MQ-HCN-based pulse sequences for the measurement of 13C1′-1H1′, 13C1′-15N, 1H1′-15N, 13C1′-13C2′, 1H1′-13C2′, 13C6/8-1H6/8, 13C6/8-15N, 1H6/8-15N, 13C6-13C5, 1H6-13C5 dipolar couplings in 13C, 15N-labeled DNA (and RNA)

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Abstract
A suite of multiple quantum (MQ) HCN-based pulse sequences has been developed for the purpose of collecting dipolar coupling data in labeled nucleic acids. All the pulse sequences are based on the robust MQ-HCN experiment which has been utilized for assignment purposes in labeled nucleic acids for a number of years and provides much-needed resolution for the dipolar coupling measurements. We have attempted to collect multiple couplings centered on the 13C1′ and 13C6/8 positions. Six pulse sequences are described, one each for measurement of one-bond 13C1′-1H1′ and 13C6/8-1H6/8 couplings, one for measurement of one-bond 13C1′-15N and two-bond 1H1′-15N couplings, one for measurement of one-bond13C6/8-15N and two-bond 1H6/8-15N couplings, one for measurement of one-bond 13C1′-13C2′ and two-bond 1H1′-13C2′ couplings, and one for measurement of one-bond 13C6-13C5 and two-bond 1H6-13C5 couplings in the bases of C and T. These sequences are demonstrated for a labeled 18 bp DNA duplex in a 47 kDa ternary complex of DNA, CBFβ, and the CBFα Runt domain, thus clearly demonstrating the robustness of the pulse sequences even for a very large complex.