Substituting CF2for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands

(2015) Sophia Bazzi et al.   CHEMISTRY-A EUROPEAN JOURNAL

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds, Interactions, and Bond/Line Paths

(2014) Cina Foroutan-Nejad et al.   CHEMISTRY-A EUROPEAN JOURNAL

The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation

(2014) Ol’ha O. Brovarets’ et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The Right Answer for the Right Electrostatics: Force Field Methods Are Able to Describe Relative Energies of DNA Guanine Quadruplexes

(2014) Jörg Grunenberg et al.   Journal of Chemical Theory and Computation

Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems

(2014) Yevgen P. Yurenko et al.   Journal of Chemical Theory and Computation

The Free Energy Landscape of Pseudorotation in 3′–5′ and 2′–5′ Linked Nucleic Acids

(2014) Li Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications

(2014) Jan Novotný et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Predicting Kinetically Unstable CC Bonds from the Ground-State Properties of a Molecule

(2013) Georgios Markopoulos et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Backbone FCH⋅⋅⋅O Hydrogen Bonds in 2′F-Substituted Nucleic Acids

(2013) Nerea Martin-Pintado et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

(2013) Osman Doluca et al.   CHEMICAL REVIEWS

Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: a comprehensive theoretical investigation

(2013) Alla G. Ponomareva et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Nucleic Acid Bases in Anionic 2′-Deoxyribonucleotides: A DFT/B3LYP Study of Structures, Relative Stability, and Proton Affinities

(2013) Gennady V. Palamarchuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations

(2013) Jiří Šponer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sugar-modified G-quadruplexes: effects of LNA-, 2′F-RNA– and 2′F-ANA-guanosine chemistries on G-quadruplex structure and stability

(2013) Zhe Li et al.   NUCLEIC ACIDS RESEARCH

Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach

(2013) Yevgen P. Yurenko et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Are compliance constants ill-defined descriptors for weak interactions?

(2013) Jörg Grunenberg et al.   RSC Advances

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

(2013) Giampaolo Barone et al.   ChemistryOpen

5′ Unlocked Nucleic Acid Modification Improves siRNA Targeting

(2013) Nicholas M Snead et al.   Molecular Therapy-Nucleic Acids

2′-Fluoro RNA Shows Increased Watson-Crick H-Bonding Strength and Stacking Relative to RNA: Evidence from NMR and Thermodynamic Data

(2012) Amritraj Patra et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

2′-F-ANA-guanosine and 2′-F-guanosine as powerful tools for structural manipulation of G-quadruplexes

(2012) Christopher Jacques Lech et al.   CHEMICAL COMMUNICATIONS

Dependence of Deformability of Geometries and Characteristics of Intramolecular Hydrogen Bonds in Canonical 2′-Deoxyribonucleotides on DNA Conformations

(2012) Gennady V. Palamarchuk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Intramolecular CH…O Hydrogen Bonds in the AI and BI DNA-like Conformers of Canonical Nucleosides and their Watson-Crick Pairs. Quantum Chemical and AIM Analysis

(2012) Yevgen P. Yurenko et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Glycosidic Bond Cleavage in Deoxynucleotides: Effects of Solvent and the DNA Phosphate Backbone in the Computational Model

(2012) Stefan A. P. Lenz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels

(2012) Jan Novotný et al.   Journal of Physical Chemistry Letters

Measurement and Theory of Hydrogen Bonding Contribution to Isosteric DNA Base Pairs

(2012) Omid Khakshoor et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quadruply bonded carbon

(2012) Jörg Grunenberg   Nature Chemistry

The solution structure of double helical arabino nucleic acids (ANA and 2′F-ANA): effect of arabinoses in duplex-hairpin interconversion

(2012) Nerea Martín-Pintado et al.   NUCLEIC ACIDS RESEARCH

Complete conformational space of the potential HIV-1 reverse transcriptase inhibitors d4U and d4C. A quantum chemical study

(2012) Alla G. Ponomareva et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2

(2012) Bjørn Dalhus et al.   STRUCTURE

Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets

(2011) Célia Fonseca Guerra et al.   CHEMISTRY-A EUROPEAN JOURNAL

MicroRNA therapeutics

(2011) J A Broderick et al.   GENE THERAPY

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

(2011) Tatsuya Maehigashi et al.   NUCLEIC ACIDS RESEARCH

Complexity in molecular recognition

(2011) Jörg Grunenberg   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Efficient computation of compliance matrices in redundant internal coordinates from Cartesian Hessians for nonstationary points

(2010) Kai Brandhorst et al.   JOURNAL OF CHEMICAL PHYSICS

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Energetically Important C−H···F−C Pseudohydrogen Bonding in Water: Evidence and Application to Rational Design of Oligonucleotides with High Binding Affinity

(2010) Maryam Yahyaee Anzahaee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Neutral and positively charged new purine tetramer structures: a computational study of xanthine and uric acid derivatives

(2010) Gábor Paragi et al.   NEW JOURNAL OF CHEMISTRY

3-Substituted xanthines as promising candidates for quadruplex formation: computational, synthetic and analytical studies

(2010) János Szolomájer et al.   NEW JOURNAL OF CHEMISTRY

Differential stability of 2′F-ANA•RNA and ANA•RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility

(2010) Jonathan K. Watts et al.   NUCLEIC ACIDS RESEARCH

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair

(2009) Pan-Pan Zhou et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Pairing Geometry of the Hydrophobic Thymine Analogue 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

(2009) Pradeep S. Pallan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The effect of 2′-fluorine substitutions on DNA i-motif conformation and stability

(2008) Clare P. Fenna et al.   CHEMICAL COMMUNICATIONS

How strong is it? The interpretation of force and compliance constants as bond strength descriptors

(2008) Kai Brandhorst et al.   CHEMICAL SOCIETY REVIEWS

Potent inhibition of microRNA in vivo without degradation

(2008) Scott Davis et al.   NUCLEIC ACIDS RESEARCH

Ab Initio Comprehensive Conformational Analysis of 2‘-Deoxyuridine, the Biologically Significant DNA Minor Nucleoside, and Reconstruction of Its Low-Temperature Matrix Infrared Spectrum

(2007) Yevgen P. Yurenko et al.   JOURNAL OF PHYSICAL CHEMISTRY B