemical structures. ...
... in position 74 of the aptamer domain, it has been found that conversion of a cytosine to a uracil changes an aptamer from being ... Such a conversion is owed to the ability of a nucleotide in position 74 to Watson-Crick base pair with the ligand in the ... The xpt guanine riboswitch aptamer is stabilized by guanine in a way that allows the riboswitch to more easily bind magnesium, ... In the absence of adenine, the aptamer domain of the riboswitch instead associates with the riboswitch expression platform, ...
... alongside the four naturally occurring nucleotides, and by including individual artificial nucleotides in the culture media, ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... 2006). "An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA". Nat. ... In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, ...
... and aptamer (nucleotide) complex among many other interesting studies. Molecular dynamics is used in many fields of science. ... and a 1063 nucleotide single stranded RNA genome. One key finding is that the capsid is very unstable when there is no RNA ... RNA structure in the ribosome and other large systems has been modeled with one pseudo-atom per nucleotide. Virtual cell ... "Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex". Scientific Reports. 6 (1): 37449. Bibcode: ...
... lacking the first and the last nucleotides of 29-mer form) nucleotides. This aptamer recognizes the exosite II of thrombin, ... Despite that this aptamer only shows moderate effect on fibrinogen regulation, the affinity of this aptamer is slightly higher ... The aptamer HD22 (also known as HTDQ) is an optimized aptamer with 29 (5'-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3') or 27 ( ... These two aptamers have high affinity and good specificity and have been widely studied and used for the development of aptamer ...
Each three-nucleotide codon is translated into one of twenty naturally occurring amino acids. There is at least one tRNA for ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... The 3'-end of the tRNA is mutated from CCA to CGA, while two cytidine nucleotides in the ribosomes A- and P-sites are mutated ... However, by co-mutating the binding nucleotides in such a way, that they can still base pair, the translational fidelity can be ...
AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Chemical analogs of nucleotides can take the place of proper nucleotides and establish ... In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic ... Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non- ... The nucleotides, which encoded RNA and proteins, were successfully replicated in vitro. Since then, Benner's team has been ...
The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of ... The hachimoji DNA system produced one type of catalytic RNA (ribozyme or aptamer) in vitro. Natural DNA is a molecule carrying ... DNA and RNA are naturally composed of four nucleotide bases that form hydrogen bonds in order to pair. Hachimoji DNA uses an ... In natural DNA, each nucleotide is composed of one of four nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T ...
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 ...
SELEX is a well known selection method for fabrication and selection of nucleotide aptamers. SELEX is relatively limited by the ... When the probe surface neighboring an aptamer is blocked by an adjacent aptamer, the redox tag on the target-bound aptamer will ... The concentration of aptamer in solution that incubates a clean probe is found to be proportional to the density of aptamers ... In this method, libraries of aptamers are separated into aptamer particles and separated by FACS based on affinity. Only the ...
L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. L-RNA ... L-RNA aptamers themselves have low antigenicity. In contrast to other aptamers, L-RNA aptamers have high stability in blood ... such as PEGylated L-RNA aptamers, show a prolonged plasma half-life. Unlike other aptamers, L-RNA aptamers are not directly ... This information is used for the synthesis of the oligonucleotide's enantiomer, the L-RNA aptamer, using L-nucleotides. L-RNA ...
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 ...
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 ...
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/ ...
... forms oxidized nucleotides that impairs DNA function by mismatching nucleotides in the sequences. This is more common in PQS ... Nanopore and Aptamer Biosensor group{NAB group} G-Quadruplex World - a website to discuss publications and other information of ... Due to Guanine having a lower electron reduction potential than the other nucleotides bases,8-oxo-2'-deoxyguanosine (8-oxo-dG ... QGRS Mapper: a web-based application for predicting G-quadruplexes in nucleotide sequences and NCBI genes from Bagga's group. ...
Kaziro and his team developed RNA aptamers that inhibited Ras's interaction with Raf-1's binding domain due to the aptamer's ... The alpha subunits of these G-protein complexes are responsible for binding to the guanine nucleotide and are unique to each ... Kaziro concluded that the RNA 9A aptamer was the most potent and could be used as a tool for researchers to regulate the Ras ... He researched the role of GTP in the translocation of proteins through a ribosome, the characterization of G nucleotide binding ...
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) ...
... s should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but ... The 10-23 DNAzyme contains a 15-nucleotide catalytic core that is flanked by two substrate recognition domains. This DNAzyme ... "Controlling uncertainty in aptamer selection". Proceedings of the National Academy of Sciences of the United States of America ...
This mechanism relies on conserved nucleotide motifs, called switch (S) regions, found in DNA upstream of each constant region ... SHM results in approximately one nucleotide change per variable gene, per cell division.[10] As a consequence, any daughter B ...
Ras guanyl-nucleotide exchange factor activity. • phosphatidylinositol-4,5-bisphosphate 3-kinase activity. ... Aptamers: Against NGF: RBM-004. *Decoy receptors: LEVI-04 (p75NTR-Fc) ...
nucleotide binding. • calcium ion binding. • protein kinase activity. • kinase activity. • protein binding. • protein tyrosine ... Aptamers: Against NGF: RBM-004. *Decoy receptors: LEVI-04 (p75NTR-Fc) ... Ras guanyl-nucleotide exchange factor activity. • signaling receptor activity. • transmembrane receptor protein tyrosine kinase ...
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 ...
DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called " ... aptamer). Some transcripts act as ribozymes and self-regulate their expression. ...
A single nucleotide polymorphism-based technique for specific characterization of YO and YN isolates of Potato virus Y (PVY). J ... Once the reaction temperature is raised to 95 °C, the aptamers are removed and the DNA-dependent polymerase component will ... The 144 nucleotide 5'-NTR is particularly rich in adenine residues and has very few guanine residues. Rather than a ... Van der Vlugt, R., Allefs, S., De Haan, P. and Goldbach, R. (1989). Nucleotide sequence of the 3'-terminal region of potato ...
Aptamer. *Artificially Expanded Genetic Information System. *3-Arylpropiolonitriles. *Asilomar Conference on Recombinant DNA ... Aminoallyl nucleotide. *Amplicon. *Analog ear. *Antibody-drug conjugate. *Antibody-oligonucleotide conjugate. *Antisense ...
Aptamer. Targeting of specific receptors, requires sophisticated screening to develop Cholesterol. Stable for systemic delivery ... The dsRNA then gets cut up by a Dicer into small (21-28 nt = nucleotides long) strands of miRNAs (microRNAs) or siRNAs (short ... is a double stranded series of nucleotides. If the mechanism didn't use dsRNAs, but only single strands, there would be a ... approximately 20-30 nucleotides in length) that function as factors involved in inactivating homologous sequences, promoting ...
In this pathway, recruitment of a guanine nucleotide exchange factor by the adaptor and docking proteins leads to activation of ... Aptamers: Against NGF: RBM-004. *Decoy receptors: LEVI-04 (p75NTR-Fc) ... a membrane-associated G-protein known as Ras.[7] The guanine nucleotide exchange factor mediates Ras activation through the GDP ...
