Molecular dynamics simulations of cyclohexyl modified peptide nucleic acids (pna)

Journal of Biomolecular Structure and Dynamics

Volumn 27, Issue 5, 2010, Pages 663-676

  Sharma, Smriti ^a   Sonavane, Uddhavesh B ^a   Joshi, Rajendra R ^a  

^a CENTRE FOR DEVELOPMENT OF ADVANCED COMPUTING   (India)

Author keywords

Cyclohexyl modification; Molecular Dynamics Simulations; Peptide Nucleic Acid; PNA duplex; PNA triplex

Indexed keywords

CYCLOHEXYLAMINE; PEPTIDE NUCLEIC ACID;

ARTICLE; COMPLEX FORMATION; DNA SEQUENCE; GENE TARGETING; GENETIC STABILITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; RNA SEQUENCE; SIMULATION; STEREOISOMERISM;

EID: 76849110645     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2010.10508580     Document Type: Article

References (54)

1. Egholm, M., Buchardtz, O., Christensen, L., Behrens, C., Freier, S. M., Driver, D. A., Berg, R. H., Kim, S. K., Norden, B., and Neilsen, P. E., 1993. Nature, 92:566–568.
2. Neilson, P. E., Egholm, M., Berg, R. H., and Buchardt, O., 1991. Science, 254:1497–1500.
3. Nielsen, P. E., and Koppelhus, U., 2004. Advanced Drug Delivery Reviews, 55:267–280.
4. Pellestor, F., Paulasova, P., and Hamamah, S., 2008. Curr Pharm Des, 14:2439–2444.
5. Menchise, V., Simone, G. D., Tedeschi, T., Corradini, R., Sforza, S., Marchelli, R., Capasso, D., Saviano, M., and Pedone, C., 2003. Proc Natl Acad Sci USA, 100:12021–12026.
6. Pellestor, F., and Paulasova, P., 2004. Int J Mol Med, 13:521–525.
7. Kumar, V. A., and Ganesh, K. N., 2005. Acc Chem Res, 38:404–412.
8. Ray, A., and Norden, B., 2000. FASEB, J14:1041–1060.
9. Sen, A., and Nielson, P. E., 2007. Nucleic Acids Res, 35:3367–3374.
10. Schwarz, F. P., Robinson, S., and Butler, J. M., 1999. Nucleic Acids Res, 27:4792–4800.
11. Tripathi, S., Chaubey, B., Barton, B. E., and Pandey, V. N., 2007. Virology, 363:91–103.
12. Hamoundi, F. B., Leforestier, E., Beaufort, C. S., Nielsen, P. E., Giovannangeli, C., and Behmoaras, T. E. S., 2007. Nucleic Acids Res, 5:3907–3917.
13. Hu, J., and Corey, D. A., 2007. Biochemistry, 46:7581–7589.
14. Tan, X. X., Actor, J. K., and Chen, Y., 2005. Antimicrobial Agents and Chemotherapy, 49:3203–3207.
15. Dilek, I., Madrid, M., Singh, R., Urrea, C. P., and Armitage, B. A., 2005. J Am Chem Soc, 127:3339–3345.
16. Bentin, T., Hansen, G. I., and Nielson, P. E., 2006. Nucleic Acids Res, 34:5790–5799.
17. Ishizuka, T., Yoshida, J., Yamamoto, Y., Sumaoka, J., Tedeschi, T., Corradini, R., Sforza, S., and Komiyama, M., 2008. Nucleic Acids Res, 36:1464–1471.
18. Datta, B., Schmitt, C., and Armitage, B. A., 2003. J Am Chem Soc, 125:4111–4118.
19. Ganesh, K. N., and Neilsen, P. E., 2000. Current Organic Chemistry, 4:931–943.
20. Topham, C., and Smith, J. C., 2007. Biophys J, 92:769–786.
21. Govindraju, T., Kumar, V. A., and Ganesh, K. N., 2005. J Am Chem Soc, 127:4144–4145.
22. Govindraju, T., Gonnade, R. G., Bhadbhade, M. M., Kumar, V. A., and Ganesh, K. N., 2003. Organic Letters, 5:3013–3016.
23. Kumar, V. A., 2002. Eur J Org Chem,:2021–2032.
