Lidé

RNDr. Vladimír Sychrovský, Ph.D.

Všechny publikace

Additive transport in DNA molecular circuits

  • Autoři: Sebechlebska, T., Kolivoska, V., Sebera, J., Fukal, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Journal of Materials Chemistry C. 2022, 10(33), 12022-12031. ISSN 2050-7526.
  • Rok: 2022
  • DOI: 10.1039/d2tc01219g
  • Odkaz: https://doi.org/10.1039/d2tc01219g
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    This work describes additive transport in DNA molecules due to a self-assembly of complementary single-stranded deoxyribonucleic acid chains, i.e. DNA hybridization. Charge transport properties in the DNA junctions at the single molecule level were studied experimentally by the break junction technique in an aqueous environment and theoretically including a non-equilibrium Green's function approach within the density functional based tight-binding method and molecular orbital calculations using density functional method and molecular dynamics simulations. Two types of anchoring groups, namely, amino and thiolate moieties were used to connect the single-stranded DNA (anchor-linker-3 '-GGCACTCGG-5 '-linker-anchor) to gold electrodes. Double-stranded DNA junctions were prepared by hybridization of single-stranded DNA with a complementary oligonucleotide chain (5 '-CCGTGAGCC-3 ') not containing linkers and anchoring groups. Three stable junction configurations were observed for both single-stranded and double-stranded DNA irrespective of the anchoring group, whereas junction conductance almost doubled upon DNA hybridization. Thiolate anchoring led to more robust and longer junction configurations compared to NH2 groups. Reasons for the observed conductance enhancement and the anchoring group effect on the overall conductance are being discussed.

Physicochemical Characterization of the Catalytic Unit of Hammerhead Ribozyme and Its Relationship with the Catalytic Activity

  • Autoři: Tanaka, Y., Yamanaka, D., Morioka, S., Yamaguchi, T., Morikawa, M., Kodama, T.S., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Biophysica. 2022, 2(3), 221-239. ISSN 2673-4125.
  • Rok: 2022
  • DOI: 10.3390/biophysica2030022
  • Odkaz: https://doi.org/10.3390/biophysica2030022
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    The catalytic mechanism of hammerhead ribozymes (HHRzs) attracted great attention in relation to the chemical origin of life. However, the basicity (pKa) of the catalytic sites of HHRzs has not been studied so far. As a result, the investigation of the currently assumed mechanism from an experimentally derived pKa value has been impossible. In HHRzs, there exists a highly functionalized structural unit (A9-G10.1 site) with a catalytic residue (G12) for the nucleophile activation and metal ion-binding residue (G10.1). As inferred from this fact, there might be a possibility that HHRzs may utilize specific functions of the A9-G10.1 motif for the catalytic reaction. Therefore, here we studied the basicity of G12/G10.1-corresponding residues using RNA duplexes including the A9-G10.1 motif without other conserved residues of HHRzs.

Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA

  • Autoři: Fukal, J., Zgarbová, M., Jurečka, P., Šebera, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2022, 18(11), 6989-6999. ISSN 1549-9618.
  • Rok: 2022
  • DOI: 10.1021/acs.jctc.2c00733
  • Odkaz: https://doi.org/10.1021/acs.jctc.2c00733
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    Interpretation of 3JP,H3′ NMR scalar spin-spin coupling constants in DNA becomes more reliable by including distinct structural states such as BI and BII, using the weighted-static or, better still, the recently implemented adiabatic-MD (Ad-MD) method. The calculation method employs an adiabatic ("Ad") dependence of 3JP,H3′ coupling on NMR-assigned torsion angle, ϵ, weighted by P(ϵ) probability distribution calculated by molecular dynamics (MD). Ad-MD calculations enable cross-validation of the bsc1, OL15, and OL21 force fields and various parametrizations of the Karplus equation describing the dependence of 3JP,H3′ coupling on ϵ torsion (KE). The mean absolute deviation of Ad-MD 3JP,H3′ couplings from the experimental values in Dickerson-Drew DNA is comparable to the scatter of 3JP,H3′ couplings among four separate NMR experiments.

Quantitative Analysis of Nanorough Hydrogenated Si(111) Surfaces through Vibrational Spectral Assignment by Periodic DFT Calculations

  • DOI: 10.1021/acs.jpcc.1c09766
  • Odkaz: https://doi.org/10.1021/acs.jpcc.1c09766
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    We use periodic density functional theory (periodic DFT) to rigorously assign vibrational spectra measured on nanorough wet-processed hydrogenated Si(111) surfaces. We compare Si(111)-(1×1) surfaces etched by dilute HF and NH4F, featuring two vibrational patterns that systematically appear together. They are attributed to vibrations observed on vicinal surfaces featuring 112̅ and 1̅1̅2 steps terminated with monohydrides and dihydrides, respectively. For the first time, we fully assign vibration patterns of realistic silicon surfaces with variable nanoroughness directly by periodic DFT simulations involving contributions from isolated species but also contributions from highly coupled species forming standing waves. This work opens the path to a better quantitative characterization of imperfect and nanorough Si(111) surfaces from vibrational spectra.