Yao F, An Y, Li X, Li Z, Duan J, Yang XD (2020-03-27). "Targeted Therapy of Colon Cancer by Aptamer-Guided Holliday Junctions ... Cruciform DNA structures require at least a six nucleotide sequence of inverted repeats to form a structure consisting of a ... This opening has several adenine and thymine nucleotides distal to the inverted repeat. As the unwound section gets larger, ... "Targeted delivery of doxorubicin to cancer cells by a cruciform DNA nanostructure composed of AS1411 and FOXM1 aptamers". ...
... es are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds ... but have more significant differences than a single nucleotide mutation. SAH riboswitches bind S-adenosylhomocysteine to ... as it contains contiguous dual aptamers. Though no longer shown to be cooperative, the cause of dual aptamers still remains ... of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. In 2002, ...
Oki, T.; Yoshimoto, A.; Sato, S.; Takamatsu, A. (1975-12-18). "Purine nucleotide pyrophosphotransferase from Streptomyces ... "Self-Assembled Signaling Aptamer DNA Arrays for Protein Detection". Angewandte Chemie International Edition. 45 (32): 5296-5301 ...
... s are typically 21 nucleotides in length with a 2 nucleotide overhang at the 3' end of each strand, the same structure as ... saRNA by Pancreatic Ductal Adenocarcinoma-specific RNA Aptamers Inhibits Tumor Growth In Vivo". Molecular Therapy. 24 (6): 1106 ...
Partitioning in digital PCR increases sensitivity and allows for detection of rare events, especially single nucleotide ... 2015). "Hi-Fi SELEX: A high-fidelity digital-PCR based therapeutic aptamer discovery platform". Biotechnology and ... "Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping". Digital PCR. Methods in ... occurs when a biomarker exists within a background of a highly abundant counterpart that differs by only a single nucleotide ...
The structure of a nucleic acid molecule consists of a sequence of nucleotides distinguished by which nucleobase they contain. ... and aptamers, which can bind to specific proteins or small molecules. Structural DNA nanotechnology, sometimes abbreviated as ... an actual sequence of nucleotides that will form into the desired structure must be devised. Nucleic acid design is the process ... and the limited chemical diversity of the four nucleotides as compared to the twenty proteinogenic amino acids. The sequences ...
March 2008). "Single-nucleotide-specific siRNA targeting in a dominant-negative skin model". The Journal of Investigative ... However recently a large Phase III trial of PEGylated RNA aptamer against factor IX had to be discontinued by Regado ... The mRNA molecule is then cut precisely by cleaving the phosphodiester bond between the target nucleotides which are paired to ... Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (May 2001). "Duplexes of 21-nucleotide RNAs mediate RNA ...
These structures include riboswitches, ribozymes, interaction sites, and aptamers. Aptamer structures allow the binding of ... This is largely a result of four different nucleotides: adenine (A), cytosine (C), guanine (G) and uracil (U), and ability to ...
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 ...
The 15-mer DNA oligonucleotide 5-GGTTGGTGTGGTTGG-3, known as thrombin binding aptamer (TBA), is a highly potent inhibitor of ... Aptamers, Nucleotide / chemistry* * Aptamers, Nucleotide / genetics * Aptamers, Nucleotide / metabolism * Circular Dichroism * ... Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer FEBS J. 2013 Dec;280(24):6581- ... The 15-mer DNA oligonucleotide 5-GGTTGGTGTGGTTGG-3, known as thrombin binding aptamer (TBA), is a highly potent inhibitor of ...
Aptamers, Nucleotide / chemistry * Aptamers, Nucleotide / isolation & purification* * Aptamers, Nucleotide / metabolism * ... In Vitro Selection of DNA Aptamers that Binds Geniposide Molecules. 2017 Feb 28;22(3):383. doi: 10.3390/molecules22030383. ... These aptamers have the potential to be further developed into analytical tools for the detection of geniposide. ... Two top aptamers exhibit low micromolar binding affinity towards geniposide, but show significantly reduced affinity to genipin ...
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 ...
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 ...
... 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 ...
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 ...
The features for aptamers are extracted from Pseudo K-tuple Nucleotide Composition (PseKNC) while the features for proteins ... Rapidly and effectively predicting aptamer-protein interacting pairs is significant to design aptamers binding to certain ... which may contribute to finding novel aptamer-protein interacting pairs and understanding the relationship between aptamers and ... which will give insight into understanding mechanisms of aptamer-protein interacting pairs and developing aptamer-based ...
2012) Stepping towards highly flexible aptamers: Enzymatic recognition studies of unlocked nucleic acid nucleotides. Chemical ... Stepping towards highly flexible aptamers: Enzymatic recognition studies of unlocked nucleic acid nucleotides ... Enzymatic recognition of unlocked nucleic acid (UNA) nucleotides was successfully accomplished. Therminator DNA polymerase was ...
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 ...
Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of ... Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of ... groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of DNA. Journal of the American Chemical ...
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 ...
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 ...
The structures of aptamers, DNA and RNA constructs, and nucleotides are shown. Indicated compounds used in this study are1 (A-E ... 57mer-RNA tetracycline aptamer, (B) 77mer-RNA FMN aptamer, (C) 44mer-DNA protein C aptamer, and (D) 15mer-DNA thrombin aptamer ... 15mer-DNA thrombin aptamer, 44mer-DNA protein C aptamer, 57mer-RNA tetracycline aptamer, or 77mer-RNA FMN aptamer in ... 15mer-DNA thrombin aptamer (20 µg/mL, bar 6), 44mer-DNA protein C aptamer (8 µg/mL, bar 7), 57mer-RNA tetracycline aptamer (5 ...
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 ...
1A). Formation of helix P1 in the TPP aptamer domain is essential for ligand binding (22). In thiM, the 3′-terminal nucleotides ... Dynamic coupling of P1 and P3/L5 of the TPP aptamer. (A) Labeling pattern and population FRET histogram of the TPP aptamer with ... 3 B-D). This contact is mediated by nucleotide A69 of L5, which stacks between the neighboring nucleotide A70 and nucleoside ... E. coli thiM riboswitch aptamer. (A) Secondary structure representation of the native RNA aptamer domain under investigation. ( ...
... a DNA aptamer that binds von Willebrand factor domain A1. ... Aptamer ARC1172 Chain: B Molecule details › Chain: B. Length: ... 42 nucleotides. Theoretical weight: 12.88 KDa. Source organism: Homo sapiens. Expression system: Not provided. ... A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1. ... A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1. ...
When bound to the ABA oligo, the same tyrosines could provide stacking interactions to some of the nucleotide bases. Yet, these ... The DNA aptamer and Flag peptide competed for binding to the M2 antibody and the aptamer eluted Flag-tagged proteins from an ... The DNA aptamer and Flag peptide competed for binding to the M2 antibody, thereby allowing the aptamer to elute Flag-tagged ... identification of this DNA aptamer demonstrates the feasibility of using SELEX to develop aptamers that block specific ...
The selected aptamer was an 86-nucleotide DNA molecule that bound to an epitope peptide of HER2 with a Kd of 18.9 nM. The ... Figure 1. Evaluation of HER2 in breast cancer with the aptamer HB5. (a) Binding profiles of the aptamer HB5 to HER2-positive ( ... we propose a novel IHC method using a newly developed DNA aptamer (HB5). The aptamer HB5 was shown to be capable of ... Novel HER2 aptamer selectively delivers cytotoxic drug to HER2-positive breast cancer cells in vitro. J Transl Med 2012; 10: ...
