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Nucleic Acids Research, 2003, Vol. 31, No. 3 1059-1066
© 2003 Oxford University Press

DNA curvature at A tracts containing a non-polar thymine mimic

Angèle Maki, Floyd E. Brownewell, Dongyu Liu and Eric T. Kool*

Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA

*To whom correspondence should be addressed. Tel: +1 650 724 4741; Fax: +1 650 725 0259; Email: kool{at}stanford.edu
Present addresses:
Floyd E. Brownewell, Albany Molecular Research, Inc., 21 Corporate Circle, PO Box 15098, Albany, NY 12212, USA
Dongyu Liu, Genzyme Corporation, PO Box 9322, Framingham, MA 01701, USA

We report the first experimental probing of electrostatic interactions on the pyrimidine side of a bent A tract. Although the curvature of short A tracts (A4–A6) has long been studied, its physical origins remain under debate. Current hypotheses include the influence of major-groove hydrogen bonds between propeller-twisted base pairs, electrostatic effects of closely associated minor-groove cations, effects of minor-groove solvation, and stacking effects at the junctions adjacent to the A tract. We investigated this problem through the substitution of thymidines in A5 tracts by difluorotoluene deoxynucleoside (F), a non-polar molecule of the same size and shape which lacks hydrogen bonding and metal-ion complexing capabilities. Ligation experiments with phased A tracts demonstrated that F substitution has asymmetric effects on the bend angle. The strongest effects occurred at the second and third thymines where curvature was reduced from 19.8° to 5.3° and 9.6°, respectively. Moderate effects were observed with substitutions at positions 1 and 4, while substitution at position 5 had no effect on bend angle. The results support the hypothesis that highly localized electrostatic interactions are a principal cause of A-tract curvature. Furthermore, they are most consistent with the notion that local metal-ion complexation at O2 of thymine is a strong component of these interactions.


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