Publications
Publications
2024
162. L. Chen, N.T. Ingolia, M.L. Insco, J.B. Li, S. Oberdoerffer, and K.M. Weeks, Voices: challenges and opportunities in RNA biology. Cell Chem. Biol. 30, 10-13 (2024)
161. B.M. Hatfield, C.A. Weidmann and K.M. Weeks, Measuring proximity-mediated function of mRNA regulatory proteins by engineered tethering. Methods Mol. Biol. 2723, 143-159 (2024). pdf
2023
160. Y. Xiang, W. Huang, L. Tan, T. Chen, Y. He, P.S. Irving, K.M. Weeks, Q.C. Zhang and X. Dong, Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature. 621, 423–430 (2023) pdf
159. P.S. Irving and K.M. Weeks, RNAvigate: Efficient exploration of RNA chemical probing datasets. bioRxiv 2023.04.25.538311 (2023).
158. M.A. Boerneke, N.S. Gokhale, S.M. Horner and K.M. Weeks, Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication. Proc. Natl. Acad. Sci. USA 120, e2217053120 (2023). pdf
157. A.M. Mustoe, C.A. Weidmann and K.M. Weeks, Single-molecule correlated chemical probing: A revolution in RNA structure analysis. Acc. Chem. Res. 56, 763-775 (2023). pdf
156. J.T. Koehn, S. Felder and K.M. Weeks, Innovations in targeting RNA, by fragment-based ligand discovery. Curr. Opin. Struct. Biol. 79, 102550 (2023). pdf
2022
155. P.J. Grayeski, C.A. Weidmann, J. Kumar, L. Lackey, A.M. Mustoe, S. Busan, A. Laederach and K.M. Weeks, Global 5′-UTR RNA structure regulates translation of a SERPINA1 mRNA. Nucl. Acids Res. 50, 9689-9704 (2022). pdf
154. C.A. Roden, Y. Dai, C.A. Giannetti, I. Seim, M. Lee, R. Sealfon, G.A. McLaughlin, M.A. Boerneke, C. Iserman, S.A. Wey, J.L Ekena, O.G. Troyanskaya, K.M. Weeks, L. You, A. Chilkoti and A.S. Gladfelter, Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucl. Acids Res. 50, 8168-8192 (2022). pdf
153. J.W. Arney and K.M. Weeks, RNA-ligand interactions quantified by surface plasmon resonance with reference subtraction. Biochemistry 61, 1625-1632 (2022). pdf
152. J. Kumar, L. Lackey, J.M. Waldern, A. Dey, A.M. Mustoe, K.M. Weeks, D.H. Mathews and A. Laederach, Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 11, e73888 (2022). pdf
151. M.J. Zeller, O. Favorov, K. Li, A. Nuthanakanti, D. Hussein, A. Michaud, D.A. Lafontaine, S. Busan, A. Serganov, J. Aubé and Kevin M. Weeks, SHAPE-enabled fragment-based ligand discovery for RNA. Proc. Natl. Acad. Sci. USA 119, e2122660119 (2022). pdf
150. S.W. Olson, A.-M.W. Turner, J.W. Arney, I. Saleem, C.A. Weidmann, D.M. Margolis, K.M. Weeks and A.M. Mustoe, Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol. Cell 82, 1708-1723 (2022). pdf
149. M.J. Zeller, A. Nuthanakanti, K. Li, J. Aubé, A. Serganov and K.M. Weeks, Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery. ACS Chem. Biol. (2022). pdf
148. W. Stephenson, R. Razaghi, S. Busan, K.M. Weeks, W. Timp and P. Smibert, Direct detection of RNA modifications and structure using single-molecule nanopore sequencing. Cell Genomics 2, 100097 (2022). pdf
147. R.K. Przanowska, C.A. Weidmann, S. Saha, M.A. Cichewicz, K.N. Jensen, P. Przanowski, P.S. Irving, K.A. Janes, M.J. Guertin, K.M. Weeks and A. Dutta, Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep. 38, 110361 (2022). pdf
2021
146. K.M. Weeks, Piercing the fog of the RNA structure-ome. Science 373, 964-965 (2021). pdf
145. T.W. Christy, C.A. Giannetti, A. Laederach and K.M. Weeks, Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. PLoS Comput. Biol. 17, e1009632 (2021). pdf
144. T.W. Christy, C.A. Giannetti, G. Houlihan, M.J. Smola, G.M. Rice, J. Wang, N.V. Dokholyan, A. Laederach, P. Holliger and K.M. Weeks, Direct mapping of higher-order RNA interactions by SHAPE-JuMP. Biochemistry 60, 1971-1982 (2021). pdf
143. K.M. Weeks, SHAPE directed discovery of new functions in large RNAs. Acc. Chem. Res. 54, 2502-2517 (2021). pdf
142. C.A. Weidman, A.M. Mustoe, P.B. Jariwala, J. M. Calabrese and Kevin M. Weeks, Analysis of RNA-protein networks with RNP-MaP defines functional hubs on RNA. Nature Biotech. 39, 347-356 (2021). pdf
141. S. Busan and K.M. Weeks, Visualization of lncRNA and mRNA structure models within the Integrative Genomics Viewer. Methods Mol. Biol. 2254, 15-25 (2021). pdf
2020
140. C. Iserman, C.A. Roden, M.A. Boerneke, R.S.G. Sealfon, G.A. McLaughlin, I. Jungreis, E.J. Fritch, Y.J. Hou, J. Ekena, C.A. Weidmann, C.L. Theesfeld, M. Kellis, O.G. Troyanskaya, R.S. Baric, T.P. Sheahan, K.M. Weeks and A.S. Gladfelter, Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid. Mol. Cell 80, 1078-1091 (2020). pdf
139. J.E. Ehrhardt and K.M. Weeks, Time-resolved, Single-molecule, correlated chemical probing of RNA. J. Am. Chem. Soc. 142, 18735-18740 (2020). pdf
138. K. Schmidt, C.A. Weidmann, T.A. Hilimire, E. Yee, B.M. Hatfield, J.S. Schneekloth, K.M. Weeks and C.D. Novina, Targeting the oncogenic long non-coding RNA SLNCR1 by blocking its sequence-specific binding to the androgen receptor. Cell Rep. 30, 541-554 (2020). pdf
2019
137. A.M. Mustoe, N.N. Lama, P.S. Irving, S.W. Olson and K.M. Weeks, RNA base-pairing complexity in living cells visualized by correlated chemical probing. Proc. Natl. Acad. Sci. USA 116, 24574-24582 (2019). pdf
136. A. Sengupta, G.M. Rice and K.M. Weeks, Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells. PLoS Biol. 17, e3000393 (2019). pdf
135. M.A. Boerneke, J.E. Ehrhardt and K.M. Weeks, Physical and functional analysis of viral RNA genomes by SHAPE. Annu. Rev. Virol. 6, 93–117 (2019). pdf
134. C.A. Giannetti, S. Busan, C.A. Weidmann and K.M. Weeks, SHAPE probing reveals human rRNAs are largely unfolded in solution. Biochemistry 58, 3377-3385 (2019). pdf
133. E.A. Dethoff and K.M. Weeks, Effects of refolding on large-scale RNA structure. Biochemistry 58, 3069-3077 (2019). pdf
132. S. Busan, C.A. Weidmann, A. Sengupta and K.M. Weeks, Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry 58, 2655-2664 (2019). pdf
2018
131. M.A. Boerneke and K.M. Weeks, High-throughput explorations of RNA structural modularity. Biochemistry 57, 6129-6131 (2018). pdf
130. E.A. Dethoff, M.A. Boerneke, N.S. Gokhale, B.M. Muhire, D.P. Martin, M.T. Sacco, M.J. McFadden, J.B. Weinstein, W.B. Messer, S.M. Horner and K.M. Weeks, Pervasive tertiary structure in the dengue virus RNA genome. Proc. Natl. Acad. Sci. USA 115, 11513-11518 (2018). pdf | SI | data
129. J.M. Kirk, S.O. Kim, K. Inoue, M.J. Smola, D.M. Lee, M.D. Schertzer, J.S. Wooten, A.R. Baker, D. Sprague, D.W. Collins, C.R. Horning, S. Wang, Q. Chen, K.M. Weeks, P.J. Mucha and J.M. Calabrese, Functional classification of long non-coding RNAs by k-mer content. Nature Genet. 50, 1474-1482 (2018). pdf