DNA of the identified clones were isolated using the Wizard® Plus SV Minipreps DNA Purification System (Promega). Nucleotide ... A peptide aptamer library was screened using an anti-HPA-1a human monoclonal antibody as a bait to isolate an aptamer that ... 23 a peptide aptamer able to specifically bind this particular antibody should mimic the HPA-1a antigen. Such a peptide aptamer ... the variable region of the Trx-HPA-1a aptamer interacts specifically with anti-HPA-1a antibodies. Indeed this aptamer interacts ...
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 ...
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. ...
Aptamer specific to a ligand. A synthesis of ligand-specific riboswitch includes selecting aptamers from a pool of nucleotide ... The most commonly used aptamers are theophylline and tetracycline aptamers. The theophylline aptamers are known to be toxic in ... aptamer]. Riboswitches induce rely on the function of an aptamer to bind small-molecule and, ... aptamer]. Riboswitches induce rely on the function of an aptamer to bind small-molecule and, ...
A61K51/0491-Sugars, nucleosides, nucleotides, oligonucleotides, nucleic acids, e.g. DNA, RNA, nucleic acid aptamers ... Aptamers specific for thrombin and methods of use WO1992014843A1 (en) * 1991-02-21. 1992-09-03. Gilead Sciences, Inc.. Aptamer ... Aptamers specific for thrombin and methods of use WO1992014843A1 (en) * 1991-02-21. 1992-09-03. Gilead Sciences, Inc.. Aptamer ... Aptamer-toxin molecules and methods for using same US7767803B2 (en) 2002-06-18. 2010-08-03. Archemix Corp.. Stabilized aptamers ...
L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. L-RNA ... L-RNA aptamers themselves have low antigenicity. In contrast to other aptamers, L-RNA aptamers have high stability in blood ... such as PEGylated L-RNA aptamers, show a prolonged plasma half-life. Unlike other aptamers, L-RNA aptamers are not directly ... This information is used for the synthesis of the oligonucleotides enantiomer, the L-RNA aptamer, using L-nucleotides. L-RNA ...
  • Aptamers are single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) oligonucleotides, which are able to bind their target with high selectivity and affinity. (
  • We isolated specifically interacting oligonucleotides, and biochemical strategies were used to identify the protein target for one of the aptamers. (
  • Generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), aptamers are short synthetic oligonucleotides, either DNA or RNA, that specifically bind target molecule(s) with high specificity due to their specific and complex three-dimensional shape comprised stems, loops, bulges, hairpins, pseudoknots, triplexes, and quadraplexes [ 12 - 14 ]. (
  • SELEX products were named 'aptamers,' which are single-stranded RNA or DNA oligonucleotides that bind with high affinity to specific targets such as proteins, small molecules, nucleic acids and cells. (
  • L-RNA aptamers, built using L-ribose, are the enantiomers of natural oligonucleotides, which are made with D-ribose. (
  • Aptamers are single stranded DNA or RNA oligonucleotides whose three-dimensional structures are dictated by their sequences. (
  • DNA aptamers are strands of DNA oligonucleotides that have the ability to bind to target molecules, such as proteins, and could be used as diagnostic tools and therapeutic agents. (
  • The chemically synthesized single-standard oligonucleotides (a polynucleotide which contains a relatively small number of nucleotides) are aptamers. (
  • 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. (
  • We have identified two synthetic oligonucleotides (aptamers) that bind to prostate cancer cells,with low nanomolar affinity, via the extracellular portion of the prostate-specificmembrane antigen (PSMA). (
  • The report compares RNAi with other antisense approaches using oligonucleotides, aptamers, ribozymes, peptide nucleic acid and locked nucleic acid. (
  • The spectrophotometer is used daily for an average of 5-10 measurements to quantify natural and modified nucleotides and oligonucleotides. (
  • The ability of DNA and RNA oligonucleotides to make strong interactions with other types of molecules, including metal ions, small molecules and large macromolecules such as proteins and viruses, has recently been studied: such oligonucleotides are called aptamers. (
  • The exceptional ability of aptamers to bind to these non-nucleic acid targets is due to the secondary structures (e.g. hairpins, loops, quadruplexes) that oligonucleotides can adopt, rather than Watson-Crick hydrogen bonding or base stacking. (
  • Moreover, heparin-induced anti-human-PF4/heparin antibodies cross-reacted with human PF4/nucleic acid and PF4/aptamer complexes, as shown by an enzyme immunoassay and a functional platelet activation assay. (
  • Finally, administration of PF4/44mer-DNA protein C aptamer complexes in mice induced anti-PF4/aptamer antibodies, which cross-reacted with murine PF4/heparin complexes. (
  • Moreover, administration of therapeutic aptamers has the potential to induce anti-PF4/polyanion antibodies and a prothrombotic diathesis. (
  • In mouse models of systemic lupus erythematosus, attempts were made to block the function of these cross-reacting antibodies using peptide aptamers, derived either from their cognate peptide self-antigens or from phage display libraries [ 10 , 11 ]. (
  • Another viable approach to block antinuclear antibodies might be to use DNA aptamers, given the high-affinity of these antibodies for DNA and evidence of nucleotide base specificity. (
  • But this approach has clearly been underexplored, perhaps due to the lack of reports on the feasibility of developing DNA aptamers to block the function of specific antibodies. (
  • Design and Methods Peptide aptamer was used to detect and identify HPA-1a-specific antibodies in human serum that do not require human platelets. (
  • Indeed, the peptide aptamer technology allows specific peptide ligands to be isolated for any given protein or domain, including antibodies. (
  • The affinity of L-RNA aptamers to their target molecules often lies in the pico to nanomolar range and is thus comparable to antibodies. (
  • Aptamers are developed from more reliable procedures than the manufacture of monoclonal antibodies. (
  • α-Gal-tagged aptamers lead to GAS opsonization with anti-Gal antibodies. (
  • 3 Aptamers offer several advantages as recognition elements for biosensor applications relative to antibodies. (
  • In the past 30 to 40 years, synthesis technology has significantly improved to allow the development of a wide variety of polymers, and the application of functional molecules such as aptamers 5 and single-chain antibodies 6 has improved performance. (
  • Although aptamers are similar to antibodies in their universalism as research tools, the fact that they can be accessed synthetically by standard oligonucleotide synthesis is advantageous in several respects. (
  • We have recently developed a new class of inhibitory (CTLA-4) and agonistic (4-1BB and OX-40) ligands composed of short oligonucleotide (ODN) aptamers that exhibited bioactivities comparable or superior to that of antibodies. (
  • To reduce toxicity, the immunomodulatory aptamers were targeted to the tumor by conjugation to a second aptamer that bound to a product expressed on the surface of the tumor cell, the targeting aptamer, generating a bispecific aptamer conjugate analogous to bispecific antibodies. (
  • In a proof-of-concept study in mice, we have shown that an agonistic 4-1BB-binding aptamer conjugated to a prostate-specific membrane antigen (PSMA)-binding aptamer led to the inhibition of PSMA-expressing tumors, was more effective than, and synergized with, vaccination, and exhibited a superior therapeutic index compared with nontargeted costimulation with 4-1BB antibodies or 4-1BB aptamers. (
  • The cell-free chemically synthesized ODN aptamers offer significant advantages over antibodies in terms of synthesis, cost, as well as conjugation chemistry needed to generate bispecific ligand fusions. (
  • The ability of aptamers to replicate the behaviour of antibodies has led to excitement about the potential of use of aptamers in diagnostic and therapeutic applications. (
  • Ease of synthesis: Aptamers can be synthesized using solid phase oligonucleotide synthesis, whereas antibodies have to be obtained using less efficient biochemical or biological methods. (
