New strategies for evaluation and analysis of SELEX experiments

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Beier, Rico ^a   Boschke, Elke ^b   Labudde, Dirk ^a  

^a UNIVERSITY OF APPLIED SCIENCES MITTWEIDA   (Germany)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; BINDING SITE; CHEMICAL BINDING; CONSENSUS SEQUENCE; DNA SEQUENCE; ENZYME LINKED IMMUNOSORBENT ASSAY; GENOTYPE; INFECTION CONTROL; NOROVIRUS; NOROVIRUS INFECTION; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SELEX EXPERIMENT; SEQUENCE ANALYSIS; CHEMISTRY; COMBINATORIAL CHEMISTRY; CONFORMATION; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; NUCLEOTIDE MOTIF; PROCEDURES;

APTAMER; CAPSID PROTEIN;

APTAMERS, NUCLEOTIDE; BINDING SITES; CAPSID PROTEINS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NOROVIRUS; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; SELEX APTAMER TECHNIQUE;

EID: 84897542500     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/849743     Document Type: Article

References (40)

1. Keefe A. D., Pai S., Ellington A., Aptamers as therapeutics. Nature Reviews Drug Discovery 2010 9 7 537 550 2-s2.0-77954220072 10.1038/nrd3141
2. Zhou J., Bobbin M. L., Burnett J. C., Rossi J. J., Current progress of RNA aptamer-based therapeutics. Frontiers in Genetics 2012 3, article 234 10.3389/fgene.2012.00234
3. Leontis N. B., Westhof E., Analysis of RNA motifs. Current Opinion in Structural Biology 2003 13 3 300 308 2-s2.0-0038170063 10.1016/S0959-440X(03) 00076-9 (Pubitemid 36782455)
4. Holeman L. A., Robinson S. L., Szostak J. W., Wilson C., Isolation and characterization of fluorophore-binding RNA aptamers. Folding and Design 1998 3 6 423 431 2-s2.0-0032437793 10.1016/S1359-0278(98)00059-5 (Pubitemid 29023608)
5. Harada K., Frankel A. D., Identification of two novel arginine binding DNAs. EMBO Journal 1995 14 23 5798 5811 2-s2.0-0028823341
6. Schürer H., Stembera K., Knoll D., Mayer G., Blind M., Förster H. H., Famulok M., Welzel P., Hahn U., Aptamers that bind to the antibiotic moenomycin A. Bioorganic and Medicinal Chemistry 2001 9 10 2557 2563 2-s2.0-0034847830 10.1016/S0968-0896(01)00030-X (Pubitemid 32824158)
7. Lupold S. E., Hicke B. J., Lin Y., Coffey D. S., Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Research 2002 62 14 4029 4033 2-s2.0-0037099536 (Pubitemid 34791070)
8. Raddatz M. S. L., Dolf A., Endl E., Knolle P., Famulok M., Mayer G., Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angewandte Chemie 2008 47 28 5190 5193 2-s2.0-48149099772 10.1002/anie.200800216
9. Lee J. H., Canny M. D., de Erkenez A., Krilleke D., Ng Y. S., Shima D. T., Pardi A., Jucker F., A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF165. Proceedings of the National Academy of Sciences of the United States of America 2005 102 52 18902 18907 2-s2.0-30044436689 10.1073/pnas.0509069102 (Pubitemid 43049539)
10. Wu Y., Zhong Z., Huber J., Bassi R., Finnerty B., Corcoran E., Li H., Navarro E., Balderes P., Jimenez X., Koo H., Mangalampalli V. R. M., Ludwig D. L., Tonra J. R., Hicklin D. J., Anti-vascular endothelial growth factor receptor-1 antagonist antibody as a therapeutic agent for cancer. Clinical Cancer Research 2006 12 21 6573 6584 2-s2.0-33751267529 10.1158/1078-0432.CCR- 06-0831 (Pubitemid 44799733)
11. Hoinka J., Zotenko E., Friedman A., Sauna Z. E., Przytycka T. M., Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers. Bioinformatics 2012 28 12 i215 i223
12. Pendergrast P. S., Marsh H. N., Grate D., Healy J. M., Stanton M., Nucleic acid aptamers for target validation and therapeutic applications. Journal of Biomolecular Techniques 2005 16 3 224 234 2-s2.0-33644850350
13. Metzker M. L., Sequencing technologies the next generation. Nature Reviews Genetics 2010 11 1 31 46 2-s2.0-72849144434 10.1038/nrg2626
14. Stoltenburg R., Reinemann C., Strehlitz B., SELEX-a (r) evolutionary method to generate high-affinity nucleic acid ligands. Biomolecular Engineering 2007 24 4 381 403 2-s2.0-34548551398 10.1016/j.bioeng.2007.06.001 (Pubitemid 47391579)
15. Sanger F., Nicklen S., Coulson A. R., DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 1977 74 12 5463 5467 2-s2.0-0017681196
16. Luo C., Tsementzi D., Kyrpides N., Read T., Konstantinidis K. T., Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 2012 7 2 2-s2.0-84856770811 10.1371/journal.pone.0030087 e30087
17. Beier R., Pahlke C., Quenzel P., Henseleit A., Boschke E., Cuniberti G., Labudde D., Selection of a DNA aptamer against norovirus capsid protein VP1. FEMS Microbiology Letters 2014 351 2 162 169 10.1111/1574-6968.12366
18. Zheng D. P., Ando T., Fankhauser R. L., Beard R. S., Glass R. I., Monroe S. S., Norovirus classification and proposed strain nomenclature. Virology 2006 346 2 312 323 2-s2.0-33644817227 10.1016/j.virol.2005.11.015 (Pubitemid 43357875)