128. K.D. Warner, C.E. Hajdin and K.M. Weeks, Principles for targeting RNA with drug-like small molecules. Nature Rev. Drug Discov. 17, 547-558 (2018). pdf
127. A.M. Mustoe, M. Corley, A. Laederach and K.M. Weeks, mRNA structure regulates translation initiation: A mechanism exploited from bacteria to humans. Biochemistry 57, 3537-3539 (2018). pdf
126. E.M. Langdon, Y. Qiu, N.A. Ghanbari, G.A. McLaughlin, C.A. Weidmann, T.M. Gerbich, J.A. Smith, J.M. Crutchley, C.M. Termini, K.M. Weeks, S. Myong and A. Gladfelter, mRNA structure determines specificity of a polyQ-driven phase separation. Science 360, 922-927 (2018). pdf
125. M.J. Smola and K.M. Weeks, In-cell RNA structure probing with SHAPE-MaP. Nature Prot. 13, 1181-1195 (2018). pdf
124. A.M. Mustoe, S. Busan, G.M. Rice, C.E. Hajdin, B.K. Peterson, V.M. Ruda, N. Kubica, R. Nutiu, J.L. Baryza and K.M. Weeks, Pervasive regulatory functions of mRNA structure revealed by high-resolution SHAPE probing. Cell 173, 181-195 (2018). pdf | data
123. Y. Liu, J. Chen, O.A. Nikolaitchik, B.A. Desimmie, S. Busan, V.K. Pathak, K.M. Weeks and W.S. Hu, The roles of five conserved lentiviral RNA structures in HIV-1 replication. Virol. 514, 1-8 (2018). pdf
122. S. Busan and K.M. Weeks, Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 24, 143-148 (2018). pdf | ShapeMapper software
2017
121. B. Williams, B. Zhao, A. Tandon, F. Ding, K.M. Weeks, Q. Zhang and N.V. Dokholyan, Structure modeling of RNA using sparse NMR constraints. Nucl. Acids Res. 45, 45, 12638-12647 (2017). pdf
120. M. Corley, A. Solem, G. Phillips, L. Lackey, B. Ziehr, H.A. Vincent, A.M. Mustoe, S.B.V Ramos, K.M. Weeks, N.J. Moorman and A. Laederach, An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc. Natl. Acad. Sci. USA 114, E10244 (2017). pdf
119. S. Busan and K.M. Weeks, Visualization of RNA structure models within the Integrative Genomics Viewer. RNA 23, 1012-1018 (2017). pdf
118. B.C. Larman, E.A. Dethoff and K.M. Weeks, Packaged and free STMV RNA genomes adopt distinct conformational states. Biochemistry 56, 2175-2183 (2017).pdf
117. Z. Miao et al. [N.V. Dokholyan, G.M. Rice, B. Williams, K.M. Weeks, and 40 others] and E. Westhof, RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA 23, 655-672 (2017). pdf
116. A. Krokhotin, A.M. Mustoe, K.M. Weeks and N.V. Dokholyan, Direct detection of base-paired RNA nucleotides by correlated chemical probing. RNA 23, 6-13 (2017). pdf
2016
115. M.J. Smola, T.W. Christy, K. Inoue, C.O. Nicholson, M. Friedersdorf, J.D. Keene, D.M. Lee, J.M. Calabrese and K.M. Weeks, SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells. Proc. Natl. Acad. Sci. USA 113, 10322-10327 (2016). pdf | data
114. C.A. Weidmann, A.M. Mustoe and K.M. Weeks, Direct duplex detection: An emerging tool in the RNA structure analysis toolbox. Trends Biochem. Sci. 41, 734-736 (2016). pdf
113. A.T. Kariisa, K.M. Weeks and R. Tamayo, The RNA domain Vc1 regulates downstream gene expression in response to cyclic diguanylate in Vibrio cholerae. PLoS One 11, e0148478 (2016). pdf
2015
112. M.J. Smola, J.M. Calabrese and K.M. Weeks, Detection of RNA-protein interactions in living cells with SHAPE. Biochemistry 54, 6867-6875 (2015). pdf | data | software
