SOLUTION CONFORMATION OF AN INTRAMOLECULAR DNA TRIPLEX CONTAINING A NONNUCLEOTIDE LINKER - COMPARISON WITH THE DNA DUPLEX

The solution properties of the parallel intramolecular DNA tripler d(G AGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)(8)-O-PO2-O-(CH2)(8)-O-PO2 -) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV meltin g and high-resolution nuclear magnetic resonance spectroscopy (NMR). A ll nucleotides were primarily in the S conformation (i.e. near C2'-end o) in both the duplex and the tripler, However, the sugars of the Hoog steen pyrimidine strand had a lower fraction of the S state than the W atson-Crick strands. Glycosidic torsion angles derived from nuclear Ov erhauser effect (NOE) build-up curves were found in the range -103 deg rees to -133 degrees, with a clear alternation in magnitude along the GAGAGA strand in the tripler, whereas the glycosidic torsion angles we re more similar in the duplex. Internucleotide NOEs were also consiste nt with an overall B-like geometry, rather than the A family. However, particularly in the Hoogsteen strand, some sequential NOE intensities were intermediate between those of the B and A forms. Distance and to rsion constraints derived from NMR experiments were used to generate s tructures and were refined by restrained molecular dynamics. Extensive chemical shift differences between residues in the tripler and duplex were found for the purine strand, and there were remarkable differenc es in the pattern of shift differences for the A and G residues that c orrelated with differences in glycosidic torsion angles. Although ther e are differences in structure between the free duplex and that in the tripler, they are in important respects similar, indicating that only small conformational adjustments are needed to make parallel triple h elices.