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。Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR
Chelsea M. Hull et al.
ACS CHEMICAL BIOLOGY (2016)
RNA Hairpin Folding in the Crowded Cell
Mimi Gao et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2016)
Computational modeling of RNA 3D structures and interactions
Wayne K. Dawson et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)
Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg2+, Nucleotides, and RNA
Erica A. Frankel et al.
LANGMUIR (2016)
Structure and Mechanism of RNA Mimics of Green Fluorescent Protein
Mingxu You et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 44 (2015)
Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding
Jillian Tyrrell et al.
BIOCHEMISTRY (2015)
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo
Yin Tang et al.
BIOINFORMATICS (2015)
Effects of Cosolvents on the Folding and Catalytic Activities of the Hammerhead Ribozyme
Shu-ichi Nakano et al.
CHEMBIOCHEM (2015)
Fast kinetics of calcium signaling and sensor design
Shen Tang et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2015)
Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA
Chelsea M. Hull et al.
JOURNAL OF MOLECULAR BIOLOGY (2015)
Kinetic and Thermodynamic Origins of Osmolyte-Influenced Nucleic Acid Folding
Erik D. Holmstrom et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
HOTAIR Forms an Intricate and Modular Secondary Structure
Srinivas Somarowthu et al.
MOLECULAR CELL (2015)
Structural imprints in vivo decode RNA regulatory mechanisms
Robert C. Spitale et al.
NATURE (2015)
Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq
Yiliang Ding et al.
NATURE PROTOCOLS (2015)
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data
Yang Wu et al.
NUCLEIC ACIDS RESEARCH (2015)
The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication
Chringma Sherpa et al.
NUCLEIC ACIDS RESEARCH (2015)
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch
Mingxu You et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR
Katrina M. Kutchko et al.
RNA (2015)
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Zhichao Miao et al.
RNA (2015)
The RNA structurome: transcriptome-wide structure probing with next-generation sequencing
Chun Kit Kwok et al.
TRENDS IN BIOCHEMICAL SCIENCES (2015)
TGF-β1 conjugated chitosan collagen hydrogels induce chondrogenic differentiation of human synovium-derived stem cells
Jinku Kim et al.
JOURNAL OF BIOLOGICAL ENGINEERING (2015)
Methods for SAXS-Based Structure Determination of Biomolecular Complexes
Sichun Yang
ADVANCED MATERIALS (2014)
Computational Analysis of Conserved RNA Secondary Structure in Transcriptomes and Genomes
Sean R. Eddy
ANNUAL REVIEW OF BIOPHYSICS, VOL 43 (2014)
Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA
Tian Jiang et al.
BIOCHEMISTRY (2014)
Genetically encoded reactive oxygen species (ROS) and redox indicators
Sandrine Pouvreau
BIOTECHNOLOGY JOURNAL (2014)
Engineering lead-sensing GFP through rational designing
Saravanan Prabhu Nadarajan et al.
CHEMICAL COMMUNICATIONS (2014)
Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids
Shu-ichi Nakano et al.
CHEMICAL REVIEWS (2014)
Macro-/micro-environment-sensitive chemosensing and biological imaging
Zhigang Yang et al.
CHEMICAL SOCIETY REVIEWS (2014)
Mitochondrial biosensors
Roberto De Michele et al.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY (2014)
Increased Ribozyme Activity in Crowded Solutions
Ravi Desai et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2014)
Folding Pathways of the Tetrahymena Ribozyme
David Mitchell et al.
JOURNAL OF MOLECULAR BIOLOGY (2014)
Molecular Crowding Accelerates Ribozyme Docking and Catalysis
Bishnu P. Paudel et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
Landscape and variation of RNA secondary structure across the human transcriptome
Yue Wan et al.
NATURE (2014)
A census of human RNA-binding proteins
Stefanie Gerstberger et al.
NATURE REVIEWS GENETICS (2014)
Dynalign II: common secondary structure prediction for RNA homologs with domain insertions
Yinghan Fu et al.
NUCLEIC ACIDS RESEARCH (2014)
Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics
Nicholas F. Dupuis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions
Christopher A. Strulson et al.
RNA (2014)
Mod-seq: high-throughput sequencing for chemical probing of RNA structure
Jason Talkish et al.
RNA (2014)
HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism
Sebastien M. Weyn-Vanhentenryck et al.
CELL REPORTS (2014)
Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Peng Cui et al.
GENOME BIOLOGY (2014)
Molecular Crowding Favors Reactivity of a Human Ribozyme Under Physiological Ionic Conditions
Christopher A. Strulson et al.
BIOCHEMISTRY (2013)
The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure
Jillian Tyrrell et al.
BIOCHEMISTRY (2013)
Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure
Elizabeth J. Denning et al.
BIOPHYSICAL CHEMISTRY (2013)
A FRET ratiometric fluorescence sensing system for mercury detection and intracellular colorimetric imaging in live Hela cells
Bo Hu et al.
