1H-1H correlations across N-H•••N hydrogen bonds in nucleic acids Journal Article


Authors: Majumdar, A.; Gosser, Y.; Patel, D. J.
Article Title: 1H-1H correlations across N-H•••N hydrogen bonds in nucleic acids
Abstract: In 2HJNN-COSY experiments, which correlate protons with donor/acceptor nitrogens across Nd•••HNa bonds, the receptor nitrogen needs to be assigned in order to unambiguously identify the hydrogen bond. For many situations this is a non-trivial task which is further complicated by poor dispersion of (Na,Nd) resonances. To address these problems, we present pulse sequences to obtain direct, internucleotide correlations between protons in uniformly 13C/15N labeled nucleic acids containing Nd•••HNa hydrogen bonds. Specifically, the pulse sequence H2(N1N3)H3 correlates H2(A,ω1):H3(U,ω2) protons across Watson-Crick A-U and mismatched G•A base pairs, the sequences H5(N3N1)H1/H6(N3N1)H1 correlate need for independent assignment of the donor/acceptor nitrogen and related degeneracy issues associated with poorly dispersed nitrogen resonances. The methodology is demonstrated on uniformly 13C/15N labeled samples of (a) an RNA regulatory element involving the HIV-1 TAR RNA fragment, (b) a multi-stranded DNA architecture involving a G•(C-A) triad-containing G-quadruplex and (c) a peptide-RNA complex involving an evolved peptide bound to the HIV-1 Rev response element (RRE) RNA fragment.
Keywords: controlled study; genetics; methodology; metabolism; peptide; structure activity relation; structure-activity relationship; rna; chemistry; dna; guanine; virus rna; nucleotide sequence; nucleic acids; peptides; nuclear magnetic resonance spectroscopy; base sequence; base pairing; hydrogen bond; hydrogen bonding; models, molecular; protons; chemical structure; human immunodeficiency virus; conformation; nucleic acid conformation; dna helix; nuclear magnetic resonance; nitrogen; rna, viral; human immunodeficiency virus 1; sample; hiv-1; proton; nucleotide; long terminal repeat; nucleic acid; adenine; protein rna binding; hydrogen; nuclear magnetic resonance, biomolecular; base mispairing; base pair mismatch; uracil; carbon 13; dispersion; hiv long terminal repeat; quadruplex dna; humans; human; priority journal; article; rev protein; 2hjnn; hnn-cosy; h2(n1n3)h3; h5(n3n1)h1; h6(n3n1)h1; h2(n2n7)h8; gene products, rev
Journal Title: Journal of Biomolecular NMR
Volume: 21
Issue: 4
ISSN: 0925-2738
Publisher: Springer  
Date Published: 2001-12-01
Start Page: 289
End Page: 306
Language: English
DOI: 10.1023/a:1013340227140
PUBMED: 11824750
PROVIDER: scopus
DOI/URL:
Notes: Export Date: 21 May 2015 -- Source: Scopus
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MSK Authors
  1. Yuying Gosser
    7 Gosser
  2. Dinshaw J Patel
    445 Patel