4.7 Article

A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine

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。
Article Biochemistry & Molecular Biology

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects

Jeffrey Zuber et al.

Summary: Nearest neighbor parameters are commonly used for estimating the folding stability of RNA secondary structures. In this study, we curated an expanded database and found that the terminal penalties for helices depend on the sequence identity of the adjacent penultimate base pair. By including this additional sequence dependence, new nearest neighbor parameters accurately predict the stabilities of helices and improve the fitting of base pair stacks with GU pairs.

NUCLEIC ACIDS RESEARCH (2022)

Article Multidisciplinary Sciences

Secondary structure prediction for RNA sequences including N6-methyladenosine

Elzbieta Kierzek et al.

Summary: This study addresses the issue of predicting the secondary structure of RNA with covalently modified nucleotides. The researchers developed software and determined thermodynamic parameters to enable the prediction of secondary structure for sequences containing N-6-methyladenosine (m(6)A). The study also revealed the effects of N-6-methylation on folding stability in different contexts.

NATURE COMMUNICATIONS (2022)

Article Biochemistry & Molecular Biology

RNA secondary structure dependence in METTL3-METTL14 mRNA methylation is modulated by the N-terminal domain of METTL3

Nathalie Meiser et al.

Summary: The study reveals that N-6-methyladenosine modification is the most abundant in mRNA, with the METTL3-METTL14 complex responsible for catalyzing this modification, which is dependent not only on sequence but also on the secondary structure of RNA. The zinc finger domains within the complex play a crucial role in RNA binding and methylation activity, while the N-terminal domain of METTL3 affects the dependence of methylation yield on secondary structure.

BIOLOGICAL CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

Deciphering nucleotide modification-induced structure and stability changes

Travis Hurst et al.

Summary: The study reveals the impact of nucleotide modification on RNA structure and stability, shedding light on the potential gene expression and folding mechanics changes induced by modified nucleotides. In addition, simulated exploration of hairpin structures also contributes to understanding their potential roles in the onset of chronic diseases.

RNA BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides

Melissa C. Hopfinger et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Cell Biology

Reading, writing and erasing mRNA methylation

Sara Zaccara et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Review Cell Biology

Reading, writing and erasing mRNA methylation

Sara Zaccara et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Surprising Sequence Effects on GU Closure of Symmetric 2 x 2 Nucleotide RNA Internal Loops

Kyle D. Berger et al.

BIOCHEMISTRY (2018)

Article Multidisciplinary Sciences

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

Bei Liu et al.

NATURE COMMUNICATIONS (2018)

Article Chemistry, Physical

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations

Louis G. Smith et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Biochemical Research Methods

Identification of N6-methyladenosine reader proteins

Katherine I. Zhou et al.

METHODS (2017)

Review Biochemical Research Methods

Epitranscriptome sequencing technologies: decoding RNA modifications

Xiaoyu Li et al.

NATURE METHODS (2017)

Review Cell Biology

RNA modifications and structures cooperate to guide RNA-protein interactions

Cole J. T. Lewis et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

Nian Liu et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA

Alyssa C. Hill et al.

Review Oncology

The Epitranscriptome of Noncoding RNAs in Cancer

Manel Esteller et al.

CANCER DISCOVERY (2017)

Article Biochemistry & Molecular Biology

Control of box C/D snoRNP assembly by N6-methylation of adenine

Lin Huang et al.

EMBO REPORTS (2017)

Article Biochemistry & Molecular Biology

N6-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding

Katherine I. Zhou et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Multidisciplinary Sciences

Blind tests of RNA nearest-neighbor energy prediction

Fang-Chieh Chou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Biophysics

Bridging the gap between in vitro and in vivo RNA folding

Kathleen A. Leamy et al.

QUARTERLY REVIEWS OF BIOPHYSICS (2016)

Review Multidisciplinary Sciences

Messenger RNA modifications: Form, distribution, and function

Wendy V. Gilbert et al.

SCIENCE (2016)

Article Biochemistry & Molecular Biology

Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability

Jeremy C. Tomcho et al.

