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PMID: 3357884 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Some rules for predicting the base-sequence dependence of DNA conformation.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 85 ·No. 8 ·1988-04-00 ·Pages 2579-83

Peticolas WL, Wang Y, Thomas GA

Abstract

Two tables have been constructed showing the crystal and solution conformations of short sequences of DNA. Each of these DNAs has been found to be in one of three different conformations--the A, B, or Z form--depending upon the base sequence and the environmental conditions. A set of rules is presented showing the tendency of certain base pairs to direct the DNA conformation into the A, B, or Z genus in saturated salt solutions and in crystals. These rules are based on a consideration of nearest-neighbor interactions that are interpreted in terms of 10 different two-letter code words made from the letters denoting the bases guanine (G), cytosine (C), adenine (A), and thymine (T). One table discusses the effect on DNA conformation of 3 strong words that tend to direct a DNA oligomer into either the A, B, or Z genus in crystals or in aqueous solutions containing a high salt concentration (6 M). The second table discusses the remaining 7 code words that appear to have a much weaker effect on conformation. The sequences that are most likely to lead to A-Z, B-Z, and A-B junctions are discussed, as is the possible biological significance of these rules.

MeSH Terms
Base Sequence DNA Nucleic Acid Conformation Spectrum Analysis, Raman Structure-Activity Relationship
Chemicals
DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Peticolas W L
Department of Chemistry, University of Oregon, Eugene 97403.
Wang Y
Thomas G A
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35 references, click to expand
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.85.8.2579
Published
1988-04-00
Pages
2579-83
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC280041
Subset
IM
Grants
NIGMS NIH HHS · GM15547 · United States
NIGMS NIH HHS · GM33825 · United States
External Links
PubMed source DOI: 10.1073/pnas.85.8.2579 PMC Full Text View journal details
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