Sequence-specific solution structure of d-GGTACGCGTACC

Abstract

Complete resonance assignments of nonexchangeable base protons and sugar protons in d-GGTACGCGTACC at 500 MHz have been obtained by two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser enhancement spectroscopy (NOESY). The characteristic phase-sensitive multiplet patterns of the ntrasugar cross peaks in the omega 1-scaled COSY spectrum have been used to estimate several scalar coupling constants (J). These coupling constants combined with the intranucleotide COSY cross peak intensities have been used to identify the sugar pucker of individual nucleotide units. In most cases, the deoxyribose rings adopt a conformation close to O4'-endo. Spin-diffusion has been monitored from the buildup of the normalized volumes of NOE cross peaks in NOESY spectra as a function of mixing time. A set of 55 intranucleotide and internucleotide interproton distances have been estimated from the low mixing time NOESY spectrum (tau m = 75 ms). The estimated intranucleotide proton-proton distances have been used to determine the individual glycosidic dihedral angles of the nucleotide units which lie in the anti domain. It is observed that the molecule adopts an overall conformation close to that of the B-form although there are differences in the intricate details.

Structural basis for poor uracil excision from hairpin DNA. An NMR study

“…Distances were estimated from the initial build-up rates of the build-up curves by the two spin-approximation as described earlier [10][11][12]. Six of the seven base pairs forming the stems of the hairpins showed evidence of hydrogen bonding in the .…”

“…The backbone torsion angles, which partially influence the local conformation of U12 and U14 in U1 and U3-hairpins, respectively, are probably locked in the trans conformation as in the case of U 13 in the U2-hairpin. Such a stretched-out backbone conformation in the vicinity of U 12 and U 14 is thought to be the reason why the K m value is poor for U1-and U3-hairpins as it is for the U2-hairpin. Furthermore, the bases U 12 and U 14 in both U1-and U3-hairpins adopt an anti conformation, in contrast with the base conformation of U 13 in the U2-hairpin, which adopts a syn conformation.…”

“…Such a stretched-out backbone conformation in the vicinity of U 12 and U 14 is thought to be the reason why the K m value is poor for U1-and U3-hairpins as it is for the U2-hairpin. Furthermore, the bases U 12 and U 14 in both U1-and U3-hairpins adopt an anti conformation, in contrast with the base conformation of U 13 in the U2-hairpin, which adopts a syn conformation. The clear discrepancy observed in the U-base orientation with respect to the sugar moieties could explain why the V max value is 10-to 20-fold higher for the U1-and U3-hairpins compared with the U2-hairpin.…”

Inosine — Adenosine base pairing in d-GGTACIAGTACC: Duplex and hairpin with a two-base loop

“…In several of the earlier studies, including those from our laborato¡ [21][22][23][24][25][26][27][28], the proton resonance assignments were achieved by use of the individual intranucleotide J correlations in COSY spectrum in conjuction with the conformation dependent intrastrand, intemucleotide cross peaks in NOESY spectrum. Assignment strategies have been proposed for the standard A, Band Z families of DNA cortformations.…”

Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides

“…Others have presented NMR evidence for unexpected pseudorotation phase angles in double-helical DNA oligonucleotides, with a variety of interpretations. For example, Hosur et al (1986) suggest pseudorotation phase angles ranging from O-endo to Cl'-exo for d(GAATTCGAATTC)2, Chary et al (1989) claim O-endo in d(ACATCGATGT)2, and Kim et al (1992) claim Cl'-exo for pyrimidines, and sugar conformations closer to C2'-endo for internal purines, in d(CGCGTTAACGCG)2. Gochin et al (1990), in a detailed study of the alternating purine-pyrimidine tract d(AC)4.d(GC)4, discuss both singleconformer and two-state structural models that could be used to fit their data.…”