Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

Bouř, Petr; Andrushchenko, Valery; Kabeláč, Martin; Maharaj,; Wieser, H.

doi:10.1021/jp051218g

Cited by 28 publications

(30 citation statements)

References 68 publications

(143 reference statements)

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“…Typically, the CdO stretching contributes most to the strongest IR signal within ∼1650-1750 cm -1 . 29,36,39,40 The carbonyl vibrations are also the most sensitive to the hydration. For an isolated carbonyl group or in peptidic systems, the hydrogen binding to water molecules shifts down the CdO stretching vibration by tens of centimeters -1 .…”

Section: Resultsmentioning

confidence: 99%

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.

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Section: Resultsmentioning

confidence: 99%

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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“…115 The most interesting outcome is described in the next two sections. The computed spectra will be compared to the experimental results for the same set of octanucleotides measured earlier.…”

Section: Accounting For Explicit Solvent and Dynamical Averagingmentioning

confidence: 99%

“…The details of the procedure can be found elsewhere. 115 For the fragment selection and following ab initio computations only water molecules closer than 3.6 Å (the first hydration shell) and hydrogen-bound to DNA were retained.…”

Section: Accounting For Explicit Solvent and Dynamical Averagingmentioning

confidence: 99%

“…Standard MD procedure was applied for the system minimization, equilibration and 5 ns production run, details of which can be found elsewhere. 115 An average octamer structure was obtained after the MD simulations. The averaging, however, led to a few artifacts in the geometry, which were removed by relaxing the molecule by an additional short minimization.…”

Section: Accounting For Explicit Solvent and Dynamical Averagingmentioning

confidence: 99%

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Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

Andrushchenko

Bouř

2010

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The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.

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“…IR [53][54][55][56][57] and VCD [58][59][60][61][62][63][64] band assignments for DNA and its constituents (nitrogen bases and sugar-phosphate backbone) have been extensively described in the literature. They are summarized in Table I based on a recent review 46 and two analyses of DNA interacting with manganese ions.…”

Section: Ir Experimentsmentioning

confidence: 99%

The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: Electronic and vibrational circular dichroism studies

et al. 2006

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The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.

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Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

Cited by 28 publications

References 68 publications

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: Electronic and vibrational circular dichroism studies

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