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| Description
| - The present project will characterize the interactions of metal cations with nucleic acids using high-level ab initio technique. The energetics of interactions between selected groups of cations and DNA bases, base pairs and other DNA constituents will be evaluated. This data cannot be obtained by any other theoretical technique and are not available from any currently used experimental technique. The ab initio approach thus represents an indispensable complement to experimental results, and allows to estimate the quality of molecular modeling techniques based on empirical potentials. The differences between various cations (for example zinc vs. magnesium, etc.) will be studied systematically, in order to rationalize their different biological roles. The influence of cations on base pairing and the role of cation hydration will be analyzed. Further, the ability of metal cations to stabilize rare tautomers of bases and induce point mutations via formation of mispairs will be considered. (en)
- Struktura a dynamika nukleov_ch kyselin (NK) je v_razn+ ovlivn+na kovov_mi ionty. Tento projekt má za cíl popsat interakce kovov_ch iontů s NK pomocí kvalitní ab initio teorie. Bude studována energetika interakcí vybran_ch skupin kovov_ch iontů s bázemi, páry bází a dal_ími základními stavebními jednotkami NK. Tato data nelze získat žádn_m jin_m teoretick_m pţístupem a nejsou ani dostupná ze stávajících experimentů. AB initio přístup tak představuje nenahraditelný doplněk experimentálních výsledků a dovoluje též odhadnout kvalitu molekulového modelování na bázi empirických potenciálů. Budou systematicky studovány rozdíly mezi jednotlivými ionty (např. rozdíl mezi Zn a Mg, ap.) v zájmu pochopení jejich odlišných funkcí v biosystémech. Dálebude studován vliv iontů na párování bází a úloha hydratace iontů. Kromě toho bude analyzována schopnost kovových kationtů stabilizovat vzácné tautomery bází a vést tak ke vzniku bodových mutací formováním nekanonických párů bází.
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| Title
| - Interactions of metal cations with nucleic acids and their constituents. Ab initio quantum-chemical study (en)
- Interakce kovových iontů s nukleovými kyselinami a jejich fragmenty. Ab initio kvantově-chemická studie
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| skos:notation
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| http://linked.open...avai/cep/aktivita
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| http://linked.open...kovaStatniPodpora
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| http://linked.open...ep/celkoveNaklady
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| http://linked.open...datumDodatniDoRIV
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| http://linked.open...i/cep/druhSouteze
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| http://linked.open...ep/duvernostUdaju
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| http://linked.open.../cep/fazeProjektu
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| http://linked.open...ai/cep/hlavniObor
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| http://linked.open...hodnoceniProjektu
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| http://linked.open.../cep/klicovaSlova
| - Ab initio quantum chemistry; DNA; RNA; metal cations; molecular interactions; molecular dynamics; (en)
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| http://linked.open...ep/partnetrHlavni
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| http://linked.open...inujicichPrijemcu
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| http://linked.open...cep/pocetPrijemcu
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| http://linked.open...ocetSpoluPrijemcu
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| http://linked.open.../pocetVysledkuRIV
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| http://linked.open...enychVysledkuVRIV
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| http://linked.open...iciPoslednihoRoku
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| http://linked.open...atUdajeProjZameru
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| http://linked.open...usZobrazovaneFaze
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| http://linked.open...ai/cep/typPojektu
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| http://linked.open.../cep/vedlejsiObor
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| http://linked.open...jektu+dodavatelem
| - Systematická charakterizace interakcí kovových iontů s bázemi nukleových kyselin pomocí nejmodernějších metod kvantové chemie a systematické srovnání teoretických výsledků s experimenty. (cs)
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| http://linked.open...tniCyklusProjektu
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| http://linked.open.../cep/klicoveSlovo
| - DNA
- RNA
- molecular dynamics
- molecular interactions
- metal cations
- Ab initio quantum chemistry
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| is http://linked.open...vavai/riv/projekt
of | - Metal Ions in Non-complementary DNA Base Pairs: an ab initio Study of Cu(I), Ag(I), and Au(I) Complexes with the Cytosine-Adenine Base Pair.
- Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases: N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views.
- Potential Energy and Free Energy Surfaces of Floppy Systems. Ab initio Calculations and Molecular Dynamics Simulations.
- Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations.
- Cation - .pi. and Amino-acceptor Interactions between Hydrated Metal Cations and DNA Bases. A Quantum-chemical View.
- Aromatic DNA Base Stacking and H-Bonding.
- Noncovalent Interactions: a Challenge for Experiment and Theory.
- Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G-A Mismatch Pairs.
- Protonation of Platinated Adenine Nucleobases. Gas Phase vs Condensed Phase Picture.
- Loss of Hoogsteen Pairing Ability upon N1 Adenine Platinum Binding.
- Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences Among Cations, and Flexibility of the Cation Hydration Shell.
- Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
- Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical ab initio Calculations.
- The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing.
- Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals.
- Local Conformational Variations Observed in B-DNA Crystals do not Improve Base Stacking: Computational Analysis of Base Stacking in a d(CATGGGCCCATG) 2 B<->A Intermediate Crystal Structure.
- The Interactions of Square Platinum(II) Complexes with Quanine and Adenine: a Quantum-chemical ab initio Study of Metaled Tautomeric Forms.
- Interactions of Hydrated Mg 2+ Cation with Bases, Base Pairs and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study.
- Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine
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| is http://linked.open...vavai/cep/projekt
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