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Organic & Biomolecular Chemistry Vol -5

Organic & Biomolecular Chemistry Vol -4

Organic & Biomolecular Chemistry Vol -3

Organic & Biomolecular Chemistry Vol -2

Sequence dependence in base flipping: experimental and computational studies

Content Provider	Royal Society of Chemistry (RSC)
Author	O'Neil, Lauren L. Wiest, Olaf
Copyright Year	2008
Abstract	Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc–cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.
Starting Page	485
Ending Page	492
Page Count	8
File Format	HTM / HTML PDF
ISSN	14770520
Volume Number	6
Issue Number	3
Journal	Organic & Biomolecular Chemistry
DOI	10.1039/b713318a
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	DNA Molecular dynamics AP site Dissociative Correlation and dependence Hydrogen bond
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Biochemistry Physical and Theoretical Chemistry

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