Abstract
We present the results of molecular dynamics simulations on d(C-G-C-G-A) X d(T-C-G-C-G) with fully charged phosphates with and without inclusion of counterions. The average structures found in the two simulations are similar, but the simulation with counterions does give an average helix repeat, tilt, and twist in better agreement with those found in the x-ray structure of d(C-G-C-G-A-A-T-T-C-G-C-G)2. The average sugar pucker phases and amplitudes are in qualitative agreement with those found in NMR studies of double-helical DNA, and a number of examples of sugar repuckering from C2' endo to C3' endo carbon conformations in the sugar ring are found. The hydrogen bond correlations as well as torsion correlations are analyzed, and some interesting long-range correlations between dihedral angles are found.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Calladine C. R. Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol. 1982 Oct 25;161(2):343–352. doi: 10.1016/0022-2836(82)90157-7. [DOI] [PubMed] [Google Scholar]
- Clementi E., Corongiu G. Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure. Biopolymers. 1982 Apr;21(4):763–777. doi: 10.1002/bip.360210404. [DOI] [PubMed] [Google Scholar]
- Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
- Drew H. R., Wing R. M., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179–2183. doi: 10.1073/pnas.78.4.2179. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harvey S. C., Prabhakaran M., Mao B., McCammon J. A. Phenylalanine transfer RNA: molecular dynamics simulation. Science. 1984 Mar 16;223(4641):1189–1191. doi: 10.1126/science.6560785. [DOI] [PubMed] [Google Scholar]
- Karplus M., McCammon J. A. Dynamics of proteins: elements and function. Annu Rev Biochem. 1983;52:263–300. doi: 10.1146/annurev.bi.52.070183.001403. [DOI] [PubMed] [Google Scholar]
- Levitt M. Computer simulation of DNA double-helix dynamics. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):251–262. doi: 10.1101/sqb.1983.047.01.030. [DOI] [PubMed] [Google Scholar]
- Prabhakaran M., Harvey S. C., Mao B., McCammon J. A. Molecular dynamics of phenylalanine transfer RNA. J Biomol Struct Dyn. 1983 Oct;1(2):357–369. doi: 10.1080/07391102.1983.10507447. [DOI] [PubMed] [Google Scholar]
- Tidor B., Irikura K. K., Brooks B. R., Karplus M. Dynamics of DNA oligomers. J Biomol Struct Dyn. 1983 Oct;1(1):231–252. doi: 10.1080/07391102.1983.10507437. [DOI] [PubMed] [Google Scholar]