Hostname: page-component-84b7d79bbc-lrf7s Total loading time: 0 Render date: 2024-07-26T23:26:32.306Z Has data issue: false hasContentIssue false
  • English
  • Français

Simulations of Stretching Single Stranded DNA

Published online by Cambridge University Press:  21 March 2011

Abhishek Singh  and
Yaroslava G. Yingling
Abhishek Singh
Affiliation:
Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695 USA
Yaroslava G. Yingling
Affiliation:
Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC, 27695 USA
Get access

Abstract

Molecular dynamics simulations were performed to estimate sequence dependent force required to stretch single stranded DNA (ssDNA) homo oligonucleotides. Simulations suggest that polyA and polyC oligonucleotides exhibit similar force profiles and corresponding elongation. Among single stranded DNA strands polyT is the most flexible and needs the most force to unwind from an equilibrium folded structure. In contrast, polyG had a very small recoverable deformation prior to a non-linear stretching. Our results indicate that mechanical properties of ssDNA chains are directly related to their sequence.

Keywords

biologicalsimulationstrength
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 1301: Symposium V/NN/OO/PP – Soft Matter, Biological Materials and Biomedical Materials—Synthesis, Characterization and Applications , 2011 , mrsf10-1301-oo10-06
Copyright
Copyright © Materials Research Society 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

(1) Kallenbach, N.; Ma, R.; Seeman, N. 1983.Google Scholar
(2) Sharma, J.; Chhabra, R.; Cheng, A.; Brownell, J.; Liu, Y.; Yan, H. Science 2009, 323, 112.10.1126/science.1165831Google Scholar
(3) Lozano, M.; Starkel, C.; Longo, M. Langmuir, 26, 8517.10.1021/la9044946Google Scholar
(4) Zhu, N.; Gao, H.; Xu, Q.; Lin, Y.; Su, L.; Mao, L. Biosensors and Bioelectronics, 25, 1498.Google Scholar
(5) Heddi, B.; Oguey, C.; Lavelle, C.; Foloppe, N.; Hartmann, B. Nucleic Acids Research, 38, 1034.Google Scholar
(6) Ke, C.; Humeniuk, M.; S-Gracz, H.; Marszalek, P. E. Physical Review Letters 2007, 99.Google Scholar
(7) Roe, D. R.; Chaka, A. M. Journal of Physical Chemistry B 2009, 113, 15364.10.1021/jp906749jGoogle Scholar
(8) Trahan, D. W.; Doyle, P. S. Biomicrofluidics 2009, 3.10.1063/1.3055275Google Scholar
(9) Reihani, N.; Bosanac, L.; Hansen, T. M.; Oddershede, L. B. Optical Trapping and Optical Micromanipulation III 2006, 6326, U501.Google Scholar
(10) Kim, J. H.; Shi, W. X.; Larson, R. G. Langmuir 2007, 23, 755.10.1021/la062505uGoogle Scholar
(11) Randall, G. C.; Schultz, K. M.; Doyle, P. S. Lab on a Chip 2006, 6, 516.10.1039/b515326cGoogle Scholar
(12) Kobayashi, T.; Washizu, M. MEMS 2005 Miami: Technical Digest 2005, 662.Google Scholar
(13) Mishra, G.; Giri, D.; Kumar, S. Physical Review E 2009, 79.10.1103/PhysRevE.79.031930Google Scholar
(14) Case, D. A.; Darden, T. A.; Cheatham, T. E. I.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9 University of California, San Francisco, 2006.Google Scholar
(15) Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J. M.; Kollman, P. Journal of Computational Chemistry 2003, 24, 1999.10.1002/jcc.10349Google Scholar
(16) Bashford, D.; Case, D. A. Annual Review of Physical Chemistry 2000, 51, 129.10.1146/annurev.physchem.51.1.129Google Scholar
(17) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Journal of Chemical Physics 1984, 81, 3684.10.1063/1.448118Google Scholar
(18) Morfill, J.; Kühner, F.; Blank, K.; Lugmaier, R. A.; Sedlmair, J.; Gaub, H. E. Biophysical Journal, 2007, 93, 2400.10.1529/biophysj.107.106112Google Scholar