nucleotide aptamers

Summary

Summary: Nucleotide sequences, generated by iterative rounds of SELEX APTAMER TECHNIQUE, that bind to a target molecule specifically and with high affinity.

Top Publications

  1. Rieder U, Lang K, Kreutz C, Polacek N, Micura R. Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. Chembiochem. 2009;10:1141-4 pubmed publisher
    ..How pseudoknot formation mediates the mRNA response through its expression platform is now open for investigation. ..
  2. Roth A, Breaker R. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem. 2009;78:305-34 pubmed publisher
    ..This diverse set of metabolite-sensing RNAs is found to exploit a variety of distinct mechanisms to regulate genes that are fundamental to metabolism. ..
  3. Mosing R, Bowser M. Isolating aptamers using capillary electrophoresis-SELEX (CE-SELEX). Methods Mol Biol. 2009;535:33-43 pubmed publisher
    ..CE-SELEX is capable of isolating high-affinity aptamers in as little as 2-4 rounds of selection, shortening the process time from several weeks to as little as a few days. ..
  4. Baird N, Ferré D Amaré A. Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA. 2010;16:598-609 pubmed publisher
    ..It is possible that the range of behaviors observed by SAXS, rather than being a biophysical idiosyncrasy, reflects adaptation of riboswitches to the regulatory requirements of their individual genomic context. ..
  5. Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, et al. Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus. Nucleic Acids Res. 2009;37:4621-8 pubmed publisher
    ..aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer. ..
  6. Choi Y, Hur J, Lee H, Jeong S. The RNA aptamer disrupts protein-protein interaction between beta-catenin and nuclear factor-kappaB p50 and regulates the expression of C-reactive protein. FEBS Lett. 2009;583:1415-21 pubmed publisher
    ..Taken together, beta-catenin binding RNA aptamer was an effective regulator of beta-catenin and NF-kappaB p50 mediated transcription. ..
  7. Chushak Y, Stone M. In silico selection of RNA aptamers. Nucleic Acids Res. 2009;37:e87 pubmed publisher
    ..The proposed approach reduces the RNA sequences search space by four to five orders of magnitude--significantly accelerating the experimental screening and selection of high-affinity aptamers. ..
  8. Nishikawa F, Murakami K, Matsugami A, Katahira M, Nishikawa S. Structural studies of an RNA aptamer containing GGA repeats under ionic conditions using microchip electrophoresis, circular dichroism, and 1D-NMR. Oligonucleotides. 2009;19:179-90 pubmed publisher
    ..Mutational, circular dichroism, and one-dimensional NMR studies of wt2 revealed that K(+) ions induce wt2 to assume a thermostable dimer in an intramolecular G-quadruplex with parallel orientation. ..
  9. Xu D, Shi H. Composite RNA aptamers as functional mimics of proteins. Nucleic Acids Res. 2009;37:e71 pubmed publisher

More Information

Publications62

  1. Rieder R, Hobartner C, Micura R. Enzymatic ligation strategies for the preparation of purine riboswitches with site-specific chemical modifications. Methods Mol Biol. 2009;540:15-24 pubmed publisher
    ..We exemplarily provide a detailed protocol for the preparation of adenosine deaminase (add) A-riboswitch variants with 2-aminopurine (AP) modifications at the 40-nmol scale. ..
  2. Bing T, Yang X, Mei H, Cao Z, Shangguan D. Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories. Bioorg Med Chem. 2010;18:1798-805 pubmed publisher
    ..The highly variable sequence composition of streptavidin-binding aptamer would make the design of aptameric sensor or device based on streptavidin more flexible and easy. ..
  3. Miyachi Y, Shimizu N, Ogino C, Fukuda H, Kondo A. Selection of a DNA aptamer that binds 8-OHdG using GMP-agarose. Bioorg Med Chem Lett. 2009;19:3619-22 pubmed publisher
    ..22 DNA aptamer was on the order of 0.1micromol/L. This result suggests that using an analogue will be a useful new SELEX method for obtaining various aptamers that are difficult to immobilize on a matrix. ..
