The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs

Calculation of the HOMO localization of Tetrahymena and Oxytricha telomeric quadruplex DNA

(2015) Masayuki Morikawa et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

RNABP COGEST: a resource for investigating functional RNAs

(2015) Sohini Bhattacharya et al.   Database-The Journal of Biological Databases and Curation

Why Does Substitution of Thymine by 6-Ethynylpyridone Increase the Thermostability of DNA Double Helices?

(2014) Antarip Halder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study

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

Evidence of σ- and π-Dimerization in a Series of Phenalenyls

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

Reciprocal Hydrogen Bonding–Aromaticity Relationships

(2014) Judy I. Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study

(2014) Antarip Halder et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A critical base pair in k-turns that confers folding characteristics and correlates with biological function

(2014) Scott A. McPhee et al.   Nature Communications

Energy hyperspace for stacking interaction inAU/AUdinucleotide step: Dispersion-corrected density functional theory study

(2013) Sanchita Mukherjee et al.   BIOPOLYMERS

Molecular Switching Behavior in Isosteric DNA Base Pairs

(2013) A. K. Jissy et al.   CHEMPHYSCHEM

Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations

(2013) Marianne Rooman et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

(2013) Jiří Šponer et al.   METHODS

Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold

(2013) Joseph A Liberman et al.   Nature Chemical Biology

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

(2013) Mohit Chawla et al.   NUCLEIC ACIDS RESEARCH

Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?

(2012) Harold S Bernhardt et al.   Biology Direct

Influence of 2′-Deoxy Sugar Moiety on Excited-State Protonation Equilibrium of Adenine and Adenosine with Acridine inside SDS Micelles: A Time-Resolved Study with Quantum Chemical Calculations

(2012) Manas Kumar Sarangi et al.   CHEMPHYSCHEM

Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family

(2012) Purshotam Sharma et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structure and Energy of Non-Canonical Basepairs: Comparison of Various Computational Chemistry Methods with Crystallographic Ensembles

(2012) Swati Panigrahi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines

(2012) Jing Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Comment on “Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings”

(2012) Jiří Šponer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent effects on electron-driven proton-transfer processes: adenine–thymine base pairs

(2012) Monika Dargiewicz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

HD-RNAS: An Automated Hierarchical Database of RNA Structures

(2012) Shubhra Sankar Ray et al.   Frontiers in Genetics

Charged Nucleobases and Their Potential for RNA Catalysis

(2011) Jennifer L. Wilcox et al.   ACCOUNTS OF CHEMICAL RESEARCH

A pH-driven DNA nanoswitch for responsive controlled release

(2011) Linfeng Chen et al.   CHEMICAL COMMUNICATIONS

Role of Multicentered Bonding in Controlling Magnetic Interactions in π-Stacked Bis-dithiazolyl Radical

(2011) Deepthi Jose et al.   CRYSTAL GROWTH & DESIGN

A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

(2011) Kamila Réblová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation of Base Pairs in RNA: Context Analysis and Quantum Chemical Investigations of Their Geometries and Stabilities

(2011) Mohit Chawla et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Binding Strength Sequence for Nucleic Acid Bases and C60 with Density Functional and Dispersion-Corrected Density Functional Theories: Whether C60 Could Protect Nucleic Acid Bases from Radiation-Induced Damage

(2011) Wenming Sun et al.   Journal of Physical Chemistry C

Nucleic Acid G-quartets: Insights into Diverse Patterns and Optical Properties

(2011) A.K. Jissy et al.   Journal of Physical Chemistry C

On the binding of Mg2+, Ca2+, Zn2+ and Cu+ metal cations to 2 ′ -deoxyguanosine: Changes on sugar puckering and strength of the -glycosidic bond

(2011) M.S. Ahmadi et al.   Scientia Iranica

Driving Forces for Nucleic Acid pKaShifting in an A+·C Wobble: Effects of Helix Position, Temperature, and Ionic Strength

(2010) Nathan A. Siegfried et al.   BIOCHEMISTRY

Effects of Nucleophile, Oxidative Damage, and Nucleobase Orientation on the Glycosidic Bond Cleavage in Deoxyguanosine

(2010) Eun Jung Shim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets—Quantum Chemical Insights into RNA Structural Biology

(2010) Purshotam Sharma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?

(2010) Jiří Šponer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Designing Molecular Switches Based on DNA-Base Mispairing

(2010) A. K. Jissy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of Unsatisfied Hydrogen Bond Acceptors in RNA Energetics and Specificity

(2010) Nathan A. Siegfried et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

THE INFLUENCES OF OXIDATION AND CATIONIZATION ON THE N-GLYCOSIDIC BOND STABILITY OF 8-OXO-2′-DEOXYADENOSINE — A THEORETICAL STUDY

(2010) YAN ZHENG et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

DFT STUDY ON METAL CATIONIZATION AND O6-PROTONATION ON 2′-DEOXYGUANOSINE CONFIGURATION: CHANGES ON SUGAR PUCKERING AND STRENGTH OF THE N-GLYCOSIDIC BOND

(2010) MARYAM S. AHMADI et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

The emerging field of RNA nanotechnology

(2010) Peixuan Guo   Nature Nanotechnology

A structural database for k-turn motifs in RNA

(2010) K. T. Schroeder et al.   RNA

On the mechanism of the N-glycosydic bond hydrolysis of 2′-deoxyguanosine: insights from first principles calculations

(2010) R. Rios-Font et al.   THEORETICAL CHEMISTRY ACCOUNTS

A CA+Pair Adjacent to a Sheared GA or AA Pair Stabilizes Size-Symmetric RNA Internal Loops

(2009) Gang Chen et al.   BIOCHEMISTRY

Eukaryotic DNA Polymerases α, β and ε Incorporate Guanine Opposite 2,2,4-Triamino-5(2H)-oxazolone

(2009) Katsuhito Kino et al.   CHEMBIOCHEM

Raman Spectroscopy Study and First-Principles Calculations of the Interaction between Nucleic Acid Bases and Carbon Nanotubes

(2009) Stepan G. Stepanian et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations

(2009) Arnošt Mládek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Frequency and Effect of the Binding of Mg2+, Mn2+, and Co2+Ions on the Guanine Base in Watson−Crick and Reverse Watson−Crick Base Pairs

(2009) Romina Oliva et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

(2009) Daniel Svozil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Direct Raman Measurement of an Elevated Base pKain the Active Site of a Small Ribozyme in a Precatalytic Conformation

(2009) Man Guo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Calculation of pKaValues of Nucleobases and the Guanine Oxidation Products Guanidinohydantoin and Spiroiminodihydantoin using Density Functional Theory and a Polarizable Continuum Model

(2008) Vincenzo Verdolino et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case

(2007) Fabrizio Santoro et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY