Consequences of Mg2+ binding on the geometry and stability of RNA base pairs

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

(2018) Jiří Šponer et al.   CHEMICAL REVIEWS

Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids

(2016) Ganesh N. Pandian et al.   BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN

How Mg2+ ion and water network affect the stability and structure of non-Watson–Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study

(2016) Sudhanshu Shanker et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

(2016) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

Development of Site-Specific Mg2+–RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

(2016) Lorenzo Casalino et al.   Journal of Chemical Theory and Computation

Mg2+ions: do they bind to nucleobase nitrogens?

(2016) Filip Leonarski et al.   NUCLEIC ACIDS RESEARCH

Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection

(2015) Krishna C. Suddala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How do metal ions direct ribozyme folding?

(2015) Natalia A. Denesyuk et al.   Nature Chemistry

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

(2015) Heping Zheng et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Antarip Halder et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Signal-amplification detection of small molecules by use of Mg2+- dependent DNAzyme

(2013) Zhijun Guo et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Design and Applications of Noncanonical DNA Base Pairs

(2013) A. K. Jissy et al.   Journal of Physical Chemistry Letters

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

(2013) Mohit Chawla et al.   NUCLEIC ACIDS RESEARCH

The Nucleic Acid Database: new features and capabilities

(2013) Buvaneswari Coimbatore Narayanan et al.   NUCLEIC ACIDS RESEARCH

RNA structure and dynamics: A base pairing perspective

(2013) Sukanya Halder et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Mg2+-induced conformational changes in the btuB riboswitch from E. coli

(2013) P. K. Choudhary et al.   RNA

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

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

The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch

(2012) Scott P. Hennelly et al.   NUCLEIC ACIDS RESEARCH

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

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

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

HD-RNAS: An Automated Hierarchical Database of RNA Structures

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

Nucleic Acid Based Molecular Devices

(2011) Yamuna Krishnan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Effects of Mg2+on the Free Energy Landscape for Folding a Purine Riboswitch RNA

(2011) Desirae Leipply et al.   BIOCHEMISTRY

Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions

(2011) Lars Goerigk et al.   CHEMPHYSCHEM

Rich Parameterization Improves RNA Structure Prediction

(2011) Shay Zakov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

MINAS—a database of Metal Ions in Nucleic AcidS

(2011) Joachim Schnabl et al.   NUCLEIC ACIDS RESEARCH

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

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

Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity

(2010) James M. Carothers et al.   NUCLEIC ACIDS RESEARCH

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

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

Structure of the Human Telomere in K+Solution: A Stable Basket-Type G-Quadruplex with Only Two G-Tetrad Layers

(2009) Kah Wai Lim et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Classification and energetics of the base-phosphate interactions in RNA

(2009) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

A Probabilistic Model of RNA Conformational Space

(2009) Jes Frellsen et al.   PLoS Computational Biology

Prediction of RNA secondary structure using generalized centroid estimators

(2008) Michiaki Hamada et al.   BIOINFORMATICS

Electrochemical control of a DNA Holliday Junction nanoswitch by Mg2+ ions

(2008) E.E. Ferapontova et al.   BIOSENSORS & BIOELECTRONICS

Assessment of the Performance of the M05−2X and M06−2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules

(2008) Edward G. Hohenstein et al.   Journal of Chemical Theory and Computation

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