Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases (Q34561384)

3 August 2017

1 reference

title

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases (English)

1 reference

3 August 2017

Sponer J

1

1 reference

PubMed ID

11891626

3 August 2017

Leszczynski J

series ordinal

2

1 reference

PubMed ID

11891626

3 August 2017

Hobza P

series ordinal

3

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3 August 2017

1 January 2001

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3 August 2017

1 reference

3 August 2017

61

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3 August 2017

1

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3 August 2017

3-31

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Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies.

3 August 2017

1 reference

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Experimental studies of molecular interactions between nitrogen bases of nucleic acids

21 January 2018

1 reference

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At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study

21 January 2018

1 reference

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Laser separation of geometrical isomers of weakly bound molecular complexes

21 January 2018

1 reference

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Weakly bound clusters of biological interest

21 January 2018

1 reference

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Derivation of nearest-neighbor properties from data on nucleic acid oligomers. I. Simple sets of independent sequences and the influence of absent nearest neighbors

21 January 2018

1 reference

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Thermodynamic parameters for DNA sequences with dangling ends

21 January 2018

1 reference

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A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

21 January 2018

1 reference

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Nucleic acid duplex stability: influence of base composition on cation effects

21 January 2018

1 reference

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Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions.

21 January 2018

1 reference

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A tetrameric DNA structure with protonated cytosine.cytosine base pairs

21 January 2018

1 reference

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Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA

21 January 2018

1 reference

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The physical basis of nucleic acid base stacking in water

21 January 2018

1 reference

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The electrostatic contribution to DNA base-stacking interactions.

21 January 2018

1 reference

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Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

21 January 2018

1 reference

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Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study

21 January 2018

1 reference

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Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair.

21 January 2018

1 reference

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On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.

21 January 2018

1 reference

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Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode

21 January 2018

1 reference

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Elucidation of primary radiation damage in DNA through application of ab initio molecular orbital theory

21 January 2018

1 reference

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The peculiar role of cytosine in nucleoside conformational behaviour: Hydrogen bond donor capacity of nucleic bases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Natural population analysis

21 January 2018

1 reference

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A quantum theory of molecular structure and its applications

21 January 2018

1 reference

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Evaluated Gas Phase Basicities and Proton Affinities of Molecules; Heats of Formation of Protonated Molecules

21 January 2018

1 reference

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Survey of the proton affinities of adenine, cytosine, thymine and uracil dideoxyribonucleosides, deoxyribonucleosides and ribonucleosides.

21 January 2018

1 reference

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Metal-Stabilized Rare Tautomers of Nucleobases. 6. Imino Tautomer of Adenine in a Mixed-Nucleobase Complex of Mercury(II).

21 January 2018

1 reference

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Helix geometry, hydration, and G.A mismatch in a B-DNA decamer

21 January 2018

1 reference

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The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges

21 January 2018

1 reference

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Crystal structure of a DNA Holliday junction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Unrestrained Molecular Dynamics Simulations of [d(AT)5]2Duplex in Aqueous Solution: Hydration and Binding of Sodium Ions in the Minor Groove

21 January 2018

1 reference

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A-Tract bending: insights into experimental structures by computational models

21 January 2018

1 reference

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Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Conserved geometrical base-pairing patterns in RNA.

21 January 2018

1 reference

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Triplex formation at the rat neu gene utilizing imidazole and 2'-deoxy-6-thioguanosine base substitutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Overcoming potassium-mediated triplex inhibition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation

21 January 2018

1 reference

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Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Structural characterization of a guanine-quadruplex ligand complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

A DFT study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA triplex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

The keto–amino/enol tautomerism of cytosine in aqueous solution. A theoretical study using combined discrete/self-consistent reaction field models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: NonempiricalAb InitioCalculations

21 January 2018

1 reference

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Nonempirical calculations on all the 29 possible DNA base pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Density functional theory and molecular clusters

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Global Minimum of the Adenine···Thymine Base Pair Corresponds Neither to Watson−Crick Nor to Hoogsteen Structures. Molecular Dynamic/Quenching/AMBER and ab Initio beyond Hartree−Fock Studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Already two water molecules change planar H-bonded structures of the adenine···thymine base pair to the stacked ones: a molecular dynamics simulations study

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Nonplanar geometries of DNA bases. Ab initio second-order Moeller-Plesset study

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

H-Bonded and Stacked DNA Base Pairs: Cytosine Dimer. An Ab Initio Second-Order Moeller-Plesset Study

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Thioguanine and Thiouracil: Hydrogen-Bonding and Stacking Properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals

21 January 2018

1 reference

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MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Comment on “Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases”

21 January 2018

1 reference

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C−H···O Contacts in the Adenine···Uracil Watson−Crick and Uracil···Uracil Nucleic Acid Base Pairs: Nonempirical ab Initio Study with Inclusion of Electron Correlation Effects

21 January 2018

1 reference

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Ab Initio Study of the Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+)

21 January 2018

1 reference

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Interaction of DNA Base Pairs with Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction

21 January 2018

1 reference

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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

21 January 2018

1 reference

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Hydrogen bonding, stacking and cation binding of DNA bases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2961%3A1%3C3%3A%3AAID-BIP10048%3E3.0.CO%3B2-4

Interactions of Hydrated Mg2+Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study

21 January 2018

1 reference

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10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4

21 January 2018

Identifiers

DOI

1 reference

3 August 2017

1 reference

PubMed ID

11891626