DEUTERIATION OF SUGAR PROTONS SIMPLIFY NMR ASSIGNMENTS AND STRUCTURE DETERMINATION OF LARGE OLIGONUCLEOTIDE BY THE H-1-NMR WINDOW APPROACH

The concept of the H-1-NMR window has been developed and examined thro ugh a comparative study of NOESY spectra of a self-complementary Dicke rson's dodecamer (1) [5'd(5C6G7C8G9A10A11T12T13C14G15C16G)(2)3'], a se lf-complementary 20-mer (11) 5C6G7C8G9A10A11T12T13C14G15C16G17C18G19C2 0G)(2)3'] in which the core part consists of the same Dickerson's dode camer sequence with the flanking CGCG residues at both 3' and 5'-ends, and the partly-deuteriated (shown by underlined CGCG residues at both -3' and 5'-ends) analogous duplex (III) 5C6G7C8G9A10A11T12T13C14G15C16 G17C18G19C20G)(2)3'] in which the core 5C to 16G part (i.e. H-1-NMR wi ndow) consists of the natural Dickerson's dodecamer sequence. A compar ison of their NOESY spectra clearly demonstrates that the severe overl ap of proton resonances in the larger DNA duplex (11) has been success fully reduced in the partly-deuterated duplex (III) as a result of spe cific incorporations of the sugar-deuteriated nucleotide residues in t he latter [stereospecific > 97 atom % H-2 enrichment at H2', H2'' and H3' sites, approximately 85 atom % 2H enrichment at H4' and approximat ely 20 atom % H-2 enrichment at H1' (see refs. 10 and 11) in the 20-me r duplex (III)]. These simplifications of the resonance overlap by the deuteriation approach have enabled unequivocal chemical shift assignm ents and extraction of the quantitative NOE data in the H-1-NMR window part of duplex (III). A comparison of the 12-nucleotide long H-1-NMR window in (III) with that of the 12-mer duplex (I) also shows the scop e of studying the changes in conformation and dynamics of the core 12- mer region in (III) which result from the increase of molecular weight due to the DNA chain extension. it is noteworthy that such a study is clearly-impossible for the natural 20-mer (II) because of the inheren t problem of the overlap of resonances.