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Kevin Weeks

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Publications

TOP 3
Eva J Archer; Dorothy A Erie; Alex McPherson; Rory O'Kane; Mark A Simpson; Bangchen Wang; Nicholas J Watts; Kevin M Weeks
Long-range architecture in a viral RNA genome.
David M Mauger; Nathan A Siegfried; Kevin M Weeks
The genetic code as expressed through relationships between mRNA structure and protein function.
Jacob K Grohman; Colin R Lickwar; Jason D Lieb; Brian D Bower; Robert J Gorelick; Brent M Znosko; Kevin M Weeks
A guanosine-centric mechanism for RNA chaperone function.

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All Publications

2013: Eva J Archer; Dorothy A Erie; Alex McPherson; Rory O'Kane; Mark A Simpson; Bangchen Wang; Nicholas J Watts; Kevin M Weeks
Long-range architecture in a viral RNA genome.
Biochemistry 2013;52(18):3182-90.
2013: David M Mauger; Nathan A Siegfried; Kevin M Weeks
The genetic code as expressed through relationships between mRNA structure and protein function.
FEBS letters 2013;587(8):1180-8.
2013: Jacob K Grohman; Colin R Lickwar; Jason D Lieb; Brian D Bower; Robert J Gorelick; Brent M Znosko; Kevin M Weeks
A guanosine-centric mechanism for RNA chaperone function.
Science (New York, N.Y.) 2013;340(6129):190-5.
2013: Christine E Hajdin; Wayne Huggins; Christopher W Leonard; David H Mathews; Stanislav Bellaousov; Kevin M Weeks
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(14):5498-503.
2013: Elizabeth Pollom; E Lake Potter; Christina L Burch; Kristen K Dang; Robert J Gorelick; Kevin M Weeks; Ronald Swanstrom
Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs.
PLoS pathogens 2013;9(4):e1003294.
2013: Christopher W Leonard; David H Mathews; Nikolay V Dokholyan; Oleg V Favorov; Christine E Hajdin; Fethullah Karabiber; Kevin M Weeks
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.
Biochemistry 2013;52(4):588-95.
2013: Srinivas Ramachandran; Kevin M Weeks; Feng Ding; Nikolay V Dokholyan
Statistical analysis of SHAPE-directed RNA secondary structure modeling.
Biochemistry 2013;52(4):596-9.
2012: Kady-Ann Steen; Greggory M Rice; Kevin M Weeks
Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity.
Journal of the American Chemical Society 2012;134(32):13160-3.
2012: Feng Ding; Christopher A Lavender; Kevin M Weeks; Nikolay V Dokholyan
Three-dimensional RNA structure refinement by hydroxyl radical probing.
Nature methods 2012;9(6):603-8.
2012: Jennifer L McGinnis; Jamie H D Cate; Jack A Dunkle; Kevin M Weeks
The mechanisms of RNA SHAPE chemistry.
Journal of the American Chemical Society 2012;134(15):6617-24.
2012: Justin T Low; Olivier ter Brake; Joseph M Watts; Ben Berkhout; Stefanie A Knoepfel; Kevin M Weeks
SHAPE-directed discovery of potent shRNA inhibitors of HIV-1.
Molecular therapy : the journal of the American Society of Gene Therapy 2012;20(4):820-8.
2011: Kady-Ann Steen; Nathan A Siegfried; Kevin M Weeks
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA.
Nature protocols 2011;6(11):1683-94.
2011: Kevin M Weeks
RNA structure probing dash seq.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(27):10933-4.
2010: costin gherghe; Tania Lombo; Christopher W Leonard; Siddhartha A K Datta; Julian W Bess; Robert J Gorelick; Alan Rein; Kevin M Weeks
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(45):19248-53.
2010: David M Mauger; Kevin M Weeks
Toward global RNA structure analysis.
Nature biotechnology 2010;28(11):1178-9.
2010: Justin T Low; Kevin M Weeks
SHAPE-directed RNA secondary structure prediction.
Methods (San Diego, Calif.) 2010;52(2):150-8.
2010: Kady-Ann Steen; Arun Malhotra; Kevin M Weeks
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease.
Journal of the American Chemical Society 2010;132(29):9940-3.
2010: Caia D S Duncan; Kevin M Weeks
Nonhierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding.
Biochemistry 2010;49(26):5418-25.
2010: Christopher A Lavender; Feng Ding; Nikolay V Dokholyan; Kevin M Weeks
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain.
