N.m.r. determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer.

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N.m.r. determination of the solution conformation and dynamics of the A.G mismatch in the d(CGCAAATTGGCG)2 dodecamer.

Publication Date
Feb 01, 1992
Source
PMC
Keywords
Disciplines
  • Biology
  • Chemistry
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Unknown

Abstract

Biochem. J. (1991) 279, 269-281 (Printed in Great Britain) N.m.r. determination of the solution conformation and dynamics of the A. G mismatch in the d(CGCAAATTGGCG)2 dodecamer Andrew N. LANE,*§ Terence C. JENKINS,t§ Dorcas J. S. BROWNt and Tom BROWNt *Laboratory of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 IAA, U.K., tCancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey SM2 5NG, U.K., and IDepartment of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3LL, U.K. A. G base-paired mismatches that occur during replication are among the most difficult to detect by repair enzymes. Such purine * purine mispairs can exist in two conformations, one of which is stabilized by protons [Gao & Patel (1988) J. Am. Chem. Soc. 110, 5178-5182]. We have undertaken a 'H-n.m.r. and 31P-n.m.r. study of the mismatched dodecamer d(CGCAAATTGGCG)2 as a function of both temperature and pH to determine the conformational features of the A. G mismatch. At pH > 7 the mispaired bases are each in the anti conformation and are stacked in the B-like helix. As the pH is decreased, a second conformation becomes populated (apparent pK. approx. 5.9) with concomitant changes in the chemical shifts of protons of the mispaired bases and their nearest neighbours. Data from two-dimensional nuclear- Overhauser-enhancement spectroscopy show unequivocally that, at low pH, the dominant conformation is one in which the mismatched G residues are in the syn conformation and are hydrogen-bonded to the A residues that remain in the anti conformation. Residues not adjacent to the A G sites are almost unaffected by the transition or the mispairing, suggesting considerable local flexibility of the unconstrained duplexes. Despite the bulging of the mispaired bases, the conformation of the A(anti) * G(anti) duplex is very similar to the native dodecamer, whereas the AH+(anti) * G(syn) duplex shows a greater variation in the backbone c

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