The spatial configuration of a left-handed base stacked dinucleoside monophosphate

Intramolecular conformation of puromycin in solution as studied by proton magnetic resonance

The intramolecular conformation of puromycin, a broad spectrum antibiotic, in solution has been investigated by proton magnetic resonance (PMR) spectroscopy. A comparison of the proton chemical shift and proton-proton coupling constant data of puromycin with puromycin aminonucleoside suggests that puromycin in solution exists as an equilibrium blend of extended and folded conformers. These folded conformers are the result of flexibility around the C alpha -C beta bond of the aminoacyl segment of puromycin. One of the folded conformers predicted by PMR is in excellent agreement with the x-ray data.

Alternate g-g- conformation for dinucleoside phosphates in solution

An alternative g-g- conformation (conformer I') for dinucleosides in solution has been deduced, based on potential energy calculations and nuclear magnetic resonance spectroscopy. This conformation is characterized by larger glycosidic torsional angles (chi = 94-111 degrees) than those of conformer I (chi = 8-35 degrees), although the other torsional angles are similar. There are thus four stable conformers (I, I', II and III) for dinucleosides in equilibrium with the open forms. The structure of conformer I' supports that of the 'vertical' double helix constructed by Olson (W.K. Olson, Proc. Natl. Acad. Sci. U.S.A. 74, (1977) 1775). Our data may suggest the possibility of interconversion between the vertical double helix and the regular double helix of A-form DNA, RNA or A'-form RNA.

Synthesis and characterization of the dinucleoside monophosphates containing 2'-fluoro-2'-deoxyadenosine

Three dinucleoside monophosphates containing 2'-fluor-2'-deoxyadenosine (dAfl), dAfl-dAfl, dAfl-A, and A-dAfl, were synthesized chemically. Characterization of these dimers has been performed by UV absorption, CD, and 1H NMR spectroscopies. The results showed that all three dimers have a stacked conformation with a geometry similar to that of A-A but with greater extent of base-base over-lapping than A-A. This interpretation is verified by the data of chemical shifts and coupling constants of 1H NMR study on these dimers (D. M. Cheng, L. S. Kan, P. O. P. Ts'o. S. Uesugi, Y. Takatsuka, and M. Ikehara unpublished data). All three dimers form 2U.1A complexes with poly(uridylic acid). The Tm of dAfl-dAfl.2poly(U) is higher than that of dAfl-A.2poly(U), which in turn is higher than that of A-dAfl.2poly(U). The NMR results clearly indicate that the conformation of the furanose of dAfl moiety in these dimers is more favored toward 3'-endo than 2'-endo puckering in comparison with the adenosine. The effects of 3' substituents on oligo- and polynucleotide conformation are also discussed.