Observation of internucleotide NH...N hydrogen bonds in the absence of directly detectable protons.
Several structural motifs found in nucleic acids involve N-H...N hydrogen bonds in which the donor hydrogens are broadened to extinction due to chemical or conformational exchange. In such situations, it is impossible to use the well-established HNN-COSY or soft HNN-COSY experiments, which report the presence of the hydrogen bond directly on the donor proton(s). We present a pulse sequence, H(CN)N(H), for alleviating this problem in hydrogen bonds of the type NdH...Na-CH, in which the donor Nd nitrogen is correlated with the corresponding non-exchangeable C-H proton associated with the acceptor Na nitrogen. In this way, missing NdH...Na correlations in an HNN-COSY spectrum may be recovered from CH-Nd correlations in the H(CN)N(H) spectrum. By correlating a different set of nuclei relative to the HNN-COSY class of experiments, the H(CN)N(H) experiment also serves to remove ambiguities associated with degeneracies in HNN-COSY spectra. The technique is demonstrated on d(GGAGGAG)4,a quadruplex containing a novel A. (G.G.G.G). A hexad and on d(GGGCAGGT)4, containing a G.G.G.C tetrad, in which missing NH2...N7 correlations are retrieved via H8-(N2,N6) correlations in the H(CN)N(H) spectrum.
Majumdar
A
A
Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. majumdar@sbnmr1.ski.mskcc.org
Kettani
A
A
Skripkin
E
E
Patel
D J
DJ
D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D006147:Guanine / Q000737:chemistry; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011522:Protons
D011522:Protons; D006147:Guanine; D000225:Adenine