  4. Wurster S, Bida J, Her Y, Maher L. Characterization of anti-NF-kappaB RNA aptamer-binding specificity in vitro and in the yeast three-hybrid system. Nucleic Acids Res. 2009;37:6214-24 pubmed publisher
    ..These aptamers appear to be compact bulged hairpins, reminiscent of anti-p50. Y1 competitively inhibits the DNA-binding domain of NF-kappaB p65(2) in vitro. ..
  5. Dausse E, Da Rocha Gomes S, Toulmé J. Aptamers: a new class of oligonucleotides in the drug discovery pipeline?. Curr Opin Pharmacol. 2009;9:602-7 pubmed publisher
    ..Aptamers constitute promising molecules for therapeutic applications as exemplified by pegaptanib, an aptamer-derived anti-VEGF compound shown to be effective in treating age-related macular degeneration. ..
  6. Kang M, Peterson R, Feigon J. Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA. Mol Cell. 2009;33:784-90 pubmed publisher
    ..In the absence of preQ(1), the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ(1) biosynthesis. ..
  7. Kulshina N, Edwards T, Ferré D Amaré A. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA. 2010;16:186-96 pubmed publisher
  8. Poiata E, Meyer M, Ames T, Breaker R. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA. 2009;15:2046-56 pubmed publisher
    ..This tandem riboswitch arrangement exhibits an architecture that can potentially control both the transcriptional and translational stages of gene expression...
  9. Oney S, Lam R, Bompiani K, BLAKE C, Quick G, Heidel J, et al. Development of universal antidotes to control aptamer activity. Nat Med. 2009;15:1224-8 pubmed publisher
    ..The availability of universal antidotes to control the activity of any aptamer suggests that aptamers may be a particularly safe class of therapeutics. ..
  10. Mayer G. The chemical biology of aptamers. Angew Chem Int Ed Engl. 2009;48:2672-89 pubmed publisher
    ..This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed. ..
  11. Wieland M, Benz A, Klauser B, Hartig J. Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed Engl. 2009;48:2715-8 pubmed publisher
    ..The approach demonstrates that intrinsic metabolites can be utilized as external effectors of cellular functions. ..
  12. Spitale R, Torelli A, Krucinska J, Bandarian V, Wedekind J. The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem. 2009;284:11012-6 pubmed publisher
    ..The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated...
  13. Win M, Smolke C. Higher-order cellular information processing with synthetic RNA devices. Science. 2008;322:456-60 pubmed publisher
    ..RNA devices process and transmit molecular inputs to targeted protein outputs, linking computation to gene expression and thus the potential to control cellular function. ..
  14. Li T, Dong S, Wang E. G-quadruplex aptamers with peroxidase-like DNAzyme functions: which is the best and how does it work?. Chem Asian J. 2009;4:918-22 pubmed publisher
    ..Accordingly, a reaction mechanism for DNAzyme-catalyzed peroxidation is proposed. This study provides new insights into the G-quadruplex-based DNAzymes and will help us to further extend their applications in the analytical field. ..
  15. Gronewold T. Aptamers and biosensors. Methods Mol Biol. 2009;535:209-22 pubmed publisher
    ..Differences in the specificity were shown by use of the similar protein elastase. ..
  16. Zhang Y, Song M, Li T, Sai D, Wang H. [Determination of human thrombin by an aptamer based on affinity capillary electrophoresis-laser induced fluorescence detection]. Se Pu. 2009;27:333-6 pubmed
    ..6 pmol/L. Regarding the advantages of high efficiency and rapid separation, low sample consumption, and high sensitivity, CE-LIF is a potential and powerful alternative to conventional immunoaffinity assays in clinical diagnostics. ..
  17. Jun B, Rho C, Byun J, Kim J, Chung W, Kang H, et al. Multilayer fluorescence optically encoded beads for protein detection. Anal Biochem. 2010;396:313-5 pubmed publisher
    ..After binding, the ligands are identified easily by their color codes. ..
