Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches

Nano Letters

Volumn 16, Issue 3, 2016, Pages 1726-1735

  Bindewald, Eckart ^a   Afonin, Kirill A ^b,c   Viard, Mathias ^a   Zakrevsky, Paul ^b   Kim, Taejin ^b   Shapiro, Bruce A ^b  

^a FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

Author keywords

Dicer; RNA interference; RNA switch; RNA DNA hybrid; secondary structure

Indexed keywords

COLLAGEN; COMPUTATION THEORY; FORECASTING; GENES; MUSCULOSKELETAL SYSTEM; PROTEINS; RNA;

COMPUTATIONAL PREDICTIONS; CONNECTIVE TISSUE GROWTH FACTOR; DICER; ENHANCED GREEN FLUORESCENT PROTEIN; EXPERIMENTAL VERIFICATION; MOLECULAR LOGIC GATES; RNA INTERFERENCE; SECONDARY STRUCTURES;

NUCLEIC ACIDS;

CONNECTIVE TISSUE GROWTH FACTOR; CTGF PROTEIN, HUMAN; DNA; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; RIBONUCLEASE III; RNA; SMALL INTERFERING RNA;

CHEMISTRY; CONFORMATION; GENETIC TRANSFECTION; GENETICS; HUMAN; METABOLISM; MOLECULAR MODEL; TUMOR CELL LINE;

CELL LINE, TUMOR; CONNECTIVE TISSUE GROWTH FACTOR; DNA; GREEN FLUORESCENT PROTEINS; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RIBONUCLEASE III; RNA; RNA, MESSENGER; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 84960510666     PISSN: 15306984     EISSN: 15306992     Source Type: Journal    
DOI: 10.1021/acs.nanolett.5b04651     Document Type: Article

References (52)

