High base pair opening rates in tracts of GC base pairs

Citation
U. Dornberger et al., High base pair opening rates in tracts of GC base pairs, J BIOL CHEM, 274(11), 1999, pp. 6957-6962
Citations number
35
Categorie Soggetti
Biochemistry & Biophysics
Journal title
JOURNAL OF BIOLOGICAL CHEMISTRY
ISSN journal
00219258 → ACNP
Volume
274
Issue
11
Year of publication
1999
Pages
6957 - 6962
Database
ISI
SICI code
0021-9258(19990312)274:11<6957:HBPORI>2.0.ZU;2-K
Abstract
Sequence-dependent structural features of the DNA double helix have a stron g influence on the base pair opening dynamics. Here we report a detailed st udy of the kinetics of base pair breathing in tracts of GC base pairs in DN A duplexes derived from H-1 NMR measurements of the imino proton exchange r ates upon titration with the exchange catalyst ammonia. In the limit of inf inite exchange catalyst concentration, the exchange times of the guanine im ino protons of the GC tracts extrapolate to much shorter base pair lifetime s than commonly observed for isolated GC base pairs. The base pair lifetime s in the GC tracts are below 5 ms for almost all of the base pairs. The unu sually rapid base pair opening dynamics of GC tracts are in striking contra st to the behavior of AT tracts, where very long base pair lifetimes are ob served, The implication of these findings for the structural principles gov erning spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.