BIOSENSORS & BIOELECTRONICS (2013)
A Decade of Riboswitches
Alexander Serganov et al.
CELL (2013)
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
Zhengqing Ouyang et al.
GENOME RESEARCH (2013)
The Long-Range P3 Helix of the Tetrahymena Ribozyme Is Disrupted during Folding between the Native and Misfolded Conformations
David Mitchell et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
Crowders Perturb the Entropy of RNA Energy Landscapes to Favor Folding
Duncan Kilburn et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
In Vivo X-Ray Footprinting of Pre-30S Ribosomes Reveals Chaperone-Dependent Remodeling of Late Assembly Intermediates
Sarah F. Clatterbuck Soper et al.
MOLECULAR CELL (2013)
MagFRET: The First Genetically Encoded Fluorescent Mg2+ Sensor
Laurens H. Lindenburg et al.
PLOS ONE (2013)
Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core
David M. Truong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
Christine E. Hajdin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Denaturation of RNA Secondary and Tertiary Structure by Urea: Simple Unfolded State Models and Free Energy Parameters Account for Measured m-Values
Dominic Lambert et al.
BIOCHEMISTRY (2012)
Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference
Pablo Cordero et al.
BIOCHEMISTRY (2012)
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots
Matthew G. Seetin et al.
BIOINFORMATICS (2012)
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
Zsuzsanna Sukosd et al.
BIOINFORMATICS (2012)
Analysis of energy-based algorithms for RNA secondary structure prediction
Monir Hajiaghayi et al.
BMC BIOINFORMATICS (2012)
Genome-wide Measurement of RNA Folding Energies
Yue Wan et al.
MOLECULAR CELL (2012)
RNA catalysis through compartmentalization
Christopher A. Strulson et al.
NATURE CHEMISTRY (2012)
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator
Irina V. Novikova et al.
NUCLEIC ACIDS RESEARCH (2012)
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction
Stefan Washietl et al.
NUCLEIC ACIDS RESEARCH (2012)
Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome
Fan Li et al.
PLANT CELL (2012)
High-resolution imaging of Ca2+, redox status, ROS and pH using GFP biosensors
Won-Gyu Choi et al.
PLANT JOURNAL (2012)
Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction
Kourosh Zarringhalam et al.
PLOS ONE (2012)
Fluorescence Imaging of Cellular Metabolites with RNA
Jeremy S. Paige et al.
SCIENCE (2012)
In Vivo Imaging of Ca2+, pH, and Reactive Oxygen Species Using Fluorescent Probes in Plants
Sarah J. Swanson et al.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 62 (2011)
Fluorescence Competition and Optical Melting Measurements of RNA Three-Way Multibranch Loops Provide a Revised Model for Thermodynamic Parameters
Biao Liu et al.
BIOCHEMISTRY (2011)
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences
Zhenjiang Xu et al.
BIOINFORMATICS (2011)
Time Resolved SAXS and RNA Folding
Lois Pollack
BIOPOLYMERS (2011)
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences
Arif O. Harmanci et al.
BMC BIOINFORMATICS (2011)
Molecular cloning, characterization, genomic organization and promoter analysis of the α1,6-fucosyltransferase gene (fut8) expressed in the rat hybridoma cell line YB2/0
Beatrice Teylaert et al.
BMC BIOTECHNOLOGY (2011)
Imaging Intracellular pH in Live Cells with a Genetically Encoded Red Fluorescent Protein Sensor
Mathew Tantama et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model
Shogo Koga et al.
NATURE CHEMISTRY (2011)
Understanding the transcriptome through RNA structure
Yue Wan et al.
NATURE REVIEWS GENETICS (2011)
RNA Mimics of Green Fluorescent Protein
Jeremy S. Paige et al.
SCIENCE (2011)
Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots
Biao Liu et al.
BIOCHEMISTRY (2010)
Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Markus Hafner et al.
CELL (2010)
Advances in RNA structure analysis by chemical probing
Kevin M. Weeks
CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)
Multiple Unfolding Events during Native Folding of the Tetrahymena Group I Ribozyme
Yaqi Wan et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
The Osmolyte TMAO Stabilizes Native RNA Tertiary Structures in the Absence of Mg2+: Evidence for a Large Barrier to Folding from Phosphate Dehydration
Dominic Lambert et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Multistage Collapse of a Bacterial Ribozyme Observed by Time-Resolved Small-Angle X-ray Scattering
Joon Ho Roh et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect
Duncan Kilburn et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Multiple native states reveal persistent ruggedness of an RNA folding landscape
Sergey V. Solomatin et al.
NATURE (2010)
Genome-wide measurement of RNA secondary structure in yeast
Michael Kertesz et al.
NATURE (2010)
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
Jason G. Underwood et al.
