Synthesis complete<sup>1</sup>H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]<sub>2</sub>and its fragments by high field NMR

Lown, J. William; Hanstock, Christopher C.; Bleackley, R. Chris; Imbach, Jean‐Louis; Rayner, Bernard; Vasseur, Jean‐Jacques

doi:10.1093/nar/12.5.2519

Cited by 40 publications

(4 citation statements)

References 32 publications

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“…The conformation of free (d(CGATCG)) 2 was evaluated from the intensities of NOESY cross-peaks in experiments acquired with short mixing time (70 ms) and from the values of vicinal coupling constants measured in one-dimensional and primitive exclusive COSY spectra (43)(44)(45)(46)(47). The results are consistent with a predominant B-type conformation in agreement with a previously reported study (48).…”

Section: Resultssupporting

confidence: 87%

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

Trotta

D’Ambrosio²,

Ravagnan³

et al. 1996

Journal of Biological Chemistry

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The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer (d(CGATCG))2 at a 2:1 drug/duplex ratio has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics, and molecular dynamics computations. Intermolecular nuclear Overhauser effects (NOEs), DNA structure perturbations, and resonance shifts induced by binding provide evidence that DAPI interacts with DNA hexamer by two different binding mechanisms, in fast exchange on the NMR time scale, without any significant distortion of the B-type conformation of DNA hexamer. The results indicate that the ligand binds into the minor groove of the central 5'-ATC-3' region of the hexamer and on the outside of the oligomer by a pi,pi-stacking interaction with the terminal C1:G6 base pairs. A model for both binding mechanisms that accounts for all experimental data was generated by molecular mechanics and dynamics calculations based on experimental NOEs. In the minor groove binding, N2 amino group of G2 precludes a deep insertion of phenyl ring of DAPI into the groove. Position and orientation of the drug in the external stacking interaction resemble those suggested for intercalation of DAPI between C:G base pairs.

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Section: Resultssupporting

confidence: 87%

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

Trotta

D’Ambrosio²,

Ravagnan³

et al. 1996

Journal of Biological Chemistry

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“…IS in the supplementary material. Our assignments are in agreement with those ofLown et al (1984) studied previously under similar conditions. At the mixing time of 200 ms, we have measured 703 NOE cross peaks for the 6.7 mM sample and 491 at 2.4 mM sample (out of 54 X 53/2 = 1431…”

supporting

confidence: 92%

A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy

Robinson

Wang²

1992

Biochemistry

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We have developed a simple and quantitative procedure (SPEDREF) for the refinement of DNA structures using experimental two-dimensional nuclear Overhauser effect (2D NOE) data. The procedure calculates the simulated 2D NOE spectrum using the full matrix relaxation method on the basis of a molecular model. The volume of all NOE peaks is measured and compared between the experimental and the calculated spectra. The difference of the experimental and simulated volumes is minimized by a conjugated gradient procedure to adjust the interproton distances in the model. An agreement factor (analogous to the crystallographic R-factor) is used to monitor the progress of the refinement. The procedure is an The agreement is considered to be complete when several parameters, including the R-factor, the energy associated with the molecule, the local conformation (as judged by the sugar pseudorotation), and the global conformation (as judged by the helical x-displacement), are refined to their respective convergence. With the B-DNA structure of d(CGATCG) as an example, we show that DNA structure may be refined to produce calculated NOE spectra that are in excellent agreement with the experimental 2D NOE spectra. This is judged to be effective by the low R-factor of approximately 15%. Moreover, we demonstrate that not only are NOE data very powerful in providing details of the local structure but, with appropriate weighting of the NOE constraints, the global structure of the DNA double helix can also be determined, even when starting with a grossly different model. The reliability and limitations of a DNA structure as determined by NMR spectroscopy are discussed.

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“…The self‐complementary oligonucleotides d(CGTACG) 2 (forming the duplex structure here named ds6) and d(AAGAATTCTT) 2 (forming the duplex structure here named ds10) were used as models for CG‐ and AT‐rich sequences, respectively. These duplex‐forming oligonucleotides have been extensively investigated by both 1 H and 31 P NMR proving to be good models, though short, of B‐DNA [34–37] . Folding of these oligomers into a duplex conformation was obtained at 15 °C in 110 mM Na + ‐containing buffer.…”

Section: Resultsmentioning

confidence: 99%

Plant‐Derived Stilbenoids as DNA‐Binding Agents: From Monomers to Dimers

Platella

Mazzini

Napolitano

et al. 2021

Chemistry A European J

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Stilbenoids are natural compounds endowed with several biological activities, including cardioprotection and cancer prevention. Among them, (±)‐trans‐δ‐viniferin, deriving from trans‐resveratrol dimerization, was investigated in its ability to target DNA duplex and G‐quadruplex structures by exploiting NMR spectroscopy, circular dichroism, fluorescence spectroscopy and molecular docking. (±)‐trans‐δ‐Viniferin proved to bind both the minor and major grooves of duplexes, whereas it bound the 3’‐ and 5’‐ends of a G‐quadruplex by stacking on the outer quartets, accompanied by rearrangement of flanking residues. Specifically, (±)‐trans‐δ‐viniferin demonstrated higher affinity for the investigated DNA targets than its monomeric counterpart. Additionally, the methoxylated derivatives of (±)‐trans‐δ‐viniferin and trans‐resveratrol, i. e. (±)‐pterostilbene‐trans‐dihydrodimer and trans‐pterostilbene, respectively, were evaluated, revealing similar binding modes, affinities and stoichiometries with the DNA targets as their parent analogues. All tested compounds were cytotoxic at μM concentration on several cancer cell lines, showing DNA damaging activity consistent with their ability to tightly interact with duplex and G‐quadruplex structures.

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Synthesis complete¹H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]₂and its fragments by high field NMR

Cited by 40 publications

References 32 publications

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy

Plant‐Derived Stilbenoids as DNA‐Binding Agents: From Monomers to Dimers

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Synthesis complete1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2and its fragments by high field NMR

Cited by 40 publications

References 32 publications

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy

Plant‐Derived Stilbenoids as DNA‐Binding Agents: From Monomers to Dimers

Contact Info

Product

Resources

About

Synthesis complete¹H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]₂and its fragments by high field NMR