1H-1H correlations across N-H...N hydrogen bonds in nucleic acids

J Biomol NMR. 2001 Dec;21(4):289-306. doi: 10.1023/a:1013340227140.

Abstract

In 2HJ(NN)-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,omega1):H3(U,omega2) protons across Watson-CrickA-U and mismatched G.A base pairs, the sequences H5(N3N1)H1/H6(N3N1)H1 correlate H5(C,omega1)/H6(C,omega1):H1(G,omega2) protons across Watson-Crick G-C base pairs, and the H2(N2N7)H8 sequence correlates NH2(G,A,C;omega1):H8(G,A;omega2) protons across G.G, A.A, sheared G.A and other mismatch pairs. These 1H-1H connectivities circumvent the 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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pair Mismatch
  • Base Pairing
  • Base Sequence
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • G-Quadruplexes
  • Gene Products, rev / metabolism
  • HIV Long Terminal Repeat
  • HIV-1 / chemistry
  • HIV-1 / genetics
  • Humans
  • Hydrogen / chemistry*
  • Hydrogen Bonding
  • Models, Molecular
  • Nitrogen / chemistry*
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation
  • Nucleic Acids / chemistry*
  • Peptides / chemistry
  • Protons
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism
  • Structure-Activity Relationship
  • rev Gene Products, Human Immunodeficiency Virus

Substances

  • Gene Products, rev
  • Nucleic Acids
  • Peptides
  • Protons
  • RNA, Viral
  • rev Gene Products, Human Immunodeficiency Virus
  • Hydrogen
  • DNA
  • Nitrogen