111. Y.F. Lu, D.M. Mauger, D.B. Goldstein, T.J. Urban, K.M. Weeks and S.S. Bradrick, IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance. Sci. Rep. 5, 16037 (2015). pdf
110. J. Tyrrell, K.M. Weeks and G.J. Pielak, Challenge of mimicking the influences of the cellular environment on RNA structure by PEG-induced macromolecular crowding. Biochemistry 54, 6447-6453 (2015). pdf | data
109. M.J. Smola, G.M. Rice, S. Busan, N.A. Siegfried and K.M. Weeks, Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis. Nature Protoc. 10, 1643-1669 (2015). pdf
108. K.M. Kutchko, W. Sanders, B. Ziehr, G. Phillips, A. Solem, M. Halvorsen, K.M. Weeks, N. Moorman and A. Laederach, Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR. RNA 21, 1274-1285 (2015). pdf | data
107. K.M. Weeks, RNA clubs. RNA 21, 760-761 (2015). pdf
106. D.M. Mauger, M. Golden, D. Yamane, S. Willford, S.M. Lemon, D.P. Martin and K.M. Weeks, The functionally conserved architecture of hepatitis C virus RNA genomes. Proc. Natl. Acad. Sci. USA 112, 3692-3697 (2015). pdf | data
105. J.L. McGinnis, Q. Liu, C.A. Lavender, A. Devaraj, S.P. McClory, K. Fredrick and K.M. Weeks, In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state. Proc. Natl. Acad. Sci. USA 112, 2425-2430 (2015). pdf | data
104. C.A. Lavender, R.J. Gorelick and K.M. Weeks, Structure-based alignment and consensus secondary structures for three HIV-related RNA genomes. PLoS Comput. Biol. 11, e1004230 (2015). pdf | data
103. C.A. Lavender, R. Lorenz, G. Zhang, R. Tamayo, I.L. Hofacker and K.M. Weeks, Model-free RNA sequence and structure alignment informed by SHAPE probing reveals a conserved alternative secondary structure for 16S rRNA. PLoS Comput. Biol. 11, e1004126 (2015). pdf | data
102. K.M. Weeks, Toward all RNA structures, concisely. Biopolymers 103, 438-448 (2015). pdf
101. A.I. Taylor, V.B. Pinheiro, M.J. Smola, A.S. Morgunov, S. Peak-Chew, C. Cozens, K.M. Weeks, P. Herdewijn & P. Holliger, Catalysts from synthetic genetic polymers. Nature 518, 427-430 (2015). pdf
2014
100. P.J. Homan, A. Tandon, G.M. Rice, F. Ding, N.V. Dokholyan and K.M. Weeks, RNA tertiary structure analysis by 2′-hydroxyl molecular interference. Biochemistry 53, 6825-6833 (2014). pdf
99. P.J. Homan, O.V. Favorov, C.A. Lavender, O. Kursun, X. Ge, S. Busan, N.V. Dokholyan and K.M. Weeks, Single-molecule correlated chemical probing of RNA. Proc. Natl. Acad. Sci. USA 111, 13858-13863 (2014). pdf | data | software
98. N.A. Siegfried, S. Busan, G.M. Rice, J.A.E. Nelson and K.M. Weeks, RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nature Meths. 11, 959-965 (2014). pdf | data | software
97. J.T. Low, P. Garcia-Miranda, K.D. Mouzakis, R.J. Gorelick, S.E. Butcher and K.M. Weeks, Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry 53, 4282-4291 (2014). pdf
96. G.M. Rice, S. Busan, F. Karabiber, O.V. Favorov and K.M. Weeks, SHAPE analysis of small RNAs and riboswitches. Methods Enzymol. 549, 165-187 (2014). pdf | software
95. J.L. McGinnis and K.M. Weeks, Ribosomal RNA assembly intermediates visualized in living cells. Biochemistry 53, 3237-3247 (2014). pdf | data
94. K.D. Warner, P. Homan, K.M. Weeks, A.G. Smith, C. Abell & A.R. Ferré-D’Amaré, Validating fragment-based drug discovery for biological RNAs: Lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595 (2014). pdf
93