  • 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. (
  • They are particular suitable for quantum dot-stimulated FRET-based (beacon) aptamer assays [61]. (
  • This approach can be further exploited for the characterization of aptamer specificity and ultimately facilitate the development of aptamer-based assays depending on the desired specificity. (
  • The binding specificity and affinity of aptamers have long been harnessed as the key elements in the development of aptamer-based assays, particularly aptasensing application. (
  • One promising avenue that is currently explored based on the specificity and affinity of aptamers is the application of aptamers in the decontamination assays. (
  • 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. (
  • Malachite green binding aptamers were already for screening assays [4] and aptamers in general were lately tested in mammalian cells in vivo (F. Simmel, personal communication). (
  • 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. (
  • Some of the highest affinity and most specific aptamers in the down-selected libraries were demonstrated to have diagnostic utility in lateral flow chromatographic assays and in a fluorescent aptamer-magnetic bead sandwich assay. (
  • Diagnostic utility of some of the aptamers for arbovirus detection in lateral flow chromatographic assays and a fluorescent sandwich assay on the surface of magnetic microbeads is also demonstrated. (
  • Several different approaches have been taken to development of homogeneous fluorescent aptamer assays including end-labeled beacons and signaling aptamers which are intrinsically quenched by nucleotides. (
  • Two new strategies dubbed 'intrachain' and 'competitive' FRET-aptamer assays are summarized in this review. (
  • Among these, three aptamers showed the highest affinity to PE in electrophoretic mobility shift assays and in dot blots. (
  • They called these RNA sequences-and later similarly behaving and selected single-stranded DNA molecules [ 2 ]-aptamers. (
  • Rare aptamer sequences are identified via solution-phase SELEX , thereby circumventing target tethering and epitope masking. (
  • In SELEX experiments, aptamers are identified for their abilities to bind a protein of interest from libraries containing up to 10 16 different RNA or DNA sequences [ 19 ]. (
  • From a diverse starting population of different DNA or RNA nucleotide sequences, the ones that bind best to the target molecule are selectively enriched, and the process is repeated over multiple "generations. (
  • Utilizing the intron homing process, the aptamer-coding sequences were integrated into hundreds of rRNA genes, and the aptamers were transcribed at high levels by RNA polymerase I without any additional promoter being introduced into the cell. (
  • In the article entitled 'Pharmacokinetic Properties of DNA Aptamers with Base Modifications,' Nebojsa Janjic, SomaLogic (Boulder, CO) and coauthors from SomaLogic and Otsuka Pharmaceutical (Tokushima, Japan), describe what effect the lengths of aptamer sequences have on plasma resident time. (
  • b) A sequence logo representing the nucleotide conservation as well as information content at each position in our structure-based alignment of 302 sequences. (
  • By round six, 95% of the aptamer pool consisted of just two sequences. (
  • These two aptamers, termed xPSM-A9 and xPSM-A10, were cloned and found to be unique, sharing no consensus sequences. (
  • Methods of combinatorial biochemistry allow the identification of nucleic acid sequences, or aptamers, which can bind their target molecules with high affinity and specificity and are able to efficiently inhibit their biological function. (
  • In a standard library, a randomised sequence that can vary considerably in length is flanked by known sequences of approximately 20 nucleotides that serve as primer binding sites that allow reverse transcription (in case of RNA libraries) and amplification of selected sequences by the polymerase chain reaction (PCR). (
  • The nucleotide sequences of the ligand binding core and supporting architectures of each aptamer class are highly conserved among different species as a result of their need to form a precise receptor for a specific ligand. (
  • some have coined "in silico" maturation, selected aptamer sequences undergo an iterative process of point mutations to identify variants that maintain selective binding with enhanced affinity (4). (
  • Several arbovirus DNA aptamer sequences emerged multiple times in the various down selected aptamer libraries thereby suggesting some consensus sequences for binding arbovirus envelope proteins. (
  • Additional study of the aptamer sequences and secondary structures of top-ranked anti-arboviral aptamers suggest potential virus binding motifs exist within some of the key aptamers and are highlighted in the supplemental figures for this article. (
  • This article catalogues numerous DNA aptamer sequences which can bind various important pathogenic arboviruses and have, in some cases, already demonstrated diagnostic potential. (
  • These aptamer sequences are proprietary, patent-pending, and partially characterized. (
  • The aptamer DNA sequences have been divulged in a U.S. patent application (No. 13/199,082, Publication No. 2012/0149889 A1). (
  • 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). (
  • I identify the minimal primary structure containing a pseudoknot in many of these aptamers sequences. (
  • DNA aptamers RT5, RT6 and RT47 form a group of related sequences that inhibit HIV-1 reverse transcriptase (RT). (
  • Because these three aptamers differ only in the loop sequences connecting the individual guanosine triplets of the quadruplex, we conclude that the loop sequences in RT6-B render that aptamer sensitive to ionic destabilization, while the simplified structures of R1T and SN stabilize those aptamers to ionic substitution.Figure 3. (
  • One advantage aptamers may have over small molecules is that, given an aptamer with moderate affinity for a target (e.g. as the result of a SELEX experiment) it is trivial to synthesize derivatives of that molecule with slightly different sequences, and to incorporate modifications. (
  • Researchers are now using DNA to store massive amounts of data, for example, including books and images, a Shakespearean sonnet, and even a computer operating system, with data encoded in the molecule's nucleotide sequences. (
  • In this study, we have performed in vitro selection experiments to isolate DNA aptamers that can specifically bind geniposide. (
  • The present disclosure relates to an RNA aptamer and uses thereof, in particular, an aptamer which specifically bind to EpCAM and which demonstrates superior tumor penetrating ability. (
  • Aptamers are able to bind a wide variety of targets from divalent metal ions, small organic molecules, proteins, and cells [ 15 , 16 ]. (
  • This study demonstrates that nucleic acids, including aptamers, also bind to PF4 and enhance PF4 binding to platelets. (
  • Like other aptamers, L-RNA aptamers are able to bind molecules such as peptides, proteins, and substances of low molecular weight. (
  • Aptamers in our case are defined as artificially designed single stranded nucleotides designated to specifically bind ligands. (
  • They show that their aptamers containing Ds bases at only a few positions bind to two human target proteins with an affinity that is 100 times higher than aptamers containing only natural bases. (
  • We show that a specific DNA aptamer conjugated to an α-Gal epitope at its 5′ end, herein termed an alphamer, can bind to group A Streptococcus (GAS) bacteria by recognition of a conserved region of the surface-anchored M protein. (
  • Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. (
  • These two specific aptamers were selected from an initial 40mer library of ∼6 × 10 14 random-sequence RNA molecules for their ability to bind to a recombinant protein representing the extracellular 706 amino acids of PSMA, termed xPSM. (
  • These are the first reported RNA aptamers selected to bind a tumor-associated membrane antigen and the first application of RNA aptamers to a prostate specific cell marker. (
  • Aptamers are short single-stranded nucleic acids that can bind with high affinity to a wide variety of protein targets. (
