Solution structure of [d(GCGTATACGC)]2

Cheng, Jya‐Wei; Chou, Shan‐Ho; Salazar, Miguel; Reid, Brian R.

doi:10.1016/0022-2836(92)90496-7

Cited by 29 publications

(12 citation statements)

References 53 publications

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“…The resulting values for clearly resolved crosspeaks are listed in Table I. From the distribution of the numbers of purine and pyrimidine nucleotides versus Hl'-H4' distances ( Figure 2), the distinction between purine and pyrimidine sugars is clearly visible: all pyrimidine Hl'-H4' distances are less than 3.0 A, while purine distances are greater than 3.0 A Literature data for few available sequences also support our observation (9,23,25,26,27). There is not such a clear sequence-dependence of sugar conformation and H 1'-H4' distances in highly-resolved B-DNA crystal structures, however the similar trend can be seen as in solution (Figure 3).…”

Section: Results and Discussion The Deoxyribose Ring Conformation Andsupporting

confidence: 81%

Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

Chuprina¹,

Nerdal²,

Sletten³

et al. 1993

Journal of Biomolecular Structure and Dynamics

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Analysis of 1H-NOESY solution data for eight short DNA duplexes has revealed pronounced differences between the sugar conformations of purine and pyrimidine nucleotides. It was found that the H1'-H4' interproton distance is less than ca. 3.0 A in pyrimidine sugars, while in purine sugars it is more than ca. 3.0A. This difference has been analyzed by comparison with the sugar conformations of highly resolved B-DNA crystal structures and model sugar conformations. The conclusion can be drawn that the deoxyribose conformation is of the general C2'-endo type but pyrimidine sugars are characterized by smaller phase angles of pseudorotation P (90 degrees < P < 150 degrees), while purine sugars have larger P values that are greater than ca. 140 degrees (140 degrees < P < 180 degrees). There is no such clear base dependence of sugar conformation in highly resolved B-DNA crystal structures; however the similar trend can be seen as in the solution studies. Based on B-type DNA crystal structures, J-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.

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Section: Results and Discussion The Deoxyribose Ring Conformation Andsupporting

confidence: 81%

Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

Chuprina¹,

Nerdal²,

Sletten³

et al. 1993

Journal of Biomolecular Structure and Dynamics

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“…The largest helical twist is observed at YR steps (average 41") and the smallest at the RY steps (average 32"). This anti-correlation between observed helical twist and that predicted by Calladine's rules has been observed previously (Cheng et al, 1992;Baleja et al, 1990) and is taken as evidence that Calladine's rules are an over-simplification. Particularly noteworthy is the large change in helical twist at the T3-G4 step (47") and the G4-T5 step (30").…”

Section: Structural Featuressupporting

confidence: 85%

“…Several groups (Keepers and James, 1984;Boelens et al, 1988;Borgias and James, 1988;Post et al, 1990;van der Ven et al, 1991) have pioneered the use of complete relaxation matrix techniques to overcome the limitations of the isolated spin pair approximation by accounting for spin diffusion contributions to distance estimates. Reid and coworkers (Banks et al, 1989;Kim et al, 1992;Cheng et al, 1992) have shown that distance geometry techniques can generate partially refined structures and, by utilising back calculation of the NOESY spectra, they have demonstrated that distance geometry can be effective as a refinement aid. Recent work has demonstrated that the combined NMWrestrained molecular dynamics or NMWdistance geometry techniques are as capable of determining a refined structure of a small oligonucleotide fragment as they are of determining the structure of a small protein (Lancelot et al, 1989;Baleja et al, 1990;Stolarski et al, 1992) as long as reasonable restraints are applied to the backbone torsion angles.…”

mentioning

confidence: 99%

The Solution Conformation of a Trisdecanucleotide Containing the Consensus Binding Site of the dnaA Initiation Protein

Owen

Keniry

1994

European Journal of Biochemistry

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The solution structure of a trisdecanucleotide, d (CCTGTGGATAACA) . d (TGTTATCCACAGG) containing the consensus binding site of the dnaA initiation protein has been determined by twodimensional NMR techniques and restrained molecular dynamics calculations. Interproton distances were obtained by an iterative complete relaxation matrix algorithm, MARDIGRAS. During molecular dynamics runs, the backbone was restricted with the assistance of experimentally derived distance constraints. A family of refined structures with small painvise root-mean-square deviation values (~0 . 0 8 nm) was obtained. All but one of the pyrimidines were found to adopt the C1'-exo conformation while the purines were found to adopt the C2'-endo or C1'-exo conformation. The six-membered rings of the purines were found to stack over the six-membered rings of the pyrimidines while there is virtually no overlap of the pyrimidines over the purines. 5'-purine-purine-3' and 5'-pyrimidine-pyrimidine-3' stacking resembles the observed stacking of these bases in other NMR and X-ray structures of oligonucleotides. The final refined structure exhibited a small curvature and was slightly longer than canonical B-DNA. The variation of twist angle, proposed as a recognition element for proteins, exhibited symmetry about the centre of the consensus binding site.

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“…For example, in G1, G5 and G9, the H2' resonates upfield of the H2", which is usually found only at 3' terminal residues (van de Ven and Hilbers, 1988), but has also recently been observed in tandem G . A mismatches (Li et al, 1991 ;Chou et al, 1992;Lane et al, 1992). G5 and A6 show unusual shifts for H8 ( Fig.…”

Section: Solution Structure Of [D(gagt=acga)] -[D(gagtgaacm)]mentioning

confidence: 94%

“…A mismatches in different base-stacking environments have revealed that very stable amino pairs form when a tandem G . A mismatch is flanked by a pyrimidine base on the 5' side and a purine base on the 3' side Cheng et al, 1992).…”

mentioning

confidence: 99%

Properties of multiple G · A mismatches in stable oligonucleotide duplexes

Lane¹,

Ebel²,

Brown³

1994

European Journal of Biochemistry

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The solution structure of the deoxydecanucleotide [d(GAGTUACGA)] . [d(GAGTUACGA)] has been determined by NMR methods. This duplex, which contains six G . A mismatches and four Watson-Crick base pairs, is thermodynamically more stable than a decamer where T . A base pairs are substituted for the G . A mismatches, and is less stable than the duplex that contains G . C base pairs. Circular-dichroism spectroscopy indicates an overall B-like conformation for the decamer, but stronger than usual base staclung. 'H-NMR spectroscopy revealed that the N1H groups of the mismatched guanine residues are not hydrogen bonded, and 31P-NMR showed the presence of B,, phosphate conformations for the GpA steps. Detailed analysis of the NMR data showed that all nucleotides have anti glycosidic torsion angles and S type sugar puckers. The G .

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Solution structure of [d(GCGTATACGC)]2

Cited by 29 publications

References 53 publications

Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

The Solution Conformation of a Trisdecanucleotide Containing the Consensus Binding Site of the dnaA Initiation Protein

Properties of multiple G · A mismatches in stable oligonucleotide duplexes

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