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

  • Autoři: Fukal, J., Budesinsky, M., Pav, O., Jurecka, P., Zgarbova, M., Sebera, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Journal of Computational Chemistry. 2022, 43(2), 132-143. ISSN 0192-8651.
  • Rok: 2022
  • DOI: 10.1002/jcc.26778
  • Odkaz: https://doi.org/10.1002/jcc.26778
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31P NMR shift (δ31P) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units dif- fering only in dynamic behavior. The Ad-MD method is benchmarked against the sta- tistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

FTIR Measurement of the Hydrogenated Si(100) Surface: The Structure-Vibrational Interpretation by Means of Periodic DFT Calculation

  • DOI: 10.1021/acs.jpcc.0c11176
  • Odkaz: https://doi.org/10.1021/acs.jpcc.0c11176
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    The periodic density functional theory (periodic DFT) method was employed for the interpretation of infrared radiation spectra (IR spectra) measured for the hydrogen-covered H/Si(100) surface after the standard step of native oxide removal by brief etching in 40% NH4F. The IR employed the attenuated total reflectance (ATR) method. The periodic DFT calculations of IR spectra focused on reconstructions of H/Si(100) that involved combinations of surface-terminating Si-H groups including the double-occupied dimer (DOD), dihydride (DH), and trihydride (TH). The IR spectra calculated with periodic DFT for H/Si(100) surfaces were compared with the IR spectra calculated by means of DFT in Si-H clusters. The periodic DFT provided considerably better and more reliable theoretical description of the IR spectra by keeping the periodicity of the silicon material that guaranteed proper spatial distribution of the Si-H species within H/Si(100).

Interstrand Charge Transport within Metallo-DNA: The Effect Due to Hg(II): The Ag(I)-Mediated Base Pairs

  • Autoři: Šebera, J., Řeha, D., Fukal, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Journal of Physical Chemistry C. 2020, 124(13), 7477-7486. ISSN 1932-7447.
  • Rok: 2020
  • DOI: 10.1021/acs.jpcc.9b12020
  • Odkaz: https://doi.org/10.1021/acs.jpcc.9b12020
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    Metallo-DNA is considered promising in regard to functional molecular electronic elements. From this perspective, the longitudinal charge transport within metallo-DNA is usually studied. By contrast, this work was aimed at the transversal conductance of metalloDNA, particularly at the effect of Hg and Ag metals on the conductance of base pairs. The charge transport through metal-mediated base pairs involving Hg(II) and Ag(I) metals, deoxythymidine (T) and 4- deoxythiothymidine (Ts), was studied by means of density functional theory (DFT) calculations employing the non-equilibrium

Structural interpretation of the 31P NMR chemical shifts in thiophosphate and phosphate: key effects due to spin–orbit and explicit solvent

  • Autoři: Fukal, J., Pav, O., Budesinsky, M., Rosenberg, I., Sebera, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Physical Chemistry Chemical Physics. 2019, 21(19), 9924-9934. ISSN 1463-9076.
  • Rok: 2019
  • DOI: 10.1039/c9cp01460h
  • Odkaz: https://doi.org/10.1039/c9cp01460h
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    Structural interpretation of the 31P NMR shifts measured in O,O-diethyl thiophosphate (PT), 5,5-dimethyl-2-mercapto-1,3,2-dioxaphosphorinane 2-oxide (cPT), diethylphosphate (P) and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide (cP) was obtained by means of theoretical calculations including the effects of geometry, molecular dynamics, and solvent, relativistic effects and the effect of NMR reference. NMR calculations employed the B3LYP, BP86, BPW91, M06-2X, PBE0, MP2, and HF methods, the Iglo-n (n = II, III), cc-pVnZ (n = D, T, Q, 5), and pcS-n (n = 0, 1, 2, 3, 4) Gaussian-type basis sets and the Slater-type QZ4P atomic basis. Water solvent was described explicitly and/or implicitly.

The benchmark of P-31 NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate

  • Autoři: Fukal, J., Pav, O., Budesinsky, M., Sebera, J., RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Physical Chemistry Chemical Physics. 2017, 19(47), 31830-31841. ISSN 1463-9076.
  • Rok: 2017
  • DOI: 10.1039/c7cp06969c
  • Odkaz: https://doi.org/10.1039/c7cp06969c
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    A benchmark for structural interpretation of the P-31 NMR shift and the (2)J(P),(C) NMR spin-spin coupling in the phosphate group was obtained by means of theoretical calculations and NMR measurements in diethylphosphate (DEP) and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide (cDEP). The NMR parameters were calculated employing the B3LYP, BP86, BPW91, M06-2X, PBE0, KT2, KT3, MP2, and HF methods, and the 6-31+G(d), Iglo-n (n = II, III), cc-pVnZ (n = D, T, Q, 5), aug-cc-pVnZ (n = D, T and Q), and pcS-n and pcJ-n (n = 1, 2, 3, 4) bases, including the solvent effects described with explicit water molecules and/or the implicit Polarizable Continuum Model (PCM). The effect of molecular dynamics (MD) on NMR parameters was MD-calculated using the GAFF force field inclusive of explicit hydration with TIP3P water molecules. Both the optimal geometries and the dynamic behaviors of the DEP and cDEP phosphates differed notably, which allowed a reliable theoretical benchmark of the P-31 NMR parameters for highly flexible and structurally constrained phosphate in a one-to-one relationship with the corresponding experiment. The calculated P-31 NMR shifts were referenced employing three different NMR reference schemes to highlight the effect of the P-31 NMR reference on the accuracy of the calculated P-31 NMR shift.