  18. Huang H, Zhu J. DNA aptamer-based QDs electrochemiluminescence biosensor for the detection of thrombin. Biosens Bioelectron. 2009;25:927-30 pubmed publisher
    ..In addition, the biosensor exhibited the excellent selectivity responses and good stability toward the target analyte. ..
  19. Priyakumar U, MacKerell A. Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol. 2010;396:1422-38 pubmed publisher
    ..The possibility of methodological artifacts and force-field inaccuracies impacting the present observations was checked by additional molecular dynamics simulations in the presence of 2,6-diaminopurine and in the crystal environment. ..
  20. Huang C, Lin H, Shiesh S, Lee G. Integrated microfluidic system for rapid screening of CRP aptamers utilizing systematic evolution of ligands by exponential enrichment (SELEX). Biosens Bioelectron. 2010;25:1761-6 pubmed publisher
    ..The developed microsystem demonstrated fast screening of CRP aptamers and can be used as a powerful tool to select analyte-specific aptamers for biomedical applications. ..
  21. Villa A, Wöhnert J, Stock G. Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res. 2009;37:4774-86 pubmed publisher
  22. Pastor F, Kolonias D, Giangrande P, Gilboa E. Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature. 2010;465:227-30 pubmed publisher
    ..The cell-free chemically synthesized oligonucleotide backbone of aptamer-siRNAs reduces the risk of immunogenicity and enhances the feasibility of generating reagents suitable for clinical use. ..
  23. Cekan P, Jonsson E, Sigurdsson S. Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç. Nucleic Acids Res. 2009;37:3990-5 pubmed publisher
    ..The EPR data indicate that nucleotides in helix I are more mobile than nucleotides in regular duplex regions and may reflect increased dynamics due to the short length of helix I. ..
  24. Wang C, Yang G, Luo Z, Ding H. In vitro selection of high-affinity DNA aptamers for streptavidin. Acta Biochim Biophys Sin (Shanghai). 2009;41:335-40 pubmed
    ..The method described in the study is also generally applicable to target molecules other than streptavidin. ..
  25. Latham M, Zimmermann G, Pardi A. NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. J Am Chem Soc. 2009;131:5052-3 pubmed publisher
    ..Comparisons with other ligand-receptor interactions are presented. ..
  26. Rarey K, Friberg T. Indirect laser treatment and anti-VEGF therapy of a retinal angioma, with resolution of a large serous retinal detachment, macular exudates, and macular edema. Semin Ophthalmol. 2010;25:21-6 pubmed publisher
    ..A combination of laser photocoagulation and anti-VEGF theraphy can be effective in the treatment of macular exudation and edema from a retinal angioma. ..
  27. Freeman R, Li Y, Tel Vered R, Sharon E, Elbaz J, Willner I. Self-assembly of supramolecular aptamer structures for optical or electrochemical sensing. Analyst. 2009;134:653-6 pubmed publisher
    ..The amperometric response of the system allows the detection of cocaine with a detection limit of 1 x 10(-5) M. The approach is generic and can be applied to other substrates, e.g. adenosine triphosphate. ..
  28. Zhang Z, Yang W, Wang J, Yang C, Yang F, Yang X. A sensitive impedimetric thrombin aptasensor based on polyamidoamine dendrimer. Talanta. 2009;78:1240-5 pubmed publisher
    ..The aptasensor exhibited favorable regeneration ability, selectivity and stability. It also showed the detectability in biological fluid. ..
  29. Barciszewski J, Medgaard M, Koch T, Kurreck J, Erdmann V. Locked nucleic acid aptamers. Methods Mol Biol. 2009;535:165-86 pubmed publisher
    ..LNA-Aps are attractive alternatives to antibody- and small-molecule-based therapeutics due to their stability, low toxicity and immunogenecity. ..
