Linked Life Data

11456575

Source:http://linkedlifedata.com/resource/pubmed/id/11456575

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2001-7-17
pubmed:abstractText
We present a new NMR procedure for determining the three-dimensional fold of C2-symmetric nucleic acid homodimers that relies on long-range orientational constraints derived from the measurement of two independent sets of residual dipolar couplings under two alignment conditions. The application is demonstrated on an (15)N/(13)C-enriched deoxyoligonucleotide sequence, d(G-G-G-T-T-C-A-G-G), shown previously to dimerize into a quadruplex in solution and form a pair of G.(C-A) triads and G-G-G-G tetrads (G-tetrad) motifs. One-bond (1)H-(15)N ((1)D(NH)) and (1)H-(13)C ((1)D(CH)) residual dipolar couplings have been measured between nuclei in the bases of these motifs using bacteriophage as an ordering medium, and under direct magnetic field alignment (800 MHz). By combining the two dipolar data sets in an order matrix analysis, the orientation of the G.(C-A) triad relative to the G-tetrad within a contiguous monomeric unit can directly be determined, even in the presence of interstrand/intrastrand NOE ambiguity. We further demonstrate that the orientation of the C2-axis of molecular symmetry in the homodimer relative to the G.(C-A) triad and G-tetrad motifs can unambiguously be determined using the two sets of independent dipolar coupling measurements. The three-dimensional fold of the homodimer determined using this procedure is very regular and in excellent agreement with a previously determined high-resolution NOE-based NMR structure, where interstrand/intrastrand NOEs were treated as ambiguous and where noncrystallographic symmetry constraints were implicitly imposed during the structure calculation.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
0002-7863
pubmed:author
pubmed:issnType
Print
pubmed:day
31
pubmed:volume
123
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
633-40
pubmed:dateRevised
2007-11-15
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Field- and phage-induced dipolar couplings in a homodimeric DNA quadruplex: relative orientation of G.(C-A) triad and G-tetrad motifs and direct determination of C2 symmetry axis orientation.
pubmed:affiliation
Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA. hashimi@sbnmr1.mskcc.org
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.