Selection of thrombin-binding aptamers by using computational approach for aptasensor application

Biosensors and Bioelectronics

Volumn 26, Issue 11, 2011, Pages 4411-4416

  Bini, Alessandra ^a,b   Mascini, Marcello ^c   Mascini, Marco ^a   Turner, Anthony P F ^b,d  

^a UNIVERSITY OF FLORENCE   (Italy)

^b CRANFIELD UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF TERAMO   (Italy)

^d LINKÖPING UNIVERSITY   (Sweden)

Author keywords

Aptamers; Binding score; Molecular dynamics; Surface plasmon resonance biosensor; Thrombin

Indexed keywords

ANALYTICAL PERFORMANCE; APTAMERS; BINDING SCORE; COMPUTATIONAL APPROACH; OLIGONUCLEOTIDE SEQUENCES; REPRODUCIBILITIES; SCORING FUNCTIONS; SHAPE BASED; SIGNAL AMPLITUDE; SURFACE PLASMON RESONANCE BIOSENSOR; THROMBIN; THROMBIN BINDING;

BIOSENSORS; DNA SEQUENCES; IONIC STRENGTH; MOLECULAR DYNAMICS; OLIGONUCLEOTIDES; PLASMONS; SODIUM CHLORIDE;

SURFACE PLASMON RESONANCE;

APTAMER; FIBRINOGEN; THROMBIN;

APTASENSOR; ARTICLE; BINDING AFFINITY; BIOSENSOR; CONTROLLED STUDY; DNA SEQUENCE; IONIC STRENGTH; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PROTEIN STRUCTURE; REPRODUCIBILITY; SCORING SYSTEM; SENSITIVITY ANALYSIS; SURFACE PLASMON RESONANCE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BINDING SITES; BIOSENSING TECHNIQUES; COMPUTATIONAL BIOLOGY; GENE LIBRARY; MORPHOLINES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; SELEX APTAMER TECHNIQUE; SURFACE PLASMON RESONANCE; THROMBIN;

EID: 79959260429     PISSN: 09565663     EISSN: 18734235     Source Type: Journal    
DOI: 10.1016/j.bios.2011.04.053     Document Type: Article

References (42)

