SHAPE-directed RNA secondary structure prediction.

PubWeight™: 2.40‹?› | Rank: Top 2%

🔗 View Article (PMC 2941709)

Published in Methods on June 08, 2010

Authors

Justin T Low1, Kevin M Weeks

Author Affiliations

1: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-3290, USA.

Articles citing this

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods (2010) 2.71

Exploring RNA structural codes with SHAPE chemistry. Acc Chem Res (2011) 1.78

The mechanisms of RNA SHAPE chemistry. J Am Chem Soc (2012) 1.52

Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A (2011) 1.49

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res (2012) 1.30

An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (2012) 1.19

RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA (2014) 1.18

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16

Simplified RNA secondary structure mapping by automation of SHAPE data analysis. Nucleic Acids Res (2011) 1.12

The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. Wiley Interdiscip Rev RNA (2012) 1.12

RNA-guided assembly of Rev-RRE nuclear export complexes. Elife (2014) 1.11

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. Annu Rev Biophys (2014) 1.08

HOTAIR forms an intricate and modular secondary structure. Mol Cell (2015) 1.08

Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res (2012) 1.08

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc (2013) 1.05

Correlating SHAPE signatures with three-dimensional RNA structures. RNA (2011) 1.03

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic Acids Res (2014) 1.02

High-affinity recognition of HIV-1 frameshift-stimulating RNA alters frameshifting in vitro and interferes with HIV-1 infectivity. J Med Chem (2014) 1.01

Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res (2011) 0.99

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLoS Genet (2015) 0.98

Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7). RNA (2013) 0.95

Autoregulated splicing of muscleblind-like 1 (MBNL1) Pre-mRNA. J Biol Chem (2011) 0.94

The centrality of RNA for engineering gene expression. Biotechnol J (2013) 0.94

Positional effects of AAN motifs in rpoS regulation by sRNAs and Hfq. J Mol Biol (2013) 0.94

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nat Methods (2012) 0.93

Structural map of a microRNA-122: hepatitis C virus complex. J Virol (2011) 0.92

Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome. J Am Chem Soc (2011) 0.90

Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. RNA (2013) 0.89

Slow formation of stable complexes during coincubation of minimal rRNA and ribosomal protein S4. J Mol Biol (2011) 0.88

Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res (2011) 0.86

A proposal for a new HIV-1 DLS structural model. Nucleic Acids Res (2012) 0.86

Global organization of a positive-strand RNA virus genome. PLoS Pathog (2013) 0.86

Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Mol Plant Pathol (2011) 0.86

Long-range architecture in a viral RNA genome. Biochemistry (2013) 0.86

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. RNA (2015) 0.85

Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol (2015) 0.85

Specific contacts between protein S4 and ribosomal RNA are required at multiple stages of ribosome assembly. RNA (2013) 0.84

Efficient detection of hydrogen bonds in dynamic regions of RNA by sensitivity-optimized NMR pulse sequences. Angew Chem Int Ed Engl (2013) 0.83

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic Acids Res (2015) 0.83

iFoldRNA v2: folding RNA with constraints. Bioinformatics (2015) 0.83

Highly conserved RNA pseudoknots at the Gag-Pol junction of HIV-1 suggest a novel mechanism of -1 ribosomal frameshifting. RNA (2014) 0.82

Physics-based RNA structure prediction. Biophys Rep (2015) 0.81

Rational experiment design for sequencing-based RNA structure mapping. RNA (2014) 0.81

The 3' untranslated region of Pea Enation Mosaic Virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers. J Virol (2014) 0.81

Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity. J Virol (2013) 0.81

Nucleic acid structure characterization by small angle X-ray scattering (SAXS). Curr Protoc Nucleic Acid Chem (2012) 0.81

Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun (2016) 0.80

RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA. Proc Natl Acad Sci U S A (2015) 0.80

Requirement for Host RNA-Silencing Components and the Virus-Silencing Suppressor when Second-Site Mutations Compensate for Structural Defects in the 3' Untranslated Region. J Virol (2015) 0.80

An immature retroviral RNA genome resembles a kinetically trapped intermediate state. J Virol (2014) 0.80

The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates. Nucleic Acids Res (2013) 0.80

Hepatitis delta antigen requires a flexible quasi-double-stranded RNA structure to bind and condense hepatitis delta virus RNA in a ribonucleoprotein complex. J Virol (2014) 0.79

Progress and outlook in structural biology of large viral RNAs. Virus Res (2014) 0.79

Structural analyses of Avocado sunblotch viroid reveal differences in the folding of plus and minus RNA strands. Viruses (2014) 0.79

Splicing regulation in spinal muscular atrophy by an RNA structure formed by long-distance interactions. Ann N Y Acad Sci (2015) 0.79

The matrix domain contributes to the nucleic acid chaperone activity of HIV-2 Gag. Retrovirology (2016) 0.79

Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing. RNA (2013) 0.79

Visualizing the secondary and tertiary architectural domains of lncRNA RepA. Nat Chem Biol (2017) 0.78

