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

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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 H5(C,ω1)/H6(C,ω1):H1(G,ω2) protons across Watson–Crick G-C base pairs, and the H2(N2N7)H8 sequence correlates NH2(G,A,C;ω1):H8(G,A;ω2) 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.

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Authors and Affiliations

  1. Cellular Biochemistry and Biophysics Department, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, 10021, U.S.A

    Ananya Majumdar, Yuying Gosser & Dinshaw J. Patel

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  1. Ananya Majumdar
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  2. Yuying Gosser
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  3. Dinshaw J. Patel
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Majumdar, A., Gosser, Y. & Patel, D.J. 1H-1H correlations across N–H•••N hydrogen bonds in nucleic acids. J Biomol NMR 21, 289–306 (2001). https://doi.org/10.1023/A:1013340227140

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