Article ; Online: Unusual DNA duplex and hairpin motifs.
2003 Volume 31, Issue 10, Page(s) 2461–2474
Abstract: ... duplex and hairpin motifs in the presence (trans) or absence (cis) of ligands. Several principles ... groove to form a compact loop structure. Identification of such diverse duplex or hairpin motifs greatly ... mismatches can occur in a B-DNA duplex when sheared base pairs are adjacent to each other to confer extensive ...
| Abstract | Single-stranded DNA or double-stranded DNA has the potential to adopt a wide variety of unusual duplex and hairpin motifs in the presence (trans) or absence (cis) of ligands. Several principles for the formation of those unusual structures have been established through the observation of a number of recurring structural motifs associated with different sequences. These include: (i) internal loops of consecutive mismatches can occur in a B-DNA duplex when sheared base pairs are adjacent to each other to confer extensive cross- and intra-strand base stacking; (ii) interdigitated (zipper-like) duplex structures form instead when sheared G*A base pairs are separated by one or two pairs of purine*purine mismatches; (iii) stacking is not restricted to base, deoxyribose also exhibits the potential to do so; (iv) canonical G*C or A.T base pairs are flexible enough to exhibit considerable changes from the regular H-bonded conformation. The paired bases become stacked when bracketed by sheared G.A base pairs, or become extruded out and perpendicular to their neighboring bases in the presence of interacting drugs; (v) the purine-rich and pyrimidine-rich loop structures are notably different in nature. The purine-rich loops form compact triloop structures closed by a sheared G*A, A*A, A*C or sheared-like G(anti)*C(syn) base pair that is stacked by a single residue. On the other hand, the pyrimidine-rich loops with a thymidine in the first position exhibit no base pairing but are characterized by the folding of the thymidine residue into the minor groove to form a compact loop structure. Identification of such diverse duplex or hairpin motifs greatly enlarges the repertoire for unusual DNA structural formation. |
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| MeSH term(s) | Base Pair Mismatch/genetics ; Base Pairing/genetics ; Base Sequence ; DNA/chemistry ; DNA/genetics ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/chemistry ; Nucleic Acid Heteroduplexes/genetics |
| Chemical Substances | Nucleic Acid Heteroduplexes ; DNA (9007-49-2) |
| Language | English |
| Publishing date | 2003-03-18 |
| Publishing country | England |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't ; Review |
| ZDB-ID | 186809-3 |
| ISSN | 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048 |
| ISSN (online) | 1362-4962 ; 1362-4954 |
| ISSN | 0301-5610 ; 0305-1048 |
| DOI | 10.1093/nar/gkg367 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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