相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions
Bei Liu et al.
NATURE COMMUNICATIONS (2021)
Base pairing, structural and functional insights into N4- methylcytidine (m4C) and N4, N4-dimethylcytidine (m42C) modified RNA
Song Mao et al.
NUCLEIC ACIDS RESEARCH (2020)
Distinct RNA N-demethylation pathways catalyzed by nonheme iron ALKBH5 and FTO enzymes enable regulation of formaldehyde release rates
Joel D. W. Toh et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates
Xiao Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
MODOMICS: a database of RNA modification pathways. 2017 update
Pietro Boccaletto et al.
NUCLEIC ACIDS RESEARCH (2018)
Chemical Modifications in the Life of an mRNA Transcript
Sigrid Nachtergaele et al.
ANNUAL REVIEW OF GENETICS, VOL 52 (2018)
Mechanism of tRNA-mediated+1 ribosomal frameshifting
Samuel Hong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Acetylation of Cytidine in mRNA Promotes Translation Efficiency
Daniel Arango et al.
CELL (2018)
Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine
Christian Riml et al.
JOURNAL OF ORGANIC CHEMISTRY (2017)
C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3′-end of the mRNA codons
Elzbieta Sochacka et al.
NUCLEIC ACIDS RESEARCH (2017)
Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions
Pavanapuresan P. Vaidyanathan et al.
RNA (2017)
Improved pKa Prediction of Substituted Alcohols, Phenols, and Hydroperoxides in Aqueous Medium Using Density Functional Theory and a Cluster-Continuum Solvation Model
Bishnu Thapa et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2017)
Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing Stability
Qing Dai et al.
ACS CHEMICAL BIOLOGY (2016)
The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
Dan Dominissini et al.
NATURE (2016)
m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Huiqing Zhou et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)
Base pairing and structural insights into the 5-formylcytosine in RNA duplex
Rui Wang et al.
NUCLEIC ACIDS RESEARCH (2016)
m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs
Huiqing Zhou et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)
N6-Methyladenosine: a conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5
Shui Zou et al.
SCIENTIFIC REPORTS (2016)
Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson-Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine
Marta W. Szulik et al.
BIOCHEMISTRY (2015)
Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification
Caroline Roost et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
RNA-RNA interactions in gene regulation: the coding and noncoding players
Sonia Guil et al.
TRENDS IN BIOCHEMICAL SCIENCES (2015)
Computational estimation of pKa values
Paul G. Seybold et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)
Calculations of pKa's and Redox Potentials of Nucleobases with Explicit Waters and Polarizable Continuum Solvation
Bishnu Thapa et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2015)
Predicting pKa in Implicit Solvents: Current Status and Future Directions
Junming Ho
AUSTRALIAN JOURNAL OF CHEMISTRY (2014)
Inosine in DNA and RNA
Ingrun Alseth et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2014)
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA
Ye Fu et al.
NATURE COMMUNICATIONS (2013)
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
Kate D. Meyer et al.
CELL (2012)
A reliable and efficient first principles-based method for predicting pKa values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pKa values predicted more accurately?
Shuming Zhang
JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
Dan Dominissini et al.
NATURE (2012)
Driving Forces for Nucleic Acid pKa Shifting in an A+•C Wobble: Effects of Helix Position, Temperature, and Ionic Strength
Nathan A. Siegfried et al.
BIOCHEMISTRY (2010)
A universal approach for continuum solvent pK(a) calculations: are we there yet?
Junming Ho et al.
THEORETICAL CHEMISTRY ACCOUNTS (2010)
Explicitly Representing the Solvation Shell in Continuum Solvent Calculations
Eirik F. da Silva et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2009)
Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
Aleksandr V. Marenich et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Combined approaches to site-specific modification of RNA
Christine S. Chow et al.
ACS CHEMICAL BIOLOGY (2008)
Calculation of solvation free energies of charged solutes using mixed cluster/continuum models
Vyacheslav S. Bryantsev et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Effects of N2,N2-dimethylguanosine on RNA structure and stability:: Crystal structure of an RNA duplex with tandem m22G:A pairs
Pradeep S. Pallan et al.
RNA (2008)
The wobble hypothesis revisited:: Uridine-5-oxyacetic acid is critical for reading of G-ending codons
S. Joakim Nasvall et al.
RNA (2007)
Calculation of pKas in RNA:: On the structural origins and functional roles of protonated nucleotides
Christopher L. Tang et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton
Casey P. Kelly et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants
CP Kelly et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2006)
Comment on Accurate experimental values for the free energies of hydration of H+, OH-, and H3O+
DM Camaioni et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2005)
Effects of nucleotide substitution and modification on the stability and structure of helix 69 from 28S rRNA
M Sumita et al.
RNA (2005)
Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes
P Acharya et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)
Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides, m3Ψ and Ψ
HMP Chui et al.
JOURNAL OF ORGANIC CHEMISTRY (2002)
Investigation of Overhauser effects between pseudouridine and water protons in RNA helices
MI Newby et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure
A Huppler et al.
NATURE STRUCTURAL BIOLOGY (2002)
Translation: In retrospect and prospect
CR Woese
RNA (2001)
A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture
MI Newby et al.
RNA (2001)
Solution structure of the A loop of 23S ribosomal RNA
SC Blanchard et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
I Shih et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center
GW Muth et al.
SCIENCE (2000)
Conformation and proton configuration of pyrimidine deoxynucleoside oxidation damage products in water
CJ La Francois et al.
CHEMICAL RESEARCH IN TOXICOLOGY (2000)
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
S Nakano et al.
SCIENCE (2000)