Decreased interstrand H2-H1' distance in the GC-rich part of the duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) in solution at low temperature: proton nuclear magnetic resonance investigation.

The non-self-complementary undecadeoxyribonucleotide duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) was studied by one- and two-dimensional NMR methods in solution at low and room temperatures. The width of the minor groove of the duplex was determined on the basis of the NOE's between adenine's H2 protons and H1' protons from the complementary strand. In agreement with the previous reports, we found that the A3.T3 block forms a structure with a narrow minor groove at 5 degrees C, with the H2-H1' interstrand distance decreasing in the 5'-to-3' direction along the strand of adenines. Surprisingly, this distance is still short in the GC-rich part of the duplex downstream from the A-tract. This finding is interpreted in terms of pronounced buckle angles in the oligo(purine).oligo(pyrimidine) blocks, which diminish the H2-H1' interstrand distances. Both CA(n)- and AnC- junctions have distinct patterns of the proton chemical shifts, which suggests that both junctions may have some specific conformations in solution. Also, we report the temperature-driven changes in proton chemical shifts, which are significant in all parts of the duplex, except the 5'-ends of both strands. The structural interpretation for these changes is proposed, on the basis of the following notion: at low temperature the narrow minor groove is formed between the central A3.T3 trimer and the 3'-ends of both DNA strands, while the 5'-ends remain relatively exposed to the solvent.