Abstract
Recently, it has been shown by Calladine (1982) and Dickerson (1983) that DNA distortions due to steric clashes between opposing purines and pyrimidines can be quantitated based upon four sum functions. The distortions involve helical twist, roll, torsion angle variations and propeller twist. It is the contention of the authors that these perturbations in structure act as information carriers for various external DNA interactions. This paper describes a system that incorporates these four rules and various other functions that permit the systematic interactive exploration for significant patterns as a consequence of these steric clashes.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Drew H. R., Dickerson R. E. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol. 1981 Sep 25;151(3):535–556. doi: 10.1016/0022-2836(81)90009-7. [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]
- Drew H., Takano T., Tanaka S., Itakura K., Dickerson R. E. High-salt d(CpGpCpG), a left-handed Z' DNA double helix. Nature. 1980 Aug 7;286(5773):567–573. doi: 10.1038/286567a0. [DOI] [PubMed] [Google Scholar]
- Lennon G. G., Nussinov R. Homonyms, synonyms and mutations of the sequence/structure vocabulary. J Mol Biol. 1984 May 25;175(3):425–430. doi: 10.1016/0022-2836(84)90359-0. [DOI] [PubMed] [Google Scholar]
- Maizel J. V., Jr, Lenk R. P. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. doi: 10.1073/pnas.78.12.7665. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nussinov R., Shapiro B., Lipkin L. E., Maizel J. V., Jr DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation. J Mol Biol. 1984 Aug 25;177(4):591–607. doi: 10.1016/0022-2836(84)90039-1. [DOI] [PubMed] [Google Scholar]
- Nussinov R., Shapiro B., Lipkin L. E., Maizel J. V., Jr Enhancer elements share local homologous twist-angle variations with a helical periodicity. Biochim Biophys Acta. 1984 Dec 14;783(3):246–257. doi: 10.1016/0167-4781(84)90035-6. [DOI] [PubMed] [Google Scholar]