Abstract
Synthesis, complete 1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2 and its fragments by high field NMR ABSTRACT The two deoxyribonucleotides [d(CpGpApTpCpG)] and [d(CpGpCpG)] were synthesized by the phosphotriester method. Their guplex form under {he conditions of the 1H-nmr experiments was proven by end 32p labeling with T4 polynucleotide kinase followed by butt end joining employing the absolute specificity of T4 ligase for double stranded DNA and analysis using gel electro-phoresis and autoradiography. Complete nmr assignment of the YH chemical shifts and coupling constants was achieved. The assignments were secured using sequential decoupling, NOE difference measurements, and two-dimensional COSY and SECSY experiments. Spectrum simulation confirmed the experimental values of chemical shifts and joupling constants. The techniques for the assignment outlined together with Jlp and 2-D heteronuclear shift correlation permit an approach to a systematic analysis of more complex single-strand and duplex ol i godeoxyri bonucl eotides.