a p a n
Synopsis
Two short DNA helices, d-(CpCpCpG)y and d-(CpGpCpGpCpG),, in dilute salt solutions have been studied thoroughly by 'Hand ."P-nmr spectroscopy as model systems for the calibration of nmr theory in its application to nucleic acids research. A [ / the nonexchangeable proton resonances of' these two short helices have heen assigned by the "incremental method." "sequential homodecoupling" ol' the sugar protons, thermal perturbation, and computer spectral simulation, as well as the NOE technique.
T h e CD and uv data were also obtained a t either identical or half concentrations ofthe 01igomer used in the nmr studies in order to have comparable optical data for estimating helical content and for assigning conformation. The precise assignment of the sugar proton resonances and their corresponding coupling-constant values provide valuable information about the backbone conformation. T h e sugar conformation was shown to he predominantly in the 'ICl'orm (>TO%). The rotation of the C,t,-Ch, is in favor of the ,qg conformation (55-95'%), the rotation of the Ch,-O;,, bond is highly in favor ofg'g' (8:i ~9 1 7 ) , and the rotation of the C.~,-O.r~ bond is restricted to the domain of'$' = 195'. T h e CII data and the sugar conformational analyses indicate that these CG helices are in the R-form in dilute salt solutions. The assignment of' NH-N hydrogen-bonded resonances o f these t w ) helices are based on their thermal stabilit.?;. T h e through-space magnetic field effects on the base protons and the NH-N protons in the helices were calculated and compared with the experimental values. This comparison yields two general conclusions: ( I ) For the base protons, application of both ring-current effects and local anisotropic effects in the computations are pref'erred; but for the NH-N protons, the application of the ringcurrent effect alone is preferred over the application of both ring-current effects and local anisotropic effects; and (2) while the computed values in the best theoretical treatment cited above did support the conclusion that these CG helices are in the B-conformation, the differences among the computed values for the three conformations. A, A', and R, are not very large, a t least for the CG sequence. All the "'P resonances of these CG helices are unamhiguously assigned through a specific heterodecoupling technique established previously [ Cheng et al. (1982) Hiopoiymcrs 21,697-7011. The complete assignment of all proton resonances and :"P resonances of d-(CpGpCpG), and d-(CpGpCpGpCpC), helices in the B-form establishes these two deoxy C(; helices as valuahle model systems for the study of the nmr and polymorphism of' nucleic acids.