  • Nucleic acid aptamers have long demonstrated the capacity to bind viral envelope proteins and to inhibit the progression of pathogenic virus infections. (
  • Some of the reported aptamers may also be able to bind viral envelope proteins in vivo and therefore may have antiviral potential in passive immunity or prophylactic applications. (
  • One sequence segment (ACGGGTCCGGACA) emerged 60 times in the anti-CCHF aptamer library, but nowhere else in the anti-arbovirus library and only a few other times in a larger library of aptamers known to bind bacteria and rickettsia or other targets. (
  • A new study has demonstrated the enhanced ability of an optimized 20-nucleotide derivative of a larger DNA aptamer to bind myelin in a mouse model of multiple sclerosis. (
  • Oligonucleotide aptamers bind and inhibit the RNA- and DNA-dependent polymerization activities of HIV RT. (
  • Nucleic acid aptamers bind RT in the primer/template binding site. (
  • To identify novel inhibitory molecules of PE, we used an in vitro selection method based on systematic evolution of ligands by exponential enrichment known as SELEX in order to select 2'F-modified RNA aptamers that specifically bind to PE. (
  • To facilitate analysis of cellular RNAs, aptamers Spinach and Spinach2 that bind and activate the conditional fluorophore 3, 5-difluoro-4-hydroxybenzylidene imidazolinon have been developed. (
  • It is a single-stranded oligonucleotide (a biological polymer consisting of a relatively small number of nucleotides chemically bound in a linear sequence that forms a chain-like structure) and, importantly, has no pharmacologic activity other than to bind to and modulate the therapeutic effect of pegnivacogin. (
  • SYBR Green based ELISA was conducted to evaluate the specific binding affinity of the DNA aptamer by incubating 50 µL of multiple concentrations of soluble HSV-1 gD, gB proteins. (
  • The development of more aptamers specific to cancer cells or marker proteins is urgently needed, especially for these applications. (
  • By their targeting of short, linear motif type of interactions, peptide aptamers have joined nucleic acid aptamers for use in signaling studies because of their ease of production, their stability, their high specificity and affinity for individual target proteins, and their use in high-throughput screening protocols. (
  • Nucleic acid aptamers are short, single-stranded RNAs and DNAs that represent high-affinity and highly selective ligands for different targets, ranging from large proteins to peptides, nucleotides, drugs and small compounds, and even metal ions. (
  • Rapidly and effectively predicting aptamer-protein interacting pairs is significant to design aptamers binding to certain interested proteins, which will give insight into understanding mechanisms of aptamer-protein interacting pairs and developing aptamer-based therapies. (
  • The features for aptamers are extracted from Pseudo K-tuple Nucleotide Composition (PseKNC) while the features for proteins incorporate Discrete Cosine Transformation (DCT), disorder information, and bi-gram Position Specific Scoring Matrix (PSSM). (
  • These results suggest that the proposed method can be a potential candidate for aptamer-protein interacting pair prediction, which may contribute to finding novel aptamer-protein interacting pairs and understanding the relationship between aptamers and proteins. (
  • Due to the physiological functions and practical applications of aptamers, designing aptamers binding to certain interested proteins is crucial to gain insight into mechanisms of aptamer-protein interacting pairs and develop aptamer-based therapies for various diseases. (
  • Obviously, it is time-consuming and costly to design aptamers for specific proteins using experimental methods. (
  • Our goal was to generate oligonucleotide ligands that recognize tumor-associated proteins on/within living cells, simultaneously identifying target proteins and DNA aptamers. (
  • In addition, the aptamer eluted FLAG-tagged proteins from the antibody, suggesting a commercial application in protein purification. (
  • Peptide aptamers are recombinant proteins which can interact with any given protein target with high specificity. (
  • Studies have shown that small target molecules enable a greater signal gain for low density aptamer packing, while larger proteins as a target generate the greatest signal at intermediate probe packing densities. (
  • Iso lated aptamers may directly inhibit the function of target proteins, or they can also be formulated for use as delivery agents for other therapeutic or imaging cargoes. (
  • However, conventional DNA aptamers consisting of natural or modified natural nucleotides often lack the desired binding affinity and specificity to target proteins. (
  • Since then, hundreds of aptamers have been selected that recognise a plethora of targets such as small molecules, peptides, proteins and even living cells or viruses (3). (
  • Aptamers are nucleic acid or peptide based binders that specifically recognized proteins, nucleic acids, and other molecules. (
  • Here we report on initial efforts to develop and screen DNA aptamers against recombinant envelope proteins or synthetic peptides and whole inactivated viruses from several virulent arboviruses including Chikungunya, Crimean-Congo hemorrhagic fever (CCHF), dengue, tickborne encephalitis and West Nile viruses. (
  • Such is the case with the following body of aptamer sequence, screening, and structural data for aptamers developed against recombinant proteins or synthetic peptides and whole inactivated viruses that were developed as part of several Small Business Innovative Research (SBIR) contracts with the U.S. Defense Department (see the Acknowledgments section for contract numbers) for diagnostic applications. (
  • Nanoparticles that are suitable for detection and loading with drugs can be directed to the site of their action by use of the affinity and specificity of aptamers, which are conjugated to the nanoparticles or fixed on their surface. (
  • Aptamers can facilitate cell-specific drug delivery in a selective manner to the sick cancer cells because of their binding specificity. (
  • Binding specificity and affinity of aptamers are harnessed in various applications, majorly in biosensing applications [ 10 , 11 , 17 - 26 ]. (
  • Dr Hirao and his team now working at the Division of Structural and Synthetic Biology of the RIKEN Center for Life Science Technologies in Yokohama have developed a new method to greatly increase aptamer affinity and specificity. (
  • Sensors employing split aptamers that reassemble in the presence of a target can achieve excellent specificity, but the accompanying reduction of target affinity mitigates any overall gains in sensitivity. (
  • X-aptamers incorporate chemically modified nucleotides and DNA backbones to achieve a greater range of possible targets or increase affinity and specificity. (
  • Aptamers with the desired specificity are selected using the yeast two hybrid system or established display techniques. (
  • 2011) RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers . (
  • Aptamers, first reported by Ellington and Gold in 1990 [ 1 , 2 ], are single stranded DNA/RNA molecules or peptide molecules [ 3 ]. (
  • Part II contains basic procedures about the selection and characterization of aptamer molecules, and Part III describes fundamental processes of MIP generation and application. (
  • Large combinatorial libraries of RNA or DNA molecules are used to isolate and evolve aptamers which achieve surprisingly high affinity and specifity. (
  • The devices uses small snippets of DNA called aptamers to latch onto estrogen molecules. (
  • Estrogen molecules that are caught by the short aptamer disrupt this layer, which in turn changes the current through the device. (
  • Estrogen molecules caught by the longer aptamer are likely held above the bilayer, and so do not create the electrical signal. (
  • Polymerases are also used to incorporate modified nucleotides, including those that tag, report, or signal the presence of product DNA molecules. (
  • Aptamers are special class of molecules that combine the advantages of both low molecular weight and protein molecules. (
