Issue December 2005

category image Volume 23
No. 3 (p 233-356)
December 2005
ISSN 0739-110

Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions ? An NMR Structure and Hydration Study (p. 299-330)

The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1',3'-O-anhydro-β-D-psicofuranosyl) thymine, at the T7 position of the self-complementary Dickerson-Drew dodecamer, d[(5'-C1G2C3G4A5A6T7T8C9G10C11G12-3')]2, considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and 1D NMR display a drop in melting temperature of ∼10 °C per modification for the T7 oxetane modified duplex, where the T7 block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T7 oxetane modified duplexes. The modified T7 residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T7·A6 and A6·T7 non-linear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T7 and T8 residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T7·A6/A6·T7 base pairs of the T7 oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.

J. Isakssona
O. Plashkevycha
P. I. Pradeepkumar
S. Chatterjee
J. Barman
W. Pathmasiri
P. Shrivastava
C. Petit
J. Chattopadhyaya*

Department of Bioorganic Chemistry
Biomedical Center
Uppsala University
S-751 23 Uppsala, Sweden

aAuthors have contributed equally in this paper.
*jyoti@boc.uu.se

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