The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine

  • DOI: 10.1093/nar/gkx157
  • Odkaz: https://doi.org/10.1093/nar/gkx157
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    The excision of 8-oxoguanine (oxoG) by the human 8-oxoguanine DNA glycosylase 1 (hOGG1) base-excision repair enzyme was studied by using the QM/MM (M06-2X/6-31G(d,p):OPLS2005) calculation method and nuclear magnetic resonance (NMR) spectroscopy. The calculated glycosylase reaction included excision of the oxoG base, formation of Lys249-ribose enzyme–substrate covalent adduct and formation of a Schiff base. The formation of a Schiff base with ΔG# = 17.7 kcal/mol was the rate-limiting step of the reaction. The excision of the oxoG base with ΔG# = 16.1 kcal/mol proceeded via substitution of the C1΄-N9 N-glycosidic bond with an H-N9 bond where the negative charge on the oxoG base and the positive charge on the ribose were compensated in a concerted manner by NH3+(Lys249) and CO2−(Asp268), respectively. The effect of Asp268 on the oxoG excision was demonstrated with 1H NMR for WT hOGG1 and the hOGG1(D268N) mutant: the excision of oxoG was notably suppressed when Asp268 was mutated to Asn. The loss of the base-excision function was rationalized with QM/MM calculations and Asp268 was confirmed as the electrostatic stabilizer of ribose oxocarbenium through the initial base-excision step of DNA repair. The NMR experiments and QM/MM calculations consistently illustrated the base-excision reaction operated by hOGG1.

Limits in Proton Nuclear Singlet-State Lifetimes Measured with para-Hydrogen-Induced Polarization

  • DOI: 10.1002/cphc.201600663
  • Odkaz: https://doi.org/10.1002/cphc.201600663
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    The synthesis of a hyperpolarized molecule was developed, where the polarization and the singlet state were preserved over two controlled chemical steps. Nuclear singlet-state lifetimes close to 6 min for protons are reported in dimethyl fumarate. Owing to the high symmetry (AA′X3X3′ and A2 systems), the singlet-state readout requires either a chemical desymmetrization or a long and repeated spin lock. Using DFT calculations and relaxation models, we further determine nuclear spin singlet lifetime limiting factors, which include the intramolecular dipolar coupling mechanism (proton–proton and proton–deuterium), the chemical shift anisotropy mechanism (symmetric and antisymmetric), and the intermolecular dipolar coupling mechanism (to oxygen and deuterium). If the limit of paramagnetic relaxation caused by residual oxygen could be lifted, the intramolecular dipolar coupling to deuterium would become the limiting relaxation mechanism and proton lifetimes upwards of 26 min could become available in the molecules considered here (dimethyl maleate and dimethyl fumarate).

Structure Determination of an AgI-Mediated Cytosine–Cytosine Base Pair within DNA Duplex in Solution with 1H/15N/109Ag NMR Spectroscopy

  • Autoři: Dairaku, T, Furuita, K, Sato, H, RNDr. Vladimír Sychrovský, Ph.D.,
  • Publikace: Chemistry - A European Journal. 2016, 22(37), 13028-13031. ISSN 0947-6539.
  • Rok: 2016
  • DOI: 10.1002/chem.201603048
  • Odkaz: https://doi.org/10.1002/chem.201603048
  • Pracoviště: Katedra elektrotechnologie
  • Anotace:
    The structure of an AgI-mediated cytosine–cytosine base pair, C–AgI–C, was determined with NMR spectroscopy in solution. The observation of 1-bond 15N-109Ag J-coupling (1J(15N,109Ag): 83 and 84 Hz) recorded within the C–AgI–C base pair evidenced the N3–AgI–N3 linkage in C–AgI–C. The triplet resonances of the N4 atoms in C–AgI–C demonstrated that each exocyclic N4 atom exists as an amino group (−NH2), and any isomerization and/or N4–AgI bonding can be excluded. The 3D structure of AgI–DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C–AgI–C (−18.3±3.0°). The 109Ag NMR chemical shift of C-AgI-C was recorded for cytidine/AgI complex (δ(109Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C–AgI–C base pair.

Za stránku zodpovídá: Ing. Mgr. Radovan Suk