NATURE METHODS (2010)
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
Douglas H. Turner et al.
NUCLEIC ACIDS RESEARCH (2010)
Reactive oxygen species in abiotic stress signaling
Pinja Jaspers et al.
PHYSIOLOGIA PLANTARUM (2010)
ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
Stanislav Bellaousov et al.
RNA (2010)
Facilitation of RNA Enzyme Activity in the Molecular Crowding Media of Cosolutes
Shu-ichi Nakano et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Accurate SHAPE-directed RNA structure determination
Katherine E. Deigan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators
Hiromi Imamura et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Improved RNA secondary structure prediction by maximizing expected pair accuracy
Zhi John Lu et al.
RNA (2009)
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
Chuong B. Do et al.
BIOINFORMATICS (2008)
RNAalifold: improved consensus structure prediction for RNA alignments
Stephan H. Bernhart et al.
BMC BIOINFORMATICS (2008)
Tertiary interactions determine the accuracy of RNA folding
Seema Chauhan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Donny D. Licatalosi et al.
NATURE (2008)
A practical guide to single-molecule FRET
Rahul Roy et al.
NATURE METHODS (2008)
PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction
Arif Ozgun Harmanci et al.
NUCLEIC ACIDS RESEARCH (2008)
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions
Durga M. Chadalavada et al.
RNA (2007)
5′-triphosphate-dependent activation of PKR by RNAs with short stem-loops
Subba Rao Nallagatla et al.
SCIENCE (2007)
Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions
Dominic Lambert et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Multiple structural alignment and clustering of RNA sequences
Elfar Torarinsson et al.
BIOINFORMATICS (2007)
Tertiary structure of an RNA pseudoknot is stabilized by diffuse Mg2+ ions
Ana Maria Soto et al.
BIOCHEMISTRY (2007)
Magnesium homeostasis in mammalian cells
Andrea M. P. Romani
FRONTIERS IN BIOSCIENCE-LANDMARK (2007)
RNA-dominant diseases
Robert J. Osborne et al.
HUMAN MOLECULAR GENETICS (2006)
Conversion of a putative agrobacterium sugar-binding protein into a FRET sensor with high selectivity for sucrose
Ida Lager et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
Zhi John Lu et al.
NUCLEIC ACIDS RESEARCH (2006)
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
Kourosh Salehi-Ashtiani et al.
SCIENCE (2006)
Beyond Mfold:: recent advances in RNA bioinformatics
Jens Reeder et al.
JOURNAL OF BIOTECHNOLOGY (2006)
Revolutions in RNA secondary structure prediction
David H. Mathews
JOURNAL OF MOLECULAR BIOLOGY (2006)
Nanostructured probes for RNA detection in living cells
P Santangelo et al.
ANNALS OF BIOMEDICAL ENGINEERING (2006)
The kinetics of ligand binding by an adenine-sensing riboswitch
JK Wickiser et al.
BIOCHEMISTRY (2005)
Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding
NJ Baird et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
J Reeder et al.
BIOINFORMATICS (2005)
Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast
EM Mahen et al.
MOLECULAR CELL (2005)
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
JK Wickiser et al.
MOLECULAR CELL (2005)
RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE)
EJ Merino et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
KJ Doshi et al.
BMC BIOINFORMATICS (2004)
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
DH Mathews
RNA (2004)
How do RNA folding algorithms work?
SR Eddy
NATURE BIOTECHNOLOGY (2004)
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)
Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR
T Kubodera et al.
FEBS LETTERS (2003)
A statistical sampling algorithm for RNA secondary structure prediction
Y Ding et al.
NUCLEIC ACIDS RESEARCH (2003)
Solid-phase oligodeoxynucleotide synthesis: A two-step cycle using peroxy anion deprotection
AB Sierzchala et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
In vivo imaging of the dynamics of glucose uptake in the cytosol of COS-7 cells by fluorescent nanosensors
M Fehr et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme
P Rangan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
The chemical repertoire of natural ribozymes
JA Doudna et al.
NATURE (2002)
The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots
DM Chadalavada et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Productive folding to the native state by a group II intron ribozyme
JF Swisher et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Effects of magnesium ions on the stabilization of RNA oligomers of defined structures
MJ Serra et al.
RNA (2002)
Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer
NG Walter
METHODS (2001)
Thermodynamics of three-way multibranch loops in RNA
JM Diamond et al.
BIOCHEMISTRY (2001)
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
AP Minton
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
RNA conformation and folding studied with fluorescence resonance energy transfer
D Klostermeier et al.
METHODS (2001)
A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme
DM Chadalavada et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
The structural basis of ribosome activity in peptide bond synthesis
P Nissen et al.
SCIENCE (2000)
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA
SJ Schroeder et al.
BIOCHEMISTRY (2000)
A single-molecule study of RNA catalysis and folding
XW Zhuang et al.
SCIENCE (2000)
分享论文