  • Aptamers illustrate lock-and-key relationship between aptamer molecules and binding partners i.e., target molecules. (
  • Described herein are methods and compositions relating to the treatment of cancer, e.g., breast cancer, using, e.g., aptamer-siRNA chimera molecules. (
  • Aptamers are generally non-toxic and non-immunogenic molecules making them enticing drug prospects. (
  • MTT based cytotoxicity assay for 2 different aptamer concentrations were conducted along with a random DNA sequence and mock PBS. (
  • Analogous to the point-of-care diagnostics, there is no doubt that aptamers can also be deployed in the point-of-care aptamer-based decontamination assay, whereby decontamination can be performed anywhere and anytime for instantaneous decision-making. (
  • Apart from biosensing application, aptamers have also been the subject in the aptamer-based capture assay. (
  • In the capture assay applications, aptamers are applied for the purification of their corresponding targets for a wide variety of purposes [ 11 , 27 , 28 ]. (
  • The present review seeks to present an overview of the more narrowed context of the aptamer-based capture assay, which is on the usage of the aptamer in the decontaminating process or simply abbreviated as apta-decontamination assay. (
  • 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. (
  • We developed a simple aptamer fluorescence assay for aflatoxin B1 (AFB1) detection by using an array of capillaries. (
  • 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. (
  • Screening of aptamers by enzyme-linked aptamer sorbent assay (ELASA) was useful for ranking relative aptamer affinities against their cognate viral targets. (
  • 11. The aptamer according to claim 9 or 10, wherein the cell is in vivo or in vitro. (
  • Aptamers were selected with the optimized magnetic epoxy beads method described in the Supplementary Material and used in vitro at 150 nmol/L unless otherwise specified. (
  • Generally, aptamers can be artificially generated in vitro by a process commonly referred to as SELEX (Systematic Evolution of Ligands by Exponential Enrichment) [ 18 ], which consists of several repeated rounds of binding, partition, and amplification [ 2 ]. (
  • 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. (
  • By introducing the malachite-green binding aptamer to the Parts Registry we provide a nice tool to evaluate transcription both in vitro and in vivo. (
  • The immense diversity in function and structure of nucleic acids enable numerous aptamers to be generated through an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). (
  • 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. (
  • The selection process in vitro also allows precise control about the course of the selection and thus, some manipulation of the properties of the resulting aptamers is possible. (
  • In the year 2004, 14 years after the pioneering description of the in vitro selection of aptamers, the first aptamer was approved as a drug by the Food and Drug Administration (FDA) (4). (
  • Nucleic acid aptamers are engineered through SELEX or in vitro selection. (
  • In Vitro Selection of RNA Aptamers Directed Against Protein E: A Haemophilus influenzae Adhesin. (
  • and second particles coupled to a second oligonucleotide, the second oligonucleotide complementary to at least a portion of the aptamer. (
  • 8. The system of claim 5, where the hybridization stability of the aptamer in combination with the analyte is greater than the hybridization stability of a portion of the aptamer with the second oligonucleotide. (
  • The 15-mer DNA oligonucleotide 5'-GGTTGGTGTGGTTGG-3', known as thrombin binding aptamer (TBA), is a highly potent inhibitor of the enzyme. (
  • They generated DNA aptamers through evolutionary engineering using an oligonucleotide library containing adenine, guanine, thymine, cytosine and the highly hydrophobic unnatural base, Ds. (
  • Library synthesis: Because of the way solid phase oligonucleotide synthesis works, it is trivial to generate large libraries of similar DNA and RNA aptamers, which are necessary for selection experiments. (
  • The aptamers NS5A-4 and NS5A-5 inhibit HCV RNA replication and infectious virus production without causing cytotoxicity in human hepatocytes. (
  • For identification of specific peptides that interact and inhibit the stalled-ribosome rescues, peptide aptamer library (pTRG-SN-peptides) was constructed using pTRG as vector and Staphylococcus aureus nuclease (SN) as scaffold protein, in which 16 random amino acids were introduced to form an exposed surface loop. (
  • Notably, the aptamer did not entirely inhibit HSF function, as in some cases an increase in transcription still occurred after HS. (
  • The affinity of each aptamer for PSMA was quantitated by its ability to inhibit NAALADase activity. (
  • 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 position 277 for other aptamers. (
  • Aptamers that are un-reactive to the identity of this amino acid represent a group which may inhibit RT from other viruses as well. (
  • In this work I present a set of aptamers with unknown secondary structure which in some cases inhibit polymerization activity by RT from two HIV subtypes with different polymorphisms at position 277. (
  • Novel bimodular DNA aptamers with guanosine quadruplexes inhibit phylogenetically diverse HIV-1 reverse transcriptases. (
  • Such aptamers can be isolated from combinatorial libraries by SELEX (systematic evolution of ligands by exponential enrichment) [ 3 ]. (
  • Aptamers against NS5A were screened and obtained by the selective evolution of ligands by exponential enrichment approach and the antiviral actions of the aptamers were tested. (
  • Using SELEX (systematic evolution of ligands by exponential enrichment), we serendipitously discovered a ssDNA aptamer that binds selectively to the anti-FLAG M2 antibody. (
  • A novel HER2 aptamer (HB5) has recently been developed using systematic evolution of ligands by exponential enrichment technology (SELEX). (
  • Unlike other aptamers, L-RNA aptamers are not directly made using systematic evolution of ligands by exponential enrichment (SELEX), as L-nucleic acids are not amenable to enzymatic methods, such as polymerase chain reaction (PCR), used in SELEX. (
  • 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. (
  • 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. (
  • The selected aptamer was an 86-nucleotide DNA molecule that bound to an epitope peptide of HER2 with a K d of 18.9 nM. (
  • An L-ribonucleic acid aptamer (L-RNA aptamer, trade name Spiegelmer) is an RNA-like molecule built from L-ribose units. (
  • Depending on the size and nature of target molecule, different aptamer packing densities favor signal gain. (
  • The beauty of the aptamer plus CNT FET sensors is that the aptamers can be easily replaced with new ones that target a different molecule, Plank said. (
  • However, lack of regulatory guidelines on molecule development and some of the unfavorable characteristics of the aptamers are hampers growth of the market. (
  • The procedure commonly used for the selection of aptamers for a specific target molecule is known as SELEX process. (
  • 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. (
  • Our own approach starts from the analysis of the crystal structure of RNA aptamer-small molecule complexes. (
  • The peptide aptamer PA-2 was selected from pTRG-SN-peptides by bacterial two-hybrid system (B2H) employing pBT-SmpB or pBT-ArfA as baits. (
  • Aptamer-derived peptides as potent inhibitors of the oncogenic RhoGEF Tgat. (
  • however, the small size of aptamers makes them susceptible to renal filtration (this can be overcome by conjugation to peptides or polymers… but this increases the molecular weight). (
  • 1. An isolated RNA aptamer which binds specifically to EpCAM, wherein the aptamer is not DT3 having the sequence GCGACUGGUUACCCGGUCG (SEQ ID NO:1). (
  • 9. The aptamer according to any preceding claim, wherein the aptamer specifically binds to EpCAM + cell(s). (
  • A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1. (
  • We deliver siRNAs into epithelial cancer cells by linking them to an RNA aptamer that binds to EpCAM, the first described tumor antigen, a cell surface receptor overexpressed on epithelial cancers, including basal-like TNBCs. (