Data-directed RNA secondary structure prediction using probabilistic modeling. RNA (2016) 0.78

Direct updating of an RNA base-pairing probability matrix with marginal probability constraints. J Comput Biol (2012) 0.78

Secondary structure of the Irf7 5'-UTR, analyzed using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension). BMB Rep (2014) 0.77

Bioinformatics of prokaryotic RNAs. RNA Biol (2014) 0.77

The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs. Sci Rep (2016) 0.77

RNA secondary structure prediction using high-throughput SHAPE. J Vis Exp (2013) 0.77

Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Methods (2016) 0.77

Structural analysis of adenovirus VAI RNA defines the mechanism of inhibition of PKR. Biophys J (2015) 0.77

RNA structure replaces the need for U2AF2 in splicing. Genome Res (2015) 0.77

Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing. J Comput Biol (2014) 0.76

Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem (2016) 0.75

A 3'-end structure in RNA2 of a crinivirus is essential for viral RNA synthesis and contributes to replication-associated translation activity. Sci Rep (2016) 0.75

Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data. PLoS One (2016) 0.75

Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. RNA (2017) 0.75

Metrics for rapid quality control in RNA structure probing experiments. Bioinformatics (2016) 0.75

Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D. J Virol (2017) 0.75

A peak alignment algorithm with novel improvements in application to electropherogram analysis. J Bioinform Comput Biol (2013) 0.75

Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol (2014) 0.75

Biologically-supported structural model for a viral satellite RNA. Nucleic Acids Res (2015) 0.75

The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation. Nucleic Acids Res (2015) 0.75

Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments. Nat Methods (2016) 0.75

Articles cited by this

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res (1981) 61.59

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48

On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol (1990) 10.85

Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature (1988) 10.69

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry (1998) 9.75

Probing the structure of RNAs in solution. Nucleic Acids Res (1987) 7.62

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46

How RNA folds. J Mol Biol (1999) 6.14

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14

Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12

Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44

A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol (2008) 4.40

CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics (2006) 4.31

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA (2008) 3.46

Predicting thermodynamic properties of RNA. Methods Enzymol (1995) 3.38

HIV expression strategies: ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems. Cell (1988) 3.36

Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol (2006) 3.36

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science (2003) 3.32

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol (1974) 3.25

Direct observation of hierarchical folding in single riboswitch aptamers. Science (2008) 3.22

The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol (2002) 3.11

Ribosomal pausing during translation of an RNA pseudoknot. Mol Cell Biol (1993) 2.81

Enzymatic approaches to probing of RNA secondary and tertiary structure. Methods Enzymol (1989) 2.80

In-line probing analysis of riboswitches. Methods Mol Biol (2008) 2.76

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics (2004) 2.57

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res (2009) 2.49

Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. Gene (1989) 2.45

Bridging the gap in RNA structure prediction. Curr Opin Struct Biol (2007) 2.41

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26

RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol (2005) 2.19

Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity. J Virol (2001) 2.16

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry (1993) 2.13

Mapping nucleic acid structure by hydroxyl radical cleavage. Curr Opin Chem Biol (2005) 2.06

Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science (2010) 2.00

Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency. Mol Cell Biol (2001) 1.93

tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol (2007) 1.84

Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1. Nucleic Acids Res (2002) 1.70

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA (2009) 1.68

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA (1997) 1.68

Structural principles from large RNAs. Annu Rev Biophys (2008) 1.65

Architecture of a gamma retroviral genomic RNA dimer. Biochemistry (2006) 1.64

On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61

Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat Protoc (2009) 1.60

A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol (2007) 1.56

How do RNA folding algorithms work? Nat Biotechnol (2004) 1.56

Local RNA structural changes induced by crystallization are revealed by SHAPE. RNA (2007) 1.55

Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry. Biochemistry (2008) 1.55

SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry (2008) 1.51

Structure of stem-loop IV of Tetrahymena telomerase RNA. EMBO J (2006) 1.49

Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV. Virus Res (2005) 1.48

Thermodynamics of base pairing. Curr Opin Struct Biol (1996) 1.44

Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc Natl Acad Sci U S A (2006) 1.43

Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. J Mol Biol (2005) 1.42

High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol (2009) 1.38

A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch. J Mol Biol (2008) 1.31

Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs. RNA (2008) 1.25

Beyond Mfold: recent advances in RNA bioinformatics. J Biotechnol (2006) 1.23

Extracting stacking interaction parameters for RNA from the data set of native structures. J Mol Biol (2005) 1.22

Structure of the RNA signal essential for translational frameshifting in HIV-1. J Mol Biol (2005) 1.20

Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: a model for a possible family of structurally related RNA pseudoknots. Biochemistry (1996) 1.16

Structure of a viral cap-independent translation element that functions via high affinity binding to the eIF4E subunit of eIF4F. J Biol Chem (2009) 1.13

The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem (2006) 1.11

Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain. J Virol (2009) 1.09

Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol (2009) 1.09

The frameshift stimulatory signal of human immunodeficiency virus type 1 group O is a pseudoknot. J Mol Biol (2003) 1.02

