1H-1H correlations across N-H...N hydrogen bonds in nucleic acids.
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.
Majumdar
A
A
Cellular Biochemistry and Biophysics Department, Memorial Sloan-Kettering Cancer Center, New York 10021, USA. majumdar@sbnmr1.mskcc.org
Gosser
Y
Y
Patel
D J
DJ
D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D054856:G-Quadruplexes; D015694:Gene Products, rev / Q000378:metabolism; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics; D006801:Humans; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D011522:Protons; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D054321:rev Gene Products, Human Immunodeficiency Virus
D015694:Gene Products, rev; D009696:Nucleic Acids; D010455:Peptides; D011522:Protons; D012367:RNA, Viral; D054321:rev Gene Products, Human Immunodeficiency Virus; D006859:Hydrogen; D004247:DNA; D009584:Nitrogen