Alternate g-g- conformation for dinucleoside phosphates in solution

Conformational studies of trinucleoside bisphosphates. 2. Potential energy calculations

Semi-empirical potential energy calculations were carried out for the conformations of ApApA, a trinucleoside bisphosphate (trimer), as proposed in the preceding paper in this journal. Energy minimals were obtained for these conformers, i. e. conformers I-I, I-II, III-I' and I'-I' (the first Roman numeral represents the conformation of the ApAp- moiety and the second one the -pApA moiety of ApApA), of the nearest-neighbor interactions, and conformers B1, B2 and B3 of bulged structures. The results show that the detailed conformations of the component dinuclotide (dimer) moieties in I-I, I-II, III-I' and I'-I' are close (+/- 10 degrees) to the corresponding stable conformations of dinucleotides in solution proposed by Lee and coworkers. The bulged conformations B1, B2 and B3 have open forms for each dinucleotide moiety. Their preferred local conformations are anti, gamma +, beta +, epsilon + (except for Ap- in B3, epsilon-), and 3' endo (except for Ap- in B3, 2' endo) for the glycosidic bond, C4'-C5', C5'-O5', C3'-O3' and the ribose moiety, respectively. The conformation of the phosphodiester linkage in -pApA moiety is zeta t2, alpha t3 for all the three bulged conformers, while that in ApAp- is zeta- 1, alpha t2 for B1, zeta+ 1 alpha- 2 for B2, and zeta+ 1, alpha+ 2 for B3. The calculated composite chemical shifts of the base protons from ring-current effects agree with the corresponding observed trimerization shifts. Conformers I-I and I'-I' are helix-like structures and correspond to the right-handed and the 'vertical-stacked' helices, respectively. The structure of I-II is similar to that observed in the ApApA single crystals. The bulged conformations may serve as models for frameshift mutations.

Conformational studies of 13 trinucleoside bisphosphates by 360-MHz 1H-NMR spectroscopy. 1. Ribose protons

The ribose protons of 13 trinucleoside bisphosphates (trimers) were studied, using 360-MHz proton nuclear magnetic resonance spectroscopy. Complete assignments and analyses of the NMR signals of these protons were carried out by the methods of homonuclear decoupling and computer line-shape simulations. It was shown that the trinucleotides preferred the anti, 3' endo, gamma +, beta t and epsilon t/epsilon- conformations for the glycosidic torsions, the ribose rings, the C4'-C5' bonds, the C5'-O5' bonds, and the C3'-O3' bonds, respectively. It was also found that the trimers, especially those which had noticeable population of 'bulged' structures, did not necessarily have a higher population of these preferred local conformations than their component dimers. The overall conformations of the trinucleotides are classified into two categories. The conformations in the first category involve the nearest-neighbor interactions. Each dinucleotide moiety can assume one of the four stable conformations (I, I', II and III) or the open forms of dinucleoside monophosphates. However, due to steric hindrance, there are only four cases in which both dinucleotide moieties can assume one of the four stable conformations at the same time. These four combinations of conformations are I-I, I'-I', I-II and III-I', where the first Roman numeral represents the conformation of the NpN'p-moiety and the second one, that of the -pN'pN'' moiety of the trimers. Among them, I-I and I'-I' are helical structures, capable of forming a double helix. The second category contains conformations with bulged structures which have the two dinucleotide moieties in open forms (i.e. no nearest-neighbor interactions) and the bases of the two terminal residues stacking on each other while the middle residue is bulged out. These bulged conformations may serve as structural models for frame-shift mutations.