Parameters for the Calculation of Proton NMR Chemical Shifts of Oligoribonucleotides

Abstract

A set of empirical parameters which allows the prediction of the proton NMR chemical shifts at 70 C of non-exchangeable heterobase and anomeric protons in oligoribonucleotides has been constructed. The set is based on the highly flexible nature of oligoribonucleotide single strands and the wide range of conformational states which can be populated at relatively high temperatures (70 C or greater). A pairwise subtractive procedure, using 129 ribonucleotide oligomers (all 16 dimers, all 64 trimers, 37 tetramers, and 12 pentamers), shows that significant contributions to the observed chemical shift of protons in a given nucleoside residue are made by first, second, and third neighbors on the 3' and the 5' sides. The majority of the neighbors cause shielding effects with the exception of some first neighbors on the 5' side of a given residue. The magnitude of the shielding effects is greatest for the purine heterobases and follows the order A greater than G greater than C greater than U, with first neighbors on the 3'side showing more pronounced effects than second neighbors and these in turn showing larger effects than third neighbors. Second neighbors on the 5' side showed consistently greater shieldings than first neighbors, a result attributed to the deshielding effects of the first 5' neighbor phosphate group. The parameter Tables are applied to the prediction of proton chemical shifts in one heptamer, four hexamers, and two pentamers and give average absolute differences between predicted and observed shifts less than 0.030 ppm. The parameter approach represents an excellent method of generating initial assignments of proton chemical shifts for any single strand oligoribonucleotide.

NMR study on the impact of metal ion binding and deoxynucleotide substitution upon local structure and stability of a small ribozyme

“…The guanosine, which is cleaved off in the course of the ribozymatic reaction, is destacked from the adjacent adenosine 3' of the guanosine, and is involved in the formation of a pocket of three purine residues (G2, A3 and A4). Such a destacked arrangement is also in agreement with the conclusions that can be derived from a comparison between chemical shift data expected for a random coil RNA [29], and the chemical shifts measured for the two RNA duplexes (data not shown). Whereas all residues experience upfield shift changes due to stacking in the wellordered helix, the G2 chemical shifts resonate at even lower field than expected for the random coil.…”

The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: a topological mechanism of sequence specificity.

“…These NOEs demonstrate that the isoleucine side chain enters the minor groove (in the absence of Hoogsteen base pairing; see below) and partially penetrates between A'T base pairs 8 and 9. Its upfield complexation shift presumably reflects the interior ring current of DNA bases (14). minor groove is too narrow in B-DNA to accommodate an a-helix, the data further predict that the minor groove is widened at the site of partial intercalation.…”

“…Imino resonances. Imino resonances in B-DNA ordinarily occur in discrete A-T and G-C spectral regions due to differences in intrinsic ring currents (10,14). Such separation is observed in the 1H NMR spectrum of the free SRY-binding site (Fig.…”

Synthesis, C-13 NMR, and X-ray crystal structure of N6,N9-octamethylenepurinecyclophane

“…' The sequence-dependent arrangement of single (2) and double (3) stranded polynucleotides results in a variety of chemical shift values for neighbouring exchangeable and nonexchangeable heterobase protons. The ability to predetermine the diamagnetic shielding about these aromatic systems would be beneficial for the study of detailed conformational information for a specific sequence.…”