  • As HSF1 enables and promotes malignant growth and metastasis in mammals, and this aptamer binds yeast HSF1 and its mammalian ortholog with equal affinity, the results presented here attest to the potential of this aptamer as a specific and effective inhibitor of HSF1 activity. (
  • One aptamer was truncated from 23.4 kDa to 18.5 kDa and specifically binds LNCaP human prostate cancer cells expressing PSMA but not PSMA-devoid PC-3 human prostate cancer cells. (
  • To this aim, we selected a new RNA aptamer that specifically targets IL4Rα because of the importance of this receptor in MDSC suppressive function. (
  • RNA aptamers are nanomolecules that can recognize their targets with extremely high affinity. (
  • This aptamer selectively targets MDSCs and TAM in vivo , blocks IL4Rα signaling, induces MDSCs apoptosis, and significantly delays tumor progression in 4T1-bearing mice. (
  • Figure 1 depicts the structures of two aptamers binding to specific targets. (
  • Designing new therapeutic DNA aptamers with diverse side chains can improve their ability to interact with targets, and a new study describes characteristics of these side chains that may determine how long the aptamers remain in the bloodstream. (
  • The global aptamer market was valued at nearly US$1.0 bn in 2016 and is expected to expand with a CAGR of 20.0% over the forecast period from 2017 to 2025 to attain the value of US$5.0 bn by the end of 2025. (
  • Among these, SELEX technique is expected to account for the leading share in the global market for aptamer over the forecast period from 2017 to 2025. (
  • E-AB sensors are advantageous over previously reported aptamer-based sensors, such as fluorescence generating aptamers, due to their ability to detect target binding in vivo with real-time measurements. (
  • The 34-nt aptamer having a single fluorescein (FAM) label on the 24th T nucleotide generated a remarkable fluorescence increase upon AFB1 binding. (
  • A peptide aptamer library was screened using an anti-HPA-1a human monoclonal antibody as a bait to isolate an aptamer that mimics the human platelet antigen HPA-1a. (
  • Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. (
  • The building bricks of DNA are the nucleotides, made of nitrogen bases (adenine, guanine, thymine and cytosine), deoxyribose and phosphate groups. (
  • Tgat, a Rho-specific guanine nucleotide exchange factor, activates NF-kappaB via physical association with IkappaB kinase complexes. (
  • We previously identified Tgat as the oncogene, which consists of the Rho-guanine nucleotide exchange factor (Rho-GEF) domain and the unique C-terminal region, as a consequence of alternative splicing of the Trio transcript. (
  • Aptamer-derived peptide inhibitors of Rho guanine nucleotide exchange factors. (
  • Guanine riboswitches are involved in the regulation of transport and biosynthesis of purine metabolites, which are critical for the nucleotides cellular pool. (
  • 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. (
  • 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. (
  • NS5A aptamer disrupts the interaction of NS5A with core protein. (
  • 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. (
  • Aptamer-protein interacting pairs play a variety of physiological functions and therapeutic potentials in organisms. (
  • In this study, an ensemble method is presented to predict aptamer-protein interacting pairs with hybrid features. (
  • With a deeper understanding of aptamers in terms of their conformational and protein-binding properties, aptamer-protein interacting pairs have a potential to perform a variety of functions [ 8 , 9 ]. (
  • Therefore, it would be of help to develop a computational method for rapidly and effectively predicting the aptamer-protein interacting pairs based on sequence information. (
  • Here we characterize the interaction of the DNA aptamer, GBI-10, with tenascin-C, an extracellular protein found in the tumor matrix. (
  • The aptamer also specifically bound to the extracellular domain of HER2 protein with a K d of 316 nM. (
  • The binding of the aptamer with the target protein produces a change in impedance of the membrane which is picked up by the electrochemical sensor using an impedance spectroscopy analyzer. (
  • In contrast, peptide based aptamers consist of a variable loop region that is attached on both ends to a large scaffold protein for solubility. (
  • Slow Off-rate Modified Aptamers (SOMAmers 1 ) are a particular class of aptamers that consist of a short DNA sequence that incorporate several modified bases with protein-like side chains. (
  • Hence, they exploit the potential of synthetic nucleotide modifications to confer protein like characteristics and diversity to a nucleic acid scaffold. (
  • In the reaction between a ligand (aptamer) and receptor (target, e.g. a protein), the association constant, K a , is the equilibrium constant for the forward reaction, the formation of the complex, while the dissociation constant, K d , is the equilibrium constant for the reverse reaction, the dissociation of the complex. (
  • These aptamers have the potential to be further developed into analytical tools for the detection of geniposide. (
  • The huge potential of aptamer-nanoparticle-based detection of cancer cells and biomedical in - vivo imaging has been shown, with some examples. (
  • They can additionally include organic dyes for optical detection, just as functional groups for their conjugation with aptamers [52, 61]. (
  • 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. (
  • [3] 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. (
  • The best aptamer candidates were then tested for binding to VEGF in ELASA, using a capture antibody with aptamer candidates for detection. (
  • 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. (
  • CAMBRIDGE, Mass.--(BUSINESS WIRE)--Dec 4, 2008 - Archemix Corp., a biotechnology company focused on discovering, developing and commercializing aptamer therapeutics, today announced that data from the company's Phase 2a clinical trial of ARC1779 will be presented at the 50th Annual Meeting of the American Society of Hematology in San Francisco, Calif., December 6 to 9, 2008. (
  • They must tolerate amino acid or nucleotide substitutions within their target binding regions in order to be amenable to screening of combinatorial libraries. (
  • While some researchers utilize libraries with modified bases for aptamer selection, modified nucleotide substitutions are also applied post-selection to improve the performance of natural DNA and RNA aptamers. (
  • 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. (
  • The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. (
  • HDV-like ribozymes, which have only five conserved, non-contiguous nucleotides out of approximately 50 necessary to form the minimal catalytically-proficient double-pseudoknot [ 18 , 20 ], represent a particularly striking example of a functional RNA with low sequence conservation and strict structural requirements. (
  • Here, we present a brief survey of the use of aptamers in signaling pathways, in particular of polypeptide growth factors, starting with the published as well as potential applications of aptamers targeting Epidermal Growth Factor Receptor signaling. (
  • First, aptamers can be chemically synthesized with high reproducibility at relatively low cost. (
  • Via hybridization, we detect and differentiate single-nucleotide polymorphisms sans amplification. (
  • However, for the same reason it is not possible to apply the same amplification and selection mechanisms as for RNA- and DNA-aptamers. (
  • This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. (
  • Major advances in "next generation" sequencing, which requires the use of modified nucleotides and DNA polymerases, are considered in a separate review in this series ( Chen, 2014 ). (
  • This unit helps you understand the properties of nucleotides and how they contribute to secondary and tertiary structures of nucleic acids at the molecular level. (
  • Molecular phenotype of the inhibitory HSF aptamer. (
  • Recent work has established aptamers as a powerful tool for the identification of low molecular weight lead compounds. (
  • 2011) Synthesis and radiolabeling of chelator-RNA aptamer bioconjugates with copper-64 for targeted molecular imaging . (
