Hydrogen-bonding effects and 13 of the DNA double helix

Abstract

13C-nmr chemical shifts of the nucleotides in DNA are sensitive to hydrogen bonding, especially for three of the carbons immediately bonded to exocyclic oxygen or nitrogen atoms acting as H-bond acceptors or donors. GuoC2, GuoC6 and ThdC4 are strongly deshielded (about 1 ppm) upon Watson-Crick pairing in oligodeoxynucleotide duplexes, regardless of the base sequence. Deshielding at these sites may be useful to distinguish bases involved in Watson-Crick pairs from unpaired bases.

HELP (High Efficiency Liquid Phase) new oligonucleotide synthesis on soluble polymeric support

“…The feasibility of this method was tested in the synthesis of the octanucleotide d(TAGCGCTA) following the reported protocol ( Table 2). The identity of the final product was confirmed by comparison with the same oligomer independently synthesized (22)(23) in solution by a modified phosphotriester method (24).…”

13C NMR Assignments of the Protonated Carbons of [d(TAGCGCTA)]2by Two-Dimensional Proton-Detected Heteronuclear Correlation

“…Synthesis and purification of [d(TAGCGCTA)h have been described (5). Approximately 450 A 260 units were dissolved in 0.4ml of an aqueous buffer containing 20% Dp, 0.1 M NaCl, O.lmM EDTA and DSS.…”

“…Several methods have been proposed for assigning Be nmr resonances of oligonucleotides. Briefly, the comparative method (3,5) compares the natural abundance 13 C nmr chemical shifts, and melting curves of various oligomer sequences. This 1089 Downloaded by [New York University] at 05:51 15 May 2015 method is useful for assigning both protonated and quaternary carbons of the bases.…”

High‐Resolution Studies of Uniformly 13C,15N‐Labeled RNA by Solid‐State NMR Spectroscopy

“…[28] Stacking in nucleic acids is known to shift the 13 C resonances of the nucleobases upfield, [29] while hydrogen bonding of the adjacent heteroatoms causes the opposite, downfield shifts. [30,31] In the 14-mer RNA, the C2, C4, C5, and C8 resonances of A4 are shifted upfield relative to free ATP, while the C6 resonance is shifted downfield (see Table S2 in the Supporting Information). Similar shifts of the C6 signals of G1 and G10 could result from hydrogen bonding between O6 and external (solid) water.…”