Biochemistry 2010;49(24):4931-3.
2010: Kevin M Weeks
Advances in RNA structure analysis by chemical probing.
Current opinion in structural biology 2010;20(3):295-304.
2010: Caia D S Duncan; Kevin M Weeks
The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs.
PloS one 2010;5(2):e8983.
2010: Cristina Gherghe; Christopher W Leonard; Robert J Gorelick; Kevin M Weeks
Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain.
Journal of virology 2010;84(2):898-906.
2009: Stefanie A Mortimer; Kevin M Weeks
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(37):15622-7.
2009: Joseph M Watts; Kristen K Dang; Robert J Gorelick; Christopher W Leonard; Julian W Bess; Ronald Swanstrom; Christina L Burch; Kevin M Weeks
Architecture and secondary structure of an entire HIV-1 RNA genome.
Nature 2009;460(7256):711-6.
2009: Kevin A Wilkinson; Suzy M Vasa; Katherine E Deigan; Stefanie A Mortimer; Morgan C Giddings; Kevin M Weeks
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA.
RNA (New York, N.Y.) 2009;15(7):1314-21.
2009: Stefanie A Mortimer; Jeffrey S Johnson; Kevin M Weeks
Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine.
Biochemistry 2009;48(10):2109-14.
2009: costin gherghe; Christopher W Leonard; Feng Ding; Nikolay V Dokholyan; Kevin M Weeks
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics.
Journal of the American Chemical Society 2009;131(7):2541-6.
2009: Katherine E Deigan; Tian W Li; David H Mathews; Kevin M Weeks
Accurate SHAPE-directed RNA structure determination.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(1):97-102.
2009: Stefanie A Mortimer; Kevin M Weeks
Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution.
Nature protocols 2009;4(10):1413-21.
2008: Stefanie A Mortimer; Kevin M Weeks
Time-resolved RNA SHAPE chemistry.
Journal of the American Chemical Society 2008;130(48):16178-80.
2008: Tuhin Subhra Maity; HM Fried; Kevin M Weeks
Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle.
The Biochemical journal 2008;415(3):429-37.
2008: Suzy M Vasa; Nicolas Guex; Kevin A Wilkinson; Kevin M Weeks; Morgan C Giddings
ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis.
RNA (New York, N.Y.) 2008;14(10):1979-90.
2008: Caia D S Duncan; Kevin M Weeks
SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA.
Biochemistry 2008;47(33):8504-13.
2008: costin gherghe; Stefanie A Mortimer; Joseph M Krahn; Nancy L Thompson; Kevin M Weeks
Slow conformational dynamics at C2'-endo nucleotides in RNA.
Journal of the American Chemical Society 2008;130(28):8884-5.
2008: Christie N Jones; Kevin A Wilkinson; Kimberly T Hung; Kevin M Weeks; Linda Spremulli
Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs.
RNA (New York, N.Y.) 2008;14(5):862-71.
2008: Kevin A Wilkinson; Robert J Gorelick; Suzy M Vasa; Nicolas Guex; Alan Rein; David H Mathews; Morgan C Giddings; Kevin M Weeks
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.
PLoS biology 2008;6(4):e96.
2008: Bin Wang; Kevin A Wilkinson; Kevin M Weeks
Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry.
Biochemistry 2008;47(11):3454-61.
2007: Tuhin Subhra Maity; Kevin M Weeks
A threefold RNA-protein interface in the signal recognition particle gates native complex assembly.
Journal of molecular biology 2007;369(2):512-24.
2007: Stefanie A Mortimer; Kevin M Weeks
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry.
Journal of the American Chemical Society 2007;129(14):4144-5.
2006: Tuhin Subhra Maity; Christopher W Leonard; Marsha A Rose; HM Fried; Kevin M Weeks
Compartmentalization directs assembly of the signal recognition particle.
Biochemistry 2006;45(50):14955-64.
2006: Costin M Gherghe; Kevin M Weeks
The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer.
The Journal of biological chemistry 2006;281(49):37952-61.
2006: Christopher S Badorrek; Kevin M Weeks
Architecture of a gamma retroviral genomic RNA dimer.
Biochemistry 2006;45(42):12664-72.
2006: Christopher S Badorrek; costin gherghe; Kevin M Weeks
Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(37):13640-5.
2006: Tian W Li; Kevin M Weeks
Structure-independent and quantitative ligation of single-stranded DNA.
Analytical biochemistry 2006;349(2):242-6.
