Conformational analysis of the tetranucleotides m⁶₂A‐m⁶₂A‐U‐m⁶₂A (m⁶₂A =N⁶‐dimethyladenosine) and U‐m⁶₂A‐U‐m⁶₂A and of the hybrid dA‐r(U‐A)

Abstract

A 1H-NMR investigation was carried out on the tetranucleotides U-m6(2)A-U-m6(2)A and m6(2)A-m6(2)A-U-m6(2)A (m6(2) = N6-dimethyladenosine) as well as on the hybrid trinucleotide dA-r(U-A). An extensive comparison with m6(2)A-U-m6(2)A and other relevant compounds is made. Previous proton NMR studies on trinucleotides have shown that purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as a common feature that the interior pyrimidine residue bulges out, whereas the flanking purine residues stack upon each other. A stacking interaction on the 3' side of the bulge is known to have no measurable effect on the bulge population. Chemical-shift data, ribose ring conformational analysis and information from NOE experiments now show unambiguously that the moderate U(1)-m6(2)A(2) stack in U-m6(2)A-U-m6(2)A diminishes the population of bulged-out structures in favour of a regular stack. This tendency towards conformational transmission in the downstream 5'----3' direction is fully confirmed by the fact that the strong m6(2)A(1)-m6(2)A(2) stack in the tetranucleotide m6(2)A-m6(2)A-U-m6(2)A virtually precludes the formation of bulged-out structures. The conformational characteristics of dA-r(U-A) appear comparable with those of m6(2)A-U-m6(2)A, which indicates that the presence of a 2'-hydroxyl group in the first purine residue is not a necessary prerequisite for the formation of a bulge.

Dipolar Order Parameters in Large Systems With Fast Spinning

“…External KBr ( Thurber and Tycko, 2009 ) and neat methanol ( Ammann et al, 1982 ) were used as external standards to calibrate the temperature. The samples did not have adequate resolution to unambiguously identify the bulk water signal from the isopropanol and methyl-pentane-diol OH signals, which precluded temperature calibration by the chemical shift difference between water and DSS ( Hoogen et al, 1988 ; Wishart et al, 1995 ). Temperatures derived using either the chemical shift or the T 1 of KBr ( Thurber and Tycko, 2009 ) were not self-consistent on the 700 MHz instrument at either 10 or 60 kHz spinning.…”