1. Ou-Yang, S. S.; Lu, J. Y.; Kong, X. Q.; Liang, Z. J.; Luo, C.; Jiang, H. Acta Pharmacol. Sin. 2012, 33 (9) 1131-40 10.1038/aps.2012.109
2. Bernardo, P. H.; Tong, J. C. Methods Mol. Biol. 2012, 800, 25-31 10.1007/978-1-61779-349-3-3
3. Penchovsky, R.; Breaker, R. R. Nat. Biotechnol. 2005, 23 (11) 1424-33 10.1038/nbt1155
4. Win, M. N.; Smolke, C. D. Science 2008, 322 (5900) 456-60 10.1126/science.1160311
5. Liang, J. C.; Chang, A. L.; Kennedy, A. B.; Smolke, C. D. Nucleic Acids Res. 2012, 40 (20) e154 10.1093/nar/gks636
6. Green, A. A.; Silver, P. A.; Collins, J. J.; Yin, P. Cell 2014, 159 (4) 925-939 10.1016/j.cell.2014.10.002
7. Wachsmuth, M.; Findeiss, S.; Weissheimer, N.; Stadler, P. F.; Morl, M. Nucleic Acids Res. 2013, 41 (4) 2541-51 10.1093/nar/gks1330
8. Muranaka, N.; Yokobayashi, Y. Chem. Commun. (Cambridge, U. K.) 2010, 46 (36) 6825-7 10.1039/c0cc01438a
9. Xie, Z.; Wroblewska, L.; Prochazka, L.; Weiss, R.; Benenson, Y. Science 2011, 333 (6047) 1307-11 10.1126/science.1205527
10. Xie, Z.; Liu, S. J.; Bleris, L.; Benenson, Y. Nucleic Acids Res. 2010, 38 (8) 2692-701 10.1093/nar/gkq117
11. Rinaudo, K.; Bleris, L.; Maddamsetti, R.; Subramanian, S.; Weiss, R.; Benenson, Y. Nat. Biotechnol. 2007, 25 (7) 795-801 10.1038/nbt1307
12. Cicha, I.; Goppelt-Struebe, M. BioFactors 2009, 35 (2) 200-208 10.1002/biof.30
13. Pickles, M.; Leask, A. J. Cell Commun. Signal 2007, 1 (2) 85-90 10.1007/s12079-007-0008-9
14. Kwon, S.; Munroe, X.; Crawley, S. C.; Lee, H. Y.; Spong, S.; Bradham, D.; Gum, J. R., Jr.; Sleisenger, M. H.; Kim, Y. S. Int. J. Oncol. 2007, 31 (4) 693-703 10.3892/ijo.31.4.693
15. Bennewith, K. L.; Huang, X.; Ham, C. M.; Graves, E. E.; Erler, J. T.; Kambham, N.; Feazell, J.; Yang, G. P.; Koong, A.; Giaccia, A. J. Cancer Res. 2009, 69 (3) 775-84 10.1158/0008-5472.CAN-08-0987
16. Wang, M. Y.; Chen, P. S.; Prakash, E.; Hsu, H. C.; Huang, H. Y.; Lin, M. T.; Chang, K. J.; Kuo, M. L. Cancer Res. 2009, 69 (8) 3482-91 10.1158/0008-5472.CAN-08-2524
17. Chen, P. S.; Wang, M. Y.; Wu, S. N.; Su, J. L.; Hong, C. C.; Chuang, S. E.; Chen, M. W.; Hua, K. T.; Wu, Y. L.; Cha, S. T.; Babu, M. S.; Chen, C. N.; Lee, P. H.; Chang, K. J.; Kuo, M. L. J. Cell Sci. 2007, 120 (12) 2053-2065 10.1242/jcs.03460
18. Lorenz, R.; Bernhart, S. H.; Honer Zu Siederdissen, C.; Tafer, H.; Flamm, C.; Stadler, P. F.; Hofacker, I. L. Algorithms Mol. Biol. 2011, 6, 26 10.1186/1748-7188-6-26
19. Cao, S.; Xu, X.; Chen, S. J. RNA 2014, 20 (6) 835-45 10.1261/rna.043976.113
20. Bernhart, S. H.; Tafer, H.; Muckstein, U.; Flamm, C.; Stadler, P. F.; Hofacker, I. L. Algorithms Mol. Biol. 2006, 1 (1) 3 10.1186/1748-7188-1-3
21. Bindewald, E.; Afonin, K.; Jaeger, L.; Shapiro, B. A. ACS Nano 2011, 5 (12) 9542-51 10.1021/nn202666w
22. Andronescu, M.; Zhang, Z. C.; Condon, A. J. Mol. Biol. 2005, 345 (5) 987-1001 10.1016/j.jmb.2004.10.082
23. Dirks, R. M.; Pierce, N. A. J. Comput. Chem. 2003, 24 (13) 1664-77 10.1002/jcc.10296
24. Zadeh, J. N.; Steenberg, C. D.; Bois, J. S.; Wolfe, B. R.; Pierce, M. B.; Khan, A. R.; Dirks, R. M.; Pierce, N. A. J. Comput. Chem. 2011, 32 (1) 170-3 10.1002/jcc.21596
25. Afonin, K.; Desai, R.; Viard, M.; Kireeva, M.; Bindewald, E.; Case, C. L.; Maciag, A. E.; Kasprzak, W. K.; Kim, T.; Sappe, A.; Stepler, M.; Kewal Ramani, V. N.; Kashlev, M.; Blumenthal, R.; Shapiro, B. A. Nucleic Acids Res. 2014, 42, 2085 10.1093/nar/gkt1001