24. Siriwong, K., Chuichay, P., Saen-oon, S., Suparpprom, C., Vilaivan, T., and Hannongbua, S., 2008. Biochem Biophys Res Commun, 372:765–771.
25. Weronski, P., Jiang, Y., and Rasmussen, S., 2007. Biophys J, 92:3081–3091.
26. Rathinavelan, T., and Yathindra, N., 2005. FEBS J, 272:4055–4070.
27. Ly, D. H., 2009. J Biomol Struct Dyn, 26:903–904.
28. Sen, S., and Nilsson, L., 1998. J Am Chem Soc, 120:619–631.
29. Shields, G. C., Laughton, C. A., and Orozco, M., 1998. J Am Chem Soc, 120:5895–5904.
30. Braun, G. H., Jorge, D. M. M., Ramos, H. P., Alves, R. M., da Silva, V. B., Giuliatti, S., Sampaio, S. V., Taft, C. A., Carlos and Silva, H. T. P., 2008. J Biomol Struct Dyn, 25:347–346.
31. Yoon, J., Park, J., Jang, S., Lee, K., and Shin, S., 2008. J Biomol Struct Dyn, 25:505–516.
32. Cordomí, A., Ramon, E., Garriga, P., and Perez, J. J., 2008. J Biomol Struct Dyn, 25:573–588.
33. Chen, C. Y-C., Chen, Y-F., Wu, C-H, and Tsai, H-Y., 2008. J Biomol Struct Dyn, 26:57–64.
34. Zhao, J-H., Yang, C-T., Wu, J. W., Tsai, W-B., Lin, H-Y, Fang, H-W., Ho, Y., and Liu, H-L., 2008. J Biomol Struct Dyn, 26:65–74.
35. Macchion, B. N., Strömberg, R., and Nilsson, L., 2008. J Biomol Struct Dyn, 26:163–174.
36. Sonavane, U. B., Ramadugu, S. K., and Joshi, R. R., 2008. J Biomol Struct Dyn, 26:203–214.
37. Mehrnejad, F., and Chaparzadeh, N., 2008. J Biomol Struct Dyn, 26:255–262.
38. Yoon, J., Jang, S., Lee, K., and Shin, S., 2009. J Biomol Struct Dyn, 27:259–270.
39. Ilda, D., Giovanni, C., and Alessandro, D., 2009. J Biomol Struct Dyn, 27:307–318.
40. Cordomí, A., and Perez, J. J., 2009. J Biomol Struct Dyn, 27:127–148.
41. Bairagya, H. R., Mukhopadhyay, B. P., and Sekar, K., 2009. J Biomol Struct Dyn, 27:149–158.
42. Zhang, J., 2009. J Biomol Struct Dyn, 27:159–162.
43. Sharma, S., Sonavane, U. B., and Joshi, R. R., 2009. Int J Quantum Chem, 109:890–896.
44. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E. I., DeBolt, S., Seibel, G., and Kollman, P., 1995. Comput Phys Commun, 91:1–42.
45. Lavery, R., and Sklenar, H., 1989. J Biomol Struct Dyn, 6:655–667.
46. Lavery, R., and Sklenar, H., 1989. J Biomol Struct Dyn, 6:63–91.
47. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr, Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., and Pople, J. A., 2004. Gaussian 03, Revision C.02. Wallingford, CT:Gaussian, Inc.
48. Humphrey, W., Dalke, A., and Schulten, K., 1996. J Mol Graphics, 14:33–38.
49. Gohlke, H., and Case, D. A., 2004. J Comput Chem, 25:238–250.
50. Torres, R. A., and Bruice, T. C., 1996. Proc Natl Acad Sci USA, 93:649–653.
51. Almarsson, O., Bruice, T. C., Kerr, J., and Zuckermann, R. N., 1993. Proc Natl Acad Sci USA, 90:7518–7522.
52. Bevan, D. R., Li, L., Pedersen, L. G., and Darden, T. A., 2000. Biophys J, 78:668–682.
53. Govindraju, T., Madhuri, V., Kumar, V. A., and Ganesh, K. N., 2006. J Org Chem, 71:14–21.
54. Simmerling, C., Elber, R., and Zhang, J., 1995. Modeling of Biomolecular Structure and Mechanisms Edited by:Pullman, A., 241–265. Netherlands:Kluwer. (eds.)