19. Prasad B. V., Hardy M. E., Dokland T., Bella J., Rossmann M. G., Estes M. K., X-ray crystallographic structure of the Norwalk virus capsid. Science 1999 286 5438 287 290 2-s2.0-0033536662 10.1126/science.286.5438.287 (Pubitemid 29484691)
20. Ausar S. F., Foubert T. R., Hudson M. H., Vedvick T. S., Middaugh C. R., conformational stability and disassembly of norwalk virus-like particles: effect of ph and temperature. Journal of Biological Chemistry 2006 281 28 19478 19488 2-s2.0-33745820802 10.1074/jbc.M603313200 (Pubitemid 44035452)
21. Gray J. J., Kohli E., Ruggeri F. M., Vennema H., Sánchez-Fauquier A., Schreier E., Gallimore C. I., Iturriza-Gomara M., Giraudon H., Pothier P., di Bartolo I., Inglese N., de Bruin E., van der Veer B., Moreno S., Montero V., de Llano M. C., Höhne M., Diedrich S. M., European multicenter evaluation of commercial enzyme immunoassays for detecting norovirus antigen in fecal samples. Clinical and Vaccine Immunology 2007 14 10 1349 1355 2-s2.0-35548942716 10.1128/CVI.00214-07 (Pubitemid 350012979)
22. Bruggink L. D., Witlox K. J., Sameer R., Catton M. G., Marshall J. A., Evaluation of the RIDA QUICK immunochromatographic norovirus detection assay using specimens from Australian gastroenteritis incidents. Journal of Virological Methods 2011 173 1 121 126 2-s2.0-79952193837 10.1016/j.jviromet. 2011.01.017
23. Giegerich R., Kurtz S., From Ukkonen to McCreight and Weiner: a unifying view of linear-time suffix tree construction. Algorithmica 1997 19 3 331 353 2-s2.0-0001553729 (Pubitemid 127709320)
24. Iliopoulos C. S., Mchugh J., Peterlongo P., Pisanti N., Rytter W., Sagot M.-F., A first approach to finding common motifs with gaps. International Journal of Foundations of Computer Science 2005 16 6 1145 1154 2-s2.0-33746189871 10.1142/S0129054105003716 (Pubitemid 44099393)
25. Antoniou P., Crochemore M., Iliopoulos C., Peterlongo P., Application of suffix trees for the acquisition of common motifs with gaps in a set of strings. Proceedings of the International Conference on Language and Automata Theory and Applications 2007
26. Marsan L., Sagot M.-F., Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. Journal of Computational Biology 2000 7 3-4 345 362 2-s2.0-0033677426 10.1089/106652700750050826
27. Leibovich L., Yakhini Z., Efficient motif search in ranked lists and applications to variable gap motifs. Nucleic Acids Research 40 13 5832 5847
28. Zare-Mirakabada F., Davoodib P., Ahrabiana H., Nowzari-Dalinia A., Sadeghic M., Goliaeia B., Finding motifs based on suffix trie. Avanced Modeling and Optimization 2009 11 2
29. Sagot M. F., Spelling approximate repeated or common motifs using a suffix tree. LATIN'98: Theoretical Informatics 1998 Berlin, Germany Springer 374 390
30. Mohapatra A., Mishra P. M., Padhy S., Motif search in DNA sequences using generalized suffix tree. Proceedings of the 10th International Conference on Information Technology (ICIT '07) December 2007 Orissa, India 100 103 2-s2.0-47349104640 10.1109/ICOIT.2007.4418277
31. Brazma A., Jonassen I., Vilo J., Ukkonen E., Predicting gene regulatory elements in silico on a genomic scale. Genome Research 1998 8 11 1202 1215 2-s2.0-0032413411 (Pubitemid 29027223)
32. Lorenz R., Bernhart S. H., Höner zu Siederdissen C., Tafer H., Flamm C., Stadler P. F., Hofacker I. L., ViennaRNA package 2.0. Algorithms for Molecular Biology 2011 6 1, article 26 2-s2.0-82055164092 10.1186/1748-7188-6-26
33. Turner D. H., Mathews D. H., NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Research 2009 38 supplement 1 D280 D282 2-s2.0-75549088409 10.1093/nar/gkp892 gkp892
34. SantaLucia J. Jr., Hicks D., The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure 2004 33 415 440 2-s2.0-3042599013 10.1146/annurev.biophys.32.110601.141800 (Pubitemid 38829966)
35. Miklós I., Meyer I. M., Nagy B., Moments of the Boltzmann distribution for RNA secondary structures. Bulletin of Mathematical Biology 2005 67 5 1031 1047 2-s2.0-21444446830 10.1016/j.bulm.2004.12.003 (Pubitemid 40912465)
36. Schneider T. D., Stephens R. M., Sequence logos: a new way to display consensus sequences. Nucleic Acids Research 1990 18 20 6097 6100 2-s2.0-0025008168
37. Bailey T. L., DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 2011 27 12 1653 1659 2-s2.0-79958090979 10.1093/bioinformatics/btr261
38. Leibovich L., Paz I., Yakhini Z., Mandel-Gutfreund Y., DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. Nucleic Acids Research 2013 41 W174 W179 10.1093/nar/gkt407
39. Darty K., Denise A., Ponty Y., VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009 25 15 1974 1975 2-s2.0-67650727366 10.1093/bioinformatics/btp250
40. Keylock C. J., Simpson diversity and the Shannon-Wiener index as special cases of a generalized entropy. Oikos 2005 109 1 203 207 2-s2.0-17144428129 10.1111/j.0030-1299.2005.13735.x (Pubitemid 40518620)