B−Z Conformational Transition of DNA Monitored by Vibrational Circular Dichroism. Ab Initio Interpretation of the Experiment

Andrushchenko, Valery; Wieser, and Helmut; Bouř, Petr

doi:10.1021/jp0262721

Cited by 54 publications

(100 citation statements)

References 41 publications

(108 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We found a very small variance of the VCD signal with respect to the nucleotide sequence in this frequency region. This is in accordance with previous observations, where the signal depended only slightly on experimental conditions, 28 while its shape differed more only for the B-and Z-forms. 18 The simulated spectrum for the average MD structures (trace a) agrees reasonably with the experiment, namely, the negative lobe at 1062 (experimentally 1089 cm -1 ) and two positive peaks at 1042 and 1022 cm -1 (experimentally at 1072 and 1089 cm -1 ).…”

Section: Resultssupporting

confidence: 93%

“…Principle features of experimental RNA and DNA spectra have been described in numerous studies previously 3,4,14,15,17,18,23,26,28,29,40 and we recapitulate them only briefly. The CdO stretching region of the bases (1600-1700 cm -1 ) gives rise to a strong absorption, while relatively minor distinct features can be found in the mid-IR region of 1150-1500 cm -1 , additionally perturbed by D 2 O absorption (around 1220 cm -1 ).…”

Section: Resultsmentioning

confidence: 95%

See 1 more Smart Citation

Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

et al. 2005

Self Cite

View full text Add to dashboard Cite

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG) 2 nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.

show abstract

Section: Resultssupporting

confidence: 93%

Section: Resultsmentioning

confidence: 95%

Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

et al. 2005

Self Cite

View full text Add to dashboard Cite

show abstract

“…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%

“…Previously, this approach was successfully used for the simulation of IR and VCD spectra of peptides and regular DNA and RNA oligomers. [36][37][38][39][40] In this study, we also applied it to the irregular octamer geometry, deformed by metal binding and hydration.…”

Section: Introductionmentioning

confidence: 99%

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

2007

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…2). Based on the previously published results [1,3,5,6,10,12,16] it is possible to assign the major spectral features as summarized in the Table 1. Thus, IR/VCD spectra of large supramolecular complexes can be analyzed at higher protein to DNA ratios, unreachable for conventional UV-CD spectroscopy.…”

Section: Resultsmentioning

confidence: 99%

Structural organization of DNA–protein complexes of chromatin studied by vibrational and electronic circular dichroism

Polyanichko

Wieser

2010

Spectroscopy

Self Cite

View full text Add to dashboard Cite

Abstract. Structure and functioning of chromatin is determined by interactions of DNA with numerous nuclear proteins. The most abundant and yet not completely understood non-histone chromosomal proteins are those belonging to a High Mobility Group (HMG) namely HMGB1. The interplay of this protein on DNA with linker histone H1 and other proteins determines both structure and functioning of the chromatin. A combination of UV and IR absorption and circular dichroism (CD) spectroscopy was applied to investigate the structure and formation of large supramolecular DNA-protein complexes. This combination of techniques was used to overcome limitations of UV-CD (ECD) spectroscopy due to considerable light scattering in such solutions. Based on the analysis of FTIR and UV circular dichroism spectra and AFM imaging the interaction of DNA with high-mobility group non-histone chromatin protein HMGB1 and linker histone H1 was studied.

show abstract

B−Z Conformational Transition of DNA Monitored by Vibrational Circular Dichroism. Ab Initio Interpretation of the Experiment

Cited by 54 publications

References 41 publications

Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

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

Structural organization of DNA–protein complexes of chromatin studied by vibrational and electronic circular dichroism

Contact Info

Product

Resources

About