  30. Dobrovolsky A, Titaeva E, Khaspekova S, Spiridonova V, Kopylov A, Mazurov A. Inhibition of thrombin activity with DNA-aptamers. Bull Exp Biol Med. 2009;148:33-6 pubmed
    ..These data indicate that the studied antithrombin DNA aptamers effectively suppress its two key reactions, fibrin formation and stimulation of platelet aggregation, without modifying active center of the thrombin molecule. ..
  31. Marc D. Aptamers to explore prion protein interactions with nucleic acids. Front Biosci (Landmark Ed). 2010;15:550-63 pubmed
    ..This review will focus on these studies, their methods, the knowledge acquired from them about the prion protein, and the possibilities that they offer in the areas of diagnosis and therapy of prion diseases. ..
  32. Perrier S, Ravelet C, Guieu V, Fize J, Roy B, Perigaud C, et al. Rationally designed aptamer-based fluorescence polarization sensor dedicated to the small target analysis. Biosens Bioelectron. 2010;25:1652-7 pubmed publisher
    ..This reasoned approach was applied to the sensing of adenosine and adenosine monophosphate and their chiral analysis. ..
  33. Soontornworajit B, Zhou J, Shaw M, Fan T, Wang Y. Hydrogel functionalization with DNA aptamers for sustained PDGF-BB release. Chem Commun (Camb). 2010;46:1857-9 pubmed publisher
    ..We demonstrate that hydrogel functionalization with DNA aptamers can be applied for developing a novel sustained-release system. ..
  34. Zhang J, Wang L, Zhang H, Boey F, Song S, Fan C. Aptamer-based multicolor fluorescent gold nanoprobes for multiplex detection in homogeneous solution. Small. 2010;6:201-4 pubmed publisher
    ..This potentially generic strategy is shown to be promising for rapid screening of small molecular targets. ..
  35. Gonzalez V, Giuliari G, Banda R, Guel D. Intravitreal injection of pegaptanib sodium for proliferative diabetic retinopathy. Br J Ophthalmol. 2009;93:1474-8 pubmed publisher
    ..IVP produces short-term marked and rapid regression of diabetic retinal NV. Regression of NV was maintained throughout the study and at the final visit. ..
  36. Reinemann C, Stoltenburg R, Strehlitz B. Investigations on the specificity of DNA aptamers binding to ethanolamine. Anal Chem. 2009;81:3973-8 pubmed publisher
  37. Missailidis S, Hardy A. Aptamers as inhibitors of target proteins. Expert Opin Ther Pat. 2009;19:1073-82 pubmed publisher
    ..Despite a slow start, aptamers have been developed against various therapeutic proteins and offer the promise of providing a novel generation of therapeutic entities with a variety of applications. ..
  38. Huang Z, Pei W, Han Y, Jayaseelan S, Shekhtman A, Shi H, et al. One RNA aptamer sequence, two structures: a collaborating pair that inhibits AMPA receptors. Nucleic Acids Res. 2009;37:4022-32 pubmed publisher
    ..Thus, our results suggest more broadly that natural RNA molecules can evolve to acquire alternative structures and associated functions. Such divergence of RNA phenotype may precede gene duplication at the genome level. ..
  39. Williams B, Lin L, Lindsay S, Chaput J. Evolution of a histone H4-K16 acetyl-specific DNA aptamer. J Am Chem Soc. 2009;131:6330-1 pubmed publisher
    ..This result demonstrates that aptamers that are both modification and location specific can be generated to bind specific protein post-translational modifications. ..
  40. Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, et al. Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. RNA. 2010;16:1915-24 pubmed publisher
    ..Addition of the new element yields a sufficient binding site by the insertion criterion, binding tryptophan in 22 out of 23 tries. Random insertion testing for site sufficiency seems likely to be broadly revealing. ..
  41. Bloch S, Larsen M. [Treatment of wet age-related macular degeneration with vascular endothelial growth factor. A survey of a Cochrane review]. Ugeskr Laeger. 2009;171:3435-7 pubmed
    ..In clinical practice ranibizumab compared to pegaptanib is the drug of choice because of cost-utility analysis and the number of patients gaining visual acuity. ..
