Through-bond correlation of adenine H2 and H8 protons in unlabeled DNA fragments by HMBC spectroscopy

Abstract

SummaryA new application of the HMBC experiment is presented that provides a useful means to discriminate between H2 and H 8 proton resonances, to assign the base proton resonances to the various residue types and, most importantly, to correlate the H2 and H8 protons for adenine or inosine residues in natural abundance 13C fragments. The utility of this experiment is demonstrated for an unlabeled DNA 20-mer. Thanks to the obtained results, preliminary conclusions could be drawn regarding the molecular confor mations of the non-canonical G/I-A base pairs in the hairpin formed by this fragment.

Unusual structures of TTTA repeats in icaC gene of Staphylococcus aureus

“…As the sequential T3 H1 0 -A4 H8 and T7 H1 0 -A8 H8 NOEs were not observed in the 2D NOESY spectrum of (TTTA) 2 at a mixing time of 300 ms, in order to assign the H8 signals of A4 and A8, the NOESY experiment was repeated at a longer mixing time of 800 ms and these sequential NOEs were observed (Supporting Information, S2). For the assignments of adenine H2, they were confirmed by 1 H-13 C HMBC experiments [14] (Supporting Information, S3). Based on the H3 0 assignment results from TOCSY, the backbone 31 P signals were assigned using 1 H-31 P HSQC spectra (Supporting Information, S4 and S5).…”

“…The acquired data sets were zero-filled to give 4096 Â 4096 spectra with a cosine window function applied to both dimensions. For adenine H2 protons, the assignments were confirmed by 1 H-13 C heteronuclear multiple-bond correlation (HMBC) experiments [14] with an evolution period of 65 ms for the long-range couplings. The 13 C spectral width was set to 60 ppm and the carrier frequency was centered at 140 ppm.…”

DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly13C-Labeled Purine Nucleotides

“…Total acquisition time was less than 4 h, which was enough to identify all intraresidue H2-H8 connectivities for the 0.9 mM sample. The HMBC experiment was reported for 1.5 mM DNA of a 20-base hairpin at natural abundance to require a total acquisition time of 80 h using a 750 MHz spectrometer (58). These experiments should become a good tool for revealing intraresidue H2-H8 correlations; e.g., the sensitivity for a fully 13 C-labeled sample would be six times higher than for that of our 15%…”

Structure Determination of the Top‐Loop of the Conserved 3′‐Terminal Secondary Structure in the Genome of Flaviviruses

“…All H2 signals in adenine nucleobases were unambiguously assigned through their longrange correlation to C4, the carbon that also has cross peak with purine H8 in a [ 1 H, 13 C] HMBC spectrum ( Figure 3). [26] Heteronuclear experiments on natural-abundance samples were performed for assignment of 13 C and 31 P signals (Figure 2). Classic imino-to-imino walks in the Watergate NOESY provided assignment of imino protons (Figure 2) in the Watson-Crick base pairs of the stems of oligo 1 and oligo 2.…”