  • Systematic assessment of RNA and DNA constructs, as well as 4 aptamers of different lengths and secondary structures, revealed that increasing length and double-stranded segments of nucleic acids augment complex formation with PF4, while single nucleotides or single-stranded polyA or polyC constructs do not. (
  • 6 Finally, it is possible to generate unstructured aptamers that form specific secondary structures such as three-way junctions 7,8 or tertiary folds such as G-quadruplex structures 9,10 upon target binding. (
  • truncated the sequence to destabilize the aptamer, so that it exists in an equilibrium state consisting of both folded and unfolded structures. (
  • We also analyzed sequence data and secondary structures for commonalities that might reveal consensus binding sites among the various aptamers. (
  • Secondary structure and positional entropy plot of the aptamer domain of purine riboswitches. (
  • In most instances, riboswitches can be divided into aptamer and expression platform regions that represent two functionally distinct but usually physically overlapping domains responsible for ligand binding and gene control, respectively. (
  • The laboratory specializes in generating modified nucleoside triphosphate analogs used to isolate DNA and RNA aptamers and catalysts. (
  • 8. The aptamer according to any preceding claim comprising one or more modifications that increase aptamer stability. (
  • In contrast to other aptamers, L-RNA aptamers have high stability in blood serum, since they are less susceptible to be cleaved hydrolytically by enzymes. (
  • Additionally, factors such as high thermal stability and cost-efficiency are likely to boost adoption of the aptamer which is likely to boost growth of the global aptamer market. (
  • 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. (
  • In some cases, selected aptamers may not quite achieve the degree of affinity or stability required for a specific end-use application. (
  • It is thought that reduction of the sequence length may reduce steric hindrance, decrease the number of intermolecular interactions that must be disrupted for target binding, or improve stability of the tertiary aptamer structure (6,9). (
  • The site-specific replacements improved structural stability and aptamer activity (14). (
  • Substitution of 2'-O-methyl RNA for purines and pyrimidines at the 3' end of the aptamer were most effective at increasing stability without altering aptamer affinity or selectivity (8). (
  • More recently, researchers have added lipid-modified bases to the 5' end of an aptamer to improve in vivo stability (12). (
  • conjugation is a simple way to enhance aptamer stability. (
  • Researchers in Korea explored cholesterol conjugation as a means of increasing aptamer stability. (
  • The simplified aptamers displayed increased overall stability. (
  • Consistent with the Watson-Crick model that considers both geometric and hydrogen bonding complementarity, the Z:P pair was found to contribute more to duplex stability than any mismatches involving either nonstandard nucleotide. (
  • Ex-vivo studies on pig corneal models showed therapeutic efficacy of the aptamer in reducing productive infection over a period of 168 hours. (
  • 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. (
  • An electrochemical aptamer-based (E-AB) biosensor has the ability to generate an electrochemical signal in response to specific target binding in vivo The signal is measured by a change in Faradaic current passed through an electrode. (
  • Questo studio elegante dimostra come le modifiche del nucleotide possono attenuarsi contro degradazione della nucleasi dei aptamers, vitale una preoccupazione quanto è la consegna per le riuscite applicazioni in vivo terapeutiche o diagnostiche,„ dice l'editore esecutivo Graham C. Parker, PhD, Carman ed il dipartimento di Ann Adams della pediatria, la scuola di medicina di Wayne State University, ospedale pediatrico del Michigan, Detroit, MI. (
  • 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. (
  • 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. (
  • Adding cholesterol to the 5' end of a modified RNA aptamer doubled the in vivo half-life (from ~ 6 to 12 hours) and increased the calculated bodily exposure to drug approximately 8-fold. (
  • The bimodular ssDNA aptamers inhibited RT from diverse primate lentiviruses with low nM IC(50) values. (
  • Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. (
  • This review focuses primarily on polymerase variants that accept nucleic acids having additional nucleotide "letters" that form additional nucleobase pairs. (
  • Synthetic nucleobases presenting non-Watson-Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. (
  • a) The conserved secondary structure of the aptamer domain is depicted such that each nucleotide position is represented as a colored dot with Watson-Crick base-pairing interactions shown as a bar/line connecting the interacting nucleotides. (
  • ptamers to increase aptamer-target interactions can often be used to increase affinity and / or selectivity. (
  • Our DNA aptamer showed specific binding affinity towards HSV-1 gD (Kd = 50 nM) and was able to restrict viral entry by 70% at a 2 µM concentration. (
  • Here we describe a new RNA aptamer specific for IL4Rα/CD124. (
  • Inhibition of hepatitis C virus infection by NS5A-specific aptamer. (
  • 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. (
  • We used this system to express an aptamer against the heat shock factor 1 (HSF1), a conserved transcription factor responsible for mobilizing specific genomic expression programs in response to stressful conditions such as elevated temperature. (
  • In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. (
  • Taken together, the data show that our GE system represents a safe and promising technology for editing specific nucleotides, correcting genetic mutations or other clinically relevant applications, independent of DSB and HDR, with potential therapeutic value in non-dividing cells. (
  • Once inside the cell, this material is processed into short 21-23 nucleotide RNAs termed siRNAs that are used in a sequence-specific manner to recognize and destroy complementary RNA. (
  • We are pioneering the discovery and development of two-component drug systems consisting of a therapeutic aptamer and its specific active control agent. (
  • These studies form the basis for further development of aptamer-labelled viral RNAs that will facilitate functional studies on the dynamics of infection and clearance. (
  • R1' is a strain expressing the antisense sequence of the aptamer monomer. (
  • The difference in ratios of mRNA levels under HS and NHS conditions for the aptamer and antisense strains for each gene analyzed indicated a downregulation of HSF1 activity by the aptamer. (
  • 2. The RNA aptamer according to claim 1 which has a dissociation constant for EpCAM of about 90 nM or less. (
  • 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. (
  • The density packing of DNA or RNA aptamers, the ACV frequency administered by the potentiostat, and the chemistry of the SAM are all factors that determine signal gain as well as the signal to noise ratio of target binding. (
  • The concentration of aptamer and the surface chemistry of the self-assembling monolayer (SAM) enable variations of desired probe packing density. (
  • J. Zhou and J. J. Rossi, "The Therapeutic Potential of Cell-Internalizing Aptamers," Current topics in Medicinal Chemistry, Vol. 9. (
  • J. Zhou and J. J. Rossi, "Bivalent Aptamers Deliver the Punch," Chemistry & Biology, Vol. 15. (
  • Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of DNA. (
  • We developed a powerful expression system to produce aptamers and other types of functional RNA in yeast to examine their effects. (
  • Combinatorial mutation interference analysis reveals functional nucleotides required for DNA catalysis. (
  • The structure of a complex between human alpha-thrombin and a GGTTGGTGTGGTTGG 15-nucleotide consensus sequence has been solved by x-ray crystallography and refined at 2.9-A resolution to an R value of 0.159. (
  • Following extensive modeling of a DNA aptamer to thrombin, researchers in Italy substituted T4 and T13 thymines with 5-fluoro-2'-deoxyuridine residues. (
  • Distinct modes of inhibition suggest that each aptamer identifies a unique extracellular epitope of xPSM. (