2006: Kevin A Wilkinson; edward merino; Kevin M Weeks
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution.
Nature protocols 2006;1(3):1610-6.
2005: costin gherghe; Joseph M Krahn; Kevin M Weeks
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA.
Journal of the American Chemical Society 2005;127(39):13622-8.
2005: edward merino; Kevin M Weeks
Facile conversion of aptamers into sensors using a 2'-ribose-linked fluorophore.
Journal of the American Chemical Society 2005;127(37):12766-7.
2005: Antonella Longo; Christopher W Leonard; Gurminder S Bassi; Daniel Berndt; Joseph M Krahn; Traci M Tanaka Hall; Kevin M Weeks
Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.
Nature structural & molecular biology 2005;12(9):779-87.
2005: Christopher S Badorrek; Kevin M Weeks
RNA flexibility in the dimerization domain of a gamma retrovirus.
Nature chemical biology 2005;1(2):104-11.
2005: Kevin A Wilkinson; edward merino; Kevin M Weeks
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts.
Journal of the American Chemical Society 2005;127(13):4659-67.
2005: edward merino; Kevin A Wilkinson; Jennifer L Coughlan; Kevin M Weeks
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).
Journal of the American Chemical Society 2005;127(12):4223-31.
2004: Ivelitza Garcia; Kevin M Weeks
Structural basis for the self-chaperoning function of an RNA collapsed state.
Biochemistry 2004;43(48):15179-86.
2004: Deborah M John; edward merino; Kevin M Weeks
Mechanics of DNA flexibility visualized by selective 2'-amine acylation at nucleotide bulges.
Journal of molecular biology 2004;337(3):611-9.
2004: Karen L Buchmueller; Kevin M Weeks
Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies.
Nucleic acids research 2004;32(22):e184.
2003: Karen L Buchmueller; Kevin M Weeks
Near native structure in an RNA collapsed state.
Biochemistry 2003;42(47):13869-78.
2003: edward merino; Kevin M Weeks
Fluorogenic resolution of ligand binding by a nucleic acid aptamer.
Journal of the American Chemical Society 2003;125(41):12370-1.
2003: Karen L Buchmueller; Brian T Hill; Matthew S Platz; Kevin M Weeks
RNA-tethered phenyl azide photocrosslinking via a short-lived indiscriminant electrophile.
Journal of the American Chemical Society 2003;125(36):10850-61.
2003: Gurminder S Bassi; Kevin M Weeks
Kinetic and thermodynamic framework for assembly of the six-component bI3 group I intron ribonucleoprotein catalyst.
Biochemistry 2003;42(33):9980-8.
2003: Ivelitza Garcia; Kevin M Weeks
Small structural costs for evolution from RNA to RNP-based catalysis.
Journal of molecular biology 2003;331(1):57-73.
2003: Stacy I Chamberlin; Kevin M Weeks
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;42(4):901-9.
2002: Stacy I Chamberlin; edward merino; Kevin M Weeks
Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(23):14688-93.
2002: Deborah M John; Kevin M Weeks
Chemical interrogation of mismatches in DNA-DNA and DNA-RNA duplexes under nonstringent conditions by selective 2'-amine acylation.
Biochemistry 2002;41(21):6866-74.
2002: Gurminder S Bassi; Daniela M de Oliveira; Malcolm White; Kevin M Weeks
Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(1):128-33.
2001: AE Webb; Marsha A Rose; E Westhof; Kevin M Weeks
Protein-dependent transition states for ribonucleoprotein assembly.
Journal of molecular biology 2001;309(5):1087-100.
2001: Marsha A Rose; Kevin M Weeks
Visualizing induced fit in early assembly of the human signal recognition particle.
Nature structural biology 2001;8(6):515-20.
2001: AE Webb; Kevin M Weeks
A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex.
Nature structural biology 2001;8(2):135-40.
2000: Deborah M John; Kevin M Weeks
van't Hoff enthalpies without baselines.
Protein science : a publication of the Protein Society 2000;9(7):1416-9.
2000: Deborah M John; Kevin M Weeks
Tagging DNA mismatches by selective 2'-amine acylation.
Chemistry & biology 2000;7(6):405-10.
2000: Karen L Buchmueller; AE Webb; D A Richardson; Kevin M Weeks
A collapsed non-native RNA folding state.
Nature structural biology 2000;7(5):362-6.
1997: Kevin M Weeks
Protein-facilitated RNA folding.
Current opinion in structural biology 1997;7(3):336-42.