1. Bini A., Minunni M., Tombelli S., Centi S., Mascini M. Analytical and Bioanalytical Chemistry 2008, 390:1077-1086.
2. Bock L.C., Griffin L.C., Latham J.A., Vermaas E.H., Toole J.J. Nature 1992, 355:564-566.
3. Brown C.J., Dastidar S.G., See H.Y., Coomber D.W., Ortiz-Lombardía M., Verma C., Lane D.P. Journal of Molecular Biology 2010, 395:871-883.
4. Centi S., Tombelli S., Minunni M., Mascini M. Analytical Chemistry 2007, 79:1466-1473.
5. Chianella I., Lotierzo M., Piletsky S.A., Tothill I.E., Chen B., Karim K., Turner A.P.F. Analytical Chemistry 2002, 74:1288-1293.
6. Ellington A.D., Szostak J.W. Nature 1990, 346:818-822.
7. Goldenhuys W.J., Gaasch K.E., Watson M., Allen D.D., Van der Schyf C.J. Drug Discovery Today 2006, 11:127-132.
8. Halgren T.A. Journal of Computational Chemistry 1996, 17:490-519.
9. Hall B., Hesselberth J.R., Ellington A.D. Biosensors and Bioelectronics 2007, 22:1939-1947.
10. Hamula C.L.A., Guthrie J.W., Zhang H., Li X., Le X.C. Trends in Analytical Chemistry 2006, 25:681-691.
11. He P., Shen L., Cao Y., Li D. Analytical Chemistry 2007, 79:8024-8029.
12. Hianik T., Ostatna V., Zajacova Z., Stoikova E., Evtugyn G. Bioorganic and Medicinal Chemistry Letters 2005, 15:291-295.
13. Huang Q., Li L.L., Yang S.Y. Journal of Molecular Graphics and Modelling 2010, 28:775-787.
14. Keefe A.D., Schaub R.G. Current Opinion in Pharmacology 2008, 8:147-152.
15. Kelly J.A., Feigon J., Yeates T.O. Journal of Molecular Biology 1996, 256:417-422.
16. Kim N., Gan H.H., Schlick T. Bioinformatics 2007, 13:478-492.
17. Lai Y., Xie C., Zhang Z., Lu W., Ding J. Biomaterials 2010, 31:4809-4817.
18. Lee M., Walt D.R. Analytical Biochemistry 2000, 282:142-146.
19. Li M., Huang Y.-J., Tai P.C., Wang.B. Biochemical and Biophysical Research Communications 2008, 368:839-845.
20. Li Y., Lee H.J., Corn R.M. Analytical Chemistry 2007, 79:1082-1088.
21. Lin C., Katilius E., Liu Y., Zhang J., Yan H. Angewandte Chemie International Edition 2006, 45:5296-5301.
22. Macaya R.F., Schultze P., Smith F.W., Roe J.A., Feigon J. Proceedings of the National Academy of Sciences 1993, 90:3745-3749.
23. Mascini M., Del Carlo M., Compagnone D., Cozzani I., Tiscar P.G., Mpmhanga C.P., Chen B. Analytical Letters 2006, 39:1627-1642.
24. Mascini M., Guilbault G.G., Monk I.R., Hill C., Del Carlo M., Compagnone D. Microchimica Acta 2008, 163:227-235.
25. Mascini M., Macagnano A., Monti D., Del Carlo M., Paolesse R., Chen B., Warner P., D'Amico A., Di Natale C., Compagnone D. Biosensors and Bioelectronics 2004, 20:1203-1210.
26. Mascini M., Sergi M., Monti D., Del Carlo M., Compagnone D. Analytical Chemistry 2008, 80:9150-9156.
27. McCauley T.G., Nobuko H., Stanto M. Analytical Biochemistry 2003, 319:244-250.
28. McGann M.R., Almond H.R., Nicholls A., Grant J.A., Brown F.K. Biopolymers 2003, 68:76-90.
29. Muthusamy K., Arvidsson P.I., Govender P., Kruger H.G., Maguire G.E.M., Govender T. Bioorganic & Medicinal Chemistry Letters 2010, 20:1360-1362.
30. Padmanhabhan K., Tulinsky A. Acta Crystallographica 1996, D52:272-282.
31. Papaleo E., Russo L., Shaikh N., Cipolla L., Fantucci P., De Gioia L. Journal of Molecular Graphics and Modelling 2010, 28:834-841.
32. Piletska E.V., Tuner N.W., Turner A.P.F., Piletsky S.A. Journal of Controlled Release 2005, 108:132-139.
33. Potyrailo R.A., Conrad R.C., Ellington A.D., Hieftje G.M. Analytical Chemistry 1998, 70:3419-3425.
34. Rajamani R., Good A.C. Current Opinion in Drug Discovery & Development 2007, 10:308-315.
35. Sanchez-Barragan I., Karim K., Costa-Fernandez J.M., Piletsky S.A., Sanz-Medel A. Sensors and Actuators B 2007, 123:798-804.
36. Schlensog M.D., Gronewold T.M.A., Tewes M., Famulok M., Quandt E. Sensors and Actuators B 2004, 101:308-315.
37. Storri S., Santoni T., Minunni M., Mascini M. Biosensors and Bioelectronics 1998, 13:347-357.
38. Tasset D., Kubik M.F., Steiner W. Journal of Molecular Biology 1997, 272:688-698.
39. Tombelli S., Minunni M., Mascini M. Biosensensors & Bioelectronics 2005, 20:2424-2434.
40. Tombelli S., Minunni M., Mascini M. Biomolecular Engineering 2007, 24:191-200.
41. Yakaiah T., Lingaiah B.P.V., Narsaiah B., Shireesha B., Ashok Kumar B., Gururaj S., Parthasarathy T., Sridhar B. Bioorganic & Medicinal Chemistry Letters 2007, 17:3445-3453.
42. Zheng J., Feng W., Lin L., Zhang F., Cheng G., He P., Fang Y. Biosensors and Bioelectronics 2007, 23:341-347.