Selection of peptides interfering with a ribosomal frameshift in the human immunodeficiency virus type 1. RNA (2008) 1.01

A basis for new approaches to the chemotherapy of AIDS: novel genes in HIV-1 potentially encode selenoproteins expressed by ribosomal frameshifting and termination suppression. J Med Chem (1994) 0.96

Structural characterization of the Rous sarcoma virus RNA stability element. J Virol (2008) 0.92

Ribosomal frameshifting: an emerging drug target for HIV. Curr Opin Investig Drugs (2009) 0.89

Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol (2009) 0.86

Articles by these authors

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14

Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12

Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44

A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol (2008) 4.40

ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA (2008) 3.46

RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J Am Chem Soc (2005) 2.92

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26

RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol (2005) 2.19

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc Natl Acad Sci U S A (2013) 2.11

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA (2009) 1.68

Architecture of a gamma retroviral genomic RNA dimer. Biochemistry (2006) 1.64

On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61

QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA (2012) 1.60

Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat Protoc (2009) 1.60

Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry. Biochemistry (2008) 1.55

The mechanisms of RNA SHAPE chemistry. J Am Chem Soc (2012) 1.52

SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry (2008) 1.51

Time-resolved RNA SHAPE chemistry. J Am Chem Soc (2008) 1.48

Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome. Proc Natl Acad Sci U S A (2010) 1.46

Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc Natl Acad Sci U S A (2006) 1.43

High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol (2009) 1.38

The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry (2013) 1.38

Slow conformational dynamics at C2'-endo nucleotides in RNA. J Am Chem Soc (2008) 1.35

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33

Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs. RNA (2008) 1.25

Sharing and archiving nucleic acid structure mapping data. RNA (2011) 1.20

Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20

Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc (2012) 1.18

Two distinct binding modes of a protein cofactor with its target RNA. J Mol Biol (2006) 1.17

Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proc Natl Acad Sci U S A (2002) 1.16

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16

C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain. Proc Natl Acad Sci U S A (2009) 1.16

Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13

The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem (2006) 1.11

SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. Mol Ther (2012) 1.11

Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain. J Virol (2009) 1.09

Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs. PLoS Pathog (2013) 1.08

Near native structure in an RNA collapsed state. Biochemistry (2003) 1.06

Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. J Am Chem Soc (2010) 1.06

Structure-independent and quantitative ligation of single-stranded DNA. Anal Biochem (2005) 1.04

Ribosome RNA assembly intermediates visualized in living cells. Biochemistry (2014) 1.03

A guanosine-centric mechanism for RNA chaperone function. Science (2013) 1.03

Toward global RNA structure analysis. Nat Biotechnol (2010) 1.02

RNA structures facilitate recombination-mediated gene swapping in HIV-1. J Virol (2010) 0.99

RNA-tethered phenyl azide photocrosslinking via a short-lived indiscriminant electrophile. J Am Chem Soc (2003) 0.99

Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry (2010) 0.98

Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA. Biochemistry (2003) 0.98

Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nat Struct Mol Biol (2005) 0.97

Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups. Proc Natl Acad Sci U S A (2002) 0.96

The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One (2010) 0.93

Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA. Nat Protoc (2011) 0.93

Kinetic and thermodynamic framework for assembly of the six-component bI3 group I intron ribonucleoprotein catalyst. Biochemistry (2003) 0.92

Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome. J Am Chem Soc (2011) 0.90

A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J Mol Biol (2007) 0.90

Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine. Biochemistry (2009) 0.89

Structural basis for the self-chaperoning function of an RNA collapsed state. Biochemistry (2004) 0.87

Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry (2014) 0.87

Compartmentalization directs assembly of the signal recognition particle. Biochemistry (2006) 0.87

Long-range architecture in a viral RNA genome. Biochemistry (2013) 0.86

Chemical interrogation of mismatches in DNA-DNA and DNA-RNA duplexes under nonstringent conditions by selective 2'-amine acylation. Biochemistry (2002) 0.85

Statistical analysis of SHAPE-directed RNA secondary structure modeling. Biochemistry (2013) 0.85

Fluorogenic resolution of ligand binding by a nucleic acid aptamer. J Am Chem Soc (2003) 0.83

Role of context in RNA structure: flanking sequences reconfigure CAG motif folding in huntingtin exon 1 transcripts. Biochemistry (2013) 0.82

Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA. J Am Chem Soc (2005) 0.81

Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies. Nucleic Acids Res (2004) 0.80

An immature retroviral RNA genome resembles a kinetically trapped intermediate state. J Virol (2014) 0.80

Mechanics of DNA flexibility visualized by selective 2'-amine acylation at nucleotide bulges. J Mol Biol (2004) 0.78

Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle. Biochem J (2008) 0.78

Small structural costs for evolution from RNA to RNP-based catalysis. J Mol Biol (2003) 0.77

Facile conversion of aptamers into sensors using a 2'-ribose-linked fluorophore. J Am Chem Soc (2005) 0.77

RNA tertiary structure analysis by 2'-hydroxyl molecular interference. Biochemistry (2014) 0.77