26. Sugimoto, N.; Nakano, S.; Katoh, M.; Matsumura, A.; Nakamuta, H.; Ohmichi, T.; Yoneyama, M.; Sasaki, M. Biochemistry 1995, 34 (35) 11211-6 10.1021/bi00035a029
27. Mathews, D. H.; Sabina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288 (5) 911-40 10.1006/jmbi.1999.2700
28. SantaLucia, J., Jr. Proc. Natl. Acad. Sci. U. S. A. 1998, 95 (4) 1460-5 10.1073/pnas.95.4.1460
29. Rose, S. D.; Kim, D. H.; Amarzguioui, M.; Heidel, J. D.; Collingwood, M. A.; Davis, M. E.; Rossi, J. J.; Behlke, M. A. Nucleic Acids Res. 2005, 33 (13) 4140-56 10.1093/nar/gki732
30. Afonin, K. A.; Grabow, W. W.; Walker, F. M.; Bindewald, E.; Dobrovolskaia, M. A.; Shapiro, B. A.; Jaeger, L. Nat. Protoc. 2011, 6 (12) 2022-2034 10.1038/nprot.2011.418
31. Bindewald, E.; Grunewald, C.; Boyle, B.; O'Connor, M.; Shapiro, B. A. J. Mol. Graphics Modell. 2008, 27 (3) 299-308 10.1016/j.jmgm.2008.05.004
32. Popenda, M.; Szachniuk, M.; Antczak, M.; Purzycka, K. J.; Lukasiak, P.; Bartol, N.; Blazewicz, J.; Adamiak, R. W. Nucleic Acids Res. 2012, 40, (14), e112.
33. Case, D. A.; Cheatham, T. E., 3rd; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26 (16) 1668-88 10.1002/jcc.20290
34. Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Götz, A. W.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 12; University of California: San Francisco, 2012.
35. Andronescu, M.; Bereg, V.; Hoos, H. H.; Condon, A. BMC Bioinf. 2008, 9, 340 10.1186/1471-2105-9-340
36. Afonin, K. A.; Lindsay, B.; Shapiro, B. A. RNA Nanotechnol 2013, 1, 1-15 10.2478/rnan-2013-0001
37. Zhu, X.; Li, T.; Dang, Y.; Feng, Y.; Huang, P. Mol. Biotechnol. 2005, 31 (3) 187-92 10.1385/MB:31:3:187
38. Afonin, K. A.; Danilov, E. O.; Novikova, I. V.; Leontis, N. B. ChemBioChem 2008, 9 (12) 1902-5 10.1002/cbic.200800183
39. Afonin, K. A.; Lin, Y. P.; Calkins, E. R.; Jaeger, L. Nucleic Acids Res. 2012, 40 (5) 2168-80 10.1093/nar/gkr926
40. Lai, D.; Ho, K. C.; Hao, Y.; Yang, X. Cancer Res. 2011, 71 (7) 2728-38 10.1158/0008-5472.CAN-10-2711
41. Reeder, J.; Steffen, P.; Giegerich, R. Nucleic Acids Res. 2007, 35, W320-W324 10.1093/nar/gkm258
42. Markham, N. R.; Zuker, M. Methods Mol. Biol. 2008, 453, 3-31 10.1007/978-1-60327-429-6-1
43. Milligan, J. F.; Groebe, D. R.; Witherell, G. W.; Uhlenbeck, O. C. Nucleic Acids Res. 1987, 15 (21) 8783-98 10.1093/nar/15.21.8783
44. Lapham, J.; Crothers, D. M. RNA 1996, 2 (3) 289-96
45. Afonin, K. A.; Bindewald, E.; Yaghoubian, A. J.; Voss, N.; Jacovetty, E.; Shapiro, B. A.; Jaeger, L. Nat. Nanotechnol. 2010, 5 (9) 676-82 10.1038/nnano.2010.160
46. Grabow, W. W.; Zakrevsky, P.; Afonin, K. A.; Chworos, A.; Shapiro, B. A.; Jaeger, L. Nano Lett. 2011, 11 (2) 878-87 10.1021/nl104271s
47. Guo, P.; Sheng Wu, X.; Xue, H.; Sheng Wu Wu, Yu; Bao, L. X. Acta Biochim. Biophys. Sin. (Shanghai) 2002, 34 (5) 533-43
48. Shu, D.; Shu, Y.; Haque, F.; Abdelmawla, S.; Guo, P. Nat. Nanotechnol. 2011, 6 (10) 658-67 10.1038/nnano.2011.105
49. Xiao, F.; Zhang, H.; Guo, P. Nucleic Acids Res. 2008, 36 (20) 6620-32 10.1093/nar/gkn669
50. Chworos, A.; Severcan, I.; Koyfman, A. Y.; Weinkam, P.; Oroudjev, E.; Hansma, H. G.; Jaeger, L. Science 2004, 306 (5704) 2068-72 10.1126/science.1104686
51. Severcan, I.; Geary, C.; Chworos, A.; Voss, N.; Jacovetty, E.; Jaeger, L. Nat. Chem. 2010, 2 (9) 772-9 10.1038/nchem.733
52. Afonin, K. A.; Viard, M.; Martins, A. N.; Lockett, S. J.; Maciag, A. E.; Freed, E. O.; Heldman, E.; Jaeger, L.; Blumenthal, R.; Shapiro, B. A. Nat. Nanotechnol. 2013, 8 (4) 296-304 10.1038/nnano.2013.44