BIOCHEMISTRY (2015)

Article Chemistry, Physical

Structures and Energetics of Four Adjacent G•U Pairs That Stabilize an RNA Helix

Xiaobo Gu et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Chemistry, Physical

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations

Shun Sakuraba et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2015)

Article Chemistry, Multidisciplinary

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

Caroline Roost et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

Article Biochemical Research Methods

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

Bastian Linder et al.

NATURE METHODS (2015)

Article Chemistry, Multidisciplinary

High-Resolution N6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

Kai Chen et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Biochemistry & Molecular Biology

Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

Tian Jiang et al.

BIOCHEMISTRY (2014)

Article Biochemistry & Molecular Biology

Improved Model to Predict the Free Energy Contribution of Trinucleotide Bulges to RNA Duplex Stability

Meghan H. Murray et al.

BIOCHEMISTRY (2014)

Article Biochemistry & Molecular Biology

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

Masayuki Sakurai et al.

GENOME RESEARCH (2014)

Article Multidisciplinary Sciences

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

Thomas M. Carlile et al.

NATURE (2014)

Review Biochemistry & Molecular Biology

N6-methyl-adenosine modification in messenger and long non-coding RNA

Tao Pan

TRENDS IN BIOCHEMICAL SCIENCES (2013)

Article Biochemistry & Molecular Biology

Thermodynamic Characterization of RNA 2 x 3 Nucleotide Internal Loops

Nina Z. Hausmann et al.

BIOCHEMISTRY (2012)

Article Biochemistry & Molecular Biology

Effects of Non-Nearest Neighbors on the Thermodynamic Stability of RNA GNRA Hairpin Tetra loops

Pamela L. Vanegas et al.

BIOCHEMISTRY (2012)

Article Biochemistry & Molecular Biology

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Jonathan L. Chen et al.

BIOCHEMISTRY (2012)

Article Chemistry, Physical

The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation

Aleksandar Spasic et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Multidisciplinary Sciences

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

Dan Dominissini et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

Jeffrey E. Squires et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots

Biao Liu et al.

BIOCHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Positional and Neighboring Base Pair Effects on the Thermodynamic Stability of RNA Single Mismatches

Amber R. Davis et al.

BIOCHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Consecutive Terminal GU Pairs Stabilize RNA Helices

Mai-Thao Nguyen et al.

BIOCHEMISTRY (2010)

Article Biochemical Research Methods

RNAstructure: software for RNA secondary structure prediction and analysis

Jessica S. Reuter et al.

BMC BIOINFORMATICS (2010)

Review Cell Biology

tRNA biology charges to the front

Eric M. Phizicky et al.

GENES & DEVELOPMENT (2010)

Article Biochemistry & Molecular Biology

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

Douglas H. Turner et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

Computational approaches for RNA energy parameter estimation

Mirela Andronescu et al.

Article Biochemistry & Molecular Biology

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

Martha E. Christiansen et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

3′ Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices

Koree Clanton-Arrowood et al.

BIOCHEMISTRY (2008)

Article Biochemistry & Molecular Biology

Thermodynamic characterization of naturally occurring RNA single mismatches with G-U nearest neighbors

Amber R. Davis et al.

BIOCHEMISTRY (2008)

Article Biochemistry & Molecular Biology

Thermodynamic characterization of single mismatches found in naturally occurring RNA

Amber R. Davis et al.

BIOCHEMISTRY (2007)

Article Biochemical Research Methods

CONTRAfold: RNA secondary structure prediction without physics-based models

Chuong B. Do et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Comprehensive thermodynamic analysis of 3 ' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs

Amanda S. O'Toole et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Stability of 3' double nucleotide overhangs that model the 3' ends of siRNA

AS O'Toole et al.

Article Biochemistry & Molecular Biology

Factors affecting thermodynamic stabilities of RNA 3x3 internal loops

G Chen et al.

BIOCHEMISTRY (2004)

Article Multidisciplinary Sciences

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

DH Mathews et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion

R Micura et al.

NUCLEIC ACIDS RESEARCH (2001)

Article Biochemistry & Molecular Biology

Thermodynamics of three-way multibranch loops in RNA

JM Diamond et al.

BIOCHEMISTRY (2001)

Article Biochemistry & Molecular Biology

Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA

SJ Schroeder et al.

BIOCHEMISTRY (2000)