A direct assignment of all base and anomeric Hi' signals in the proton spectrum of a trinucleoside diphosphate, ApApA: structure implications

Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons

The 360 MHz NMR spectra of the base protons and the H1 protons of thirteen trinucleoside diphosphates have been analyzed. The sequences chosen represent all purine-pyrimidine sequences. The chemical shifts of the base protons give evidence for strong next nearest-neighbor effects in some oligonucleotides. Although increasing chain length usually increases nearest-neighbor base-base stacking, it is not always so. Comparing ApCpG, ApUpG and GpUpG to their component dimers, one finds a decrease in stacking of the center pyrimidine with the purine on either side. The coupling constants J 1'2' also show that these three trimers show less stacking for their terminal residues than expected from their component dimers. We conclude that the sequence Pu-Py-Pu favors a conformation in which the pyrimidine is bulged out and the two purines stack on each other.

The synthesis of deuterionucleosides

The synthesis of deuterionucleosides for site-specific incorporation into oligo-DNA or -RAA is herein reviewed for NMR or biological studies. The review covers the following aspects: (i) deuteration of the aglycone; (ii) single-site chemical deuteration of the sugar residues; (iii) multiple-site chemical deuteration of the sugar residues; (iv) enzymatic synthesis of deuterated nucleosides or nucleotides; and (v) synthesis of labelled nucleosides with multiple isotopes

NMR spectroscopic properties (1H at 500 MHz) of deuterated* ribonucleotide-dimers ApU*, GpC*, partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*), d(ApT*), d(GpC*) and their comparison with natural counterparts (1H-NMR window)

Pure 1'#,2',3',4'#,5',5''-2H6-ribonucleoside derivatives 10-14, 1'#,2',2'',3',4'#,5',5''-2H7-2'-deoxynucleoside blocks 15-18 and their natural-abundance counterparts were used to assemble partially deuterated ribonucleotide-dimers (* indicates deuteration at 1'#,2',3',4'#,5',5''(2H6)): ApU* 21, GpC* 22 and partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*) 23, d(ApT*) 25, d(GpC*) 26 (* indicates deuteration at 1'#,2',2'',3',4'#,5',5''(2H7)) according to the procedure described by Földesi et al. (Tetrahedron, in press). These five partially deuterated oligonucleotides were subsequently compared with their corresponding natural-abundance counterparts by 500 MHz 1H-NMR spectroscopy to evaluate the actual NMR simplifications achieved in the non-deuterated part (1H-NMR window) as a result of specific deuterium incorporation. Detailed one-dimensional 1H-NMR (500 MHz), two-dimensional correlation spectra (DQF-COSY and TOCSY) and deuterium isotope effect on the chemical shifts of oligonucleotides have been presented.

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.

RNA structure

This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.

Nucleotide rigidity

It is show that in aqueous solution the backbone conformation of adenosine is as much flexible as that of 3'-AMP, 5'-AMP and 3', 5'-ADP indicating that nucleotides are not any more rigid than nucleosides. The flexible conformation of the monomeric components is conserved in the nucleotidyl units of destacked ApA, ApApA and poly(A), but it is not conserved in base stacked conditions. The findings are extended to guanosine, uridine and cytidine systems. It is projected that in aqueous solution, conformations of the individual nucleotidyl units of yeast tRNAhe are confined to the classically stable domains in the base stacked region and non-rigid flexible structures populate in the unstacked region comprising D16, D17, G20, U47 and A76.