The transition from a neutral-pH double helix to a low-pH triple helix induces a conformational switch in the CCCG tetraloop closing a Watson-Crick stem

Journal of Molecular Biology
M J van DongenC W Hilbers

Abstract

The CCCG-loop in a DNA fragment, which is capable of forming an intramolecular triple helix as well as a hairpin structure, was investigated by NMR and molecular modeling studies. The structure of this loop is found as a type II conformation, one of the three commonly observed folding patterns of tetraloops, irrespective of the geometry of the underlying helix. In each situation, the loop exhibits a base-pair between the first cytosine and the guanine residue of the loop. The geometry of this base-pair, however, depends upon the circumstances. At neutral pH, in the hairpin form of the molecule, a Watson-Crick C.G base-pair is formed, whereas at low pH, when the strand exists as an intramolecular triple helix, a Hoogsteen C(+)-G base-pair is present. We used molecular modeling to lay the foundations for understanding the observed conformational switch. A lower amount of strain, related to the short C1'-C1' of the base-pair, and protonation effects of the structure comprising the Hoogsteen base-pair turn out to outweigh the effects of a more stable base-pair, improved stacking and more favorable interactions in the minor groove of the structure comprising the Watson-Crick C.G base-pair. The models also provide an explanation for ...Continue Reading

Citations

Apr 12, 2011·Nucleic Acids Research·Sik Lok LamLai Man Chi
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Sep 3, 2016·Journal of the American Chemical Society·Pei Guo, Sik Lok Lam
Mar 3, 2017·The Journal of Physical Chemistry. B·Yuan LiuSik Lok Lam
Jul 12, 2017·The Journal of Physical Chemistry Letters·Pei Guo, Sik Lok Lam
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Oct 21, 2017·The Journal of Physical Chemistry. B·Yuan Liu, Sik Lok Lam

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