An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: Application to the 26-kDa Dead Ringer-DNA complex

Junji Iwahara, Jonathan M. Wojciak, Robert T. Clubb

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We present a new NMR experiment for estimating the type and degree of sugar-puckering in high-molecular-weight unlabeled DNA molecules. The experiment consists of a NOESY sequence preceded by a constant-time scalar coupling period. Two subexperiments are compared, each differing in the amount of time the 3JH3′H2′ and 3JH3′H2″ couplings are active on the H3′ magnetization. The resultant data are easy to analyze, since a comparison of the signal intensities of any resolved NOE cross peak originating from H3′ atoms of the duplex can be used to estimate the sum of the 3JH3′H2′ and 3JH3′H2″ couplings and thus the puckering type of the deoxyribose ring. Isotope filters to eliminate signals of the 13C-labeled component in the F1-dimension are implemented, facilitating analyses of high-molecular-weight protein-DNA complexes containing 13C-labeled protein and unlabeled DNA. The utility of the experiment is demonstrated on the 26-kDa Dead Ringer protein-DNA complex and reveals that the DNA uniformly adopts the S-type configuration when bound to protein.

Original languageEnglish (US)
Pages (from-to)262-266
Number of pages5
JournalJournal of Magnetic Resonance
Volume153
Issue number2
DOIs
StatePublished - 2001
Externally publishedYes

Fingerprint

sugars
Sugars
deoxyribonucleic acid
Nuclear magnetic resonance
nuclear magnetic resonance
DNA
proteins
Experiments
molecular weight
Proteins
Molecular Weight
Molecular weight
Deoxyribose
Isotopes
time constant
Magnetization
estimating
isotopes
scalars
filters

Keywords

  • DNA
  • Isotope filter
  • J modulation
  • NMR
  • Protein-DNA complex
  • Sugar pucker

ASJC Scopus subject areas

  • Molecular Biology
  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Radiology Nuclear Medicine and imaging
  • Condensed Matter Physics

Cite this

An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA : Application to the 26-kDa Dead Ringer-DNA complex. / Iwahara, Junji; Wojciak, Jonathan M.; Clubb, Robert T.

In: Journal of Magnetic Resonance, Vol. 153, No. 2, 2001, p. 262-266.

Research output: Contribution to journalArticle

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