Complete 1H Assignments of the Non-Exchangeable Protons of the Non Self-Complementary Heptadeoxyribonucleotide d[(GTCGTCA)·(TGACGAC)] and its Component Strands by High Field NMR

Abstract

The non self complementary heptadeoxyribonucleotides d(GTCGTCA) and d(TGACGAC) were synthesized by the phosphotriester method. While complete ¹H-NMR assignments of the former were obtained by a combination of one and two-dimensional techniques at room temperature, extensive stacking of the latter under these conditions dictated analysis at 50°C when the lines were sharply resolved. The duplex form of the annealed strands under the conditions of the ¹H-NMR experiment was established independently of the NMR evidence by ³²P end labeling with T4 polynucleotide kinase followed by butt end joining using the absolute specificity of T4 ligase for double strand DNA. Analysis of the resulting ladder of polymers was performed using gel electrophoresis and autoradiography. Complete ¹H-NMR assignments of the non-exchangeable protons in the self complementary heptamer was achieved. The assignments were confirmed using NOE differences, and two-dimensional COSY, and HH-INADEQUATE experiments at 400 and 500 MHz. The assignments are in accord with a conformation for the heptamer belonging to the B family of structures.