Nucleic Acids Research, 2003, Vol. 31, No. 10 2461-2474
© 2003 Oxford University Press
Unusual DNA duplex and hairpin motifs
1 Department of Life Science, National Central University, Jung-Li, 320, Taiwan, ROC, 2 Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227, Taiwan, ROC and 3 Institute of Biological Chemistry, Academia Sinica, Nankang, 115, Taiwan, ROC
Correspondence may also be addressed to Andrew H.-J. Wang. Tel: +886 22 788 1981; Fax: +886 22 788 9759; Email: ahjwang{at}gate.sinica.edu.tw
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 Ganti·Csyn 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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. Kaushik and S. Kukreti Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human {beta}-globin gene cluster Nucleic Acids Res., July 19, 2006; 34(12): 3511 - 3522. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Bacolla and R. D. Wells Non-B DNA Conformations, Genomic Rearrangements, and Human Disease J. Biol. Chem., November 12, 2004; 279(46): 47411 - 47414. [Full Text] [PDF]
|
|
|
|
|
|
S. Anuradha and K. Muniyappa Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets Nucleic Acids Res., April 28, 2004; 32(8): 2378 - 2385. [Abstract] [Full Text] [PDF]
|
|