Abstract
The nonexchangeable base and sugar protons of the octanucleotide d(G-G-A-A-T-T-C-C) have been assigned by two-dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) methods in aqueous solution. The assignments are based on distance connectivities of less than 4.5 A established from NOE effects between base and sugar protons on the same strand and occasionally between strands, as well as, coupling connectivities within the protons on each sugar ring. We observe the NOEs to exhibit directionality and are consistent with the d(G-G-A-A-T-T-C-C) duplex adopting a right-handed helix in solution. The relative magnitude of the NOEs between base and sugar H2' protons of the same and 5'-adjacent sugars characterizes the AATT segment to the B-helix type in solution.
Highlights
From the Department of Biochemistryand Molecular Biophysics,College of Physicians and Surgeons, Columbia University, New York, New York I0032
The nonexchangeable base and sugar protons of theimino protons in d(TATA) [27, 28] and d(TGTG) segments octanucleotided(G-G-A-A-T-T-C-C)havebeen as- [29] exchange more rapidly than their non-alternatingpyrimsigned by two-dimensional correlate(dCOSY)and nu- idine-purine counterparts
This paper extends on these investinated right-handedA, right-handed B, and left-handed Z that gations by completelyassigning ail thebase and sugar protons have been observed in single crystals, in fibers, and inaqueous (except the super-positioned 5’,5”-sugar protons} by twosolution [1].There ismuch conformational flexibility in right- dimensional correlated (COSY) and Overhauser (NOESY)
Summary
E4.5 A.Some of the cross-peaksmay not reflect direct interactions at this mixing time so that an NOE between a base proton and a sugar H1‘ may, in part, be mediated through the sugar HZ’on the same residue. We analyze below individual regions at the AATT 8-mer COSY (Fig. IS) and NOESY (Fig. 2s) contour plots which yield the detailed spectral assignments
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