  42. Sun C, Liu X, Feng K, Jiang J, Shen G, Yu R. An aptazyme-based electrochemical biosensor for the detection of adenosine. Anal Chim Acta. 2010;669:87-93 pubmed publisher
    ..The fabricated sensor is shown to exhibit high sensitivity and desirable selectivity, which might be promising for the rational construction of aptazyme-based biosensors and the determination of adenosine in clinical examination. ..
  43. Park S, Ahn J, Jo M, Lee D, Lis J, Craighead H, et al. Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. Lab Chip. 2009;9:1206-12 pubmed publisher
    ..To our knowledge, this is the first demonstration of a chip-based selection of aptamers using microfluidics, thereby allowing development of a high throughput and efficient SELEX procedures. ..
  44. Kim N, Izzo J, Elmetwaly S, Gan H, Schlick T. Computational generation and screening of RNA motifs in large nucleotide sequence pools. Nucleic Acids Res. 2010;38:e139 pubmed publisher
    ..Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection. ..
  45. Min K, Song K, Cho M, Chun Y, Shim Y, Ku J, et al. Simultaneous electrochemical detection of both PSMA (+) and PSMA (-) prostate cancer cells using an RNA/peptide dual-aptamer probe. Chem Commun (Camb). 2010;46:5566-8 pubmed publisher
    ..This approach can be applied as a general tool for early diagnosis of prostate cancer. ..
  46. Kim E, Jung Y, Choi H, Yang J, Suh J, Huh Y, et al. Prostate cancer cell death produced by the co-delivery of Bcl-xL shRNA and doxorubicin using an aptamer-conjugated polyplex. Biomaterials. 2010;31:4592-9 pubmed publisher
    ..These results suggest that AP-mediated co-delivery of an anti-cancer drug and shRNA against Bcl-xL may widen the therapeutic window and allow for the selective destruction of cancer cells. ..
  47. Prychyna O, Dahabieh M, Chao J, O Neill M. Sequence-dependent folding and unfolding of ligand-bound purine riboswitches. Biopolymers. 2009;91:953-65 pubmed publisher
  48. Zhao Z, Xu L, Shi X, Tan W, Fang X, Shangguan D. Recognition of subtype non-small cell lung cancer by DNA aptamers selected from living cells. Analyst. 2009;134:1808-14 pubmed publisher
    ..The aptamers are expected to be new molecular probes for the investigation of the molecular bases of different NSCLC subtypes and their biological heterogeneity, which is valuable for advancing NSCLC diagnosis and treatment. ..
  49. Platt M, Rowe W, Knowles J, Day P, Kell D. Analysis of aptamer sequence activity relationships. Integr Biol (Camb). 2009;1:116-22 pubmed publisher
  50. Lu C, Shahzad M, Moreno Smith M, Lin Y, Jennings N, Allen J, et al. Targeting pericytes with a PDGF-B aptamer in human ovarian carcinoma models. Cancer Biol Ther. 2010;9:176-82 pubmed
    ..Dual targeting of endothelial cells and pericytes holds potential as an anti-vascular therapeutic approach in ovarian carcinoma. ..
  51. Barfod A, Persson T, Lindh J. In vitro selection of RNA aptamers against a conserved region of the Plasmodium falciparum erythrocyte membrane protein 1. Parasitol Res. 2009;105:1557-66 pubmed publisher
    ..The described results show that RNA aptamers are promising candidates for adjunct therapy in severe malaria. ..
  52. Liang S, Connell G. An electrochemiluminescent aptamer switch for a high-throughput assay of an RNA editing reaction. RNA. 2009;15:1929-38 pubmed publisher
    ..Chemical probing, mutagenesis, and binding affinity measurements were used to characterize the reporter. The highly sensitive assay could be adapted to a broad range of RNA processing reactions. ..
  53. Rieder U, Kreutz C, Micura R. Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci U S A. 2010;107:10804-9 pubmed publisher
    ..A model is presented how a riboswitch that provides no obvious overlap between aptamer and terminator stem-loop solves this communication problem by involving bistable sequence determinants...