NMR evidence for mechanical coupling of phosphate BI-BII transitions with deoxyribose conformational exchange in DNA

Richard J. Isaacs, H. Peter Spielmann

Research output: Contribution to journalArticlepeer-review

40 Scopus citations

Abstract

The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)2 and d(CGCTAGCG)2 have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate BI and BII conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %BI or %S. Sequence context-dependent variations in %BI and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %BI, %S, and previously calculated model free 13C order parameters (S2) were observed. The %BI of the phosphates were found to be correlated to the S2 of the flanking C3′ and C4′ atoms. The %BI was also found to be correlated with the %S and C1′ S2 of the deoxyribose ring 5′ of the phosphates. The %BI of opposing phosphates is correlated, while the %BI of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.

Original languageEnglish
Pages (from-to)149-160
Number of pages12
JournalJournal of Molecular Biology
Volume311
Issue number1
DOIs
StatePublished - Aug 3 2001

Bibliographical note

Funding Information:
We thank Dr Charlotte Gotfredsen (Carlsberg Laboratories, Copenhagen) and Professor Muriel Delepierre (Institut Pasteur, Paris) for providing the pulse-sequences that we modified to accomplish this work. This work was supported in part by NSF grant MCB-9808633.

Keywords

  • B-B equilibrium
  • Conformational exchange
  • N-S equilibrium
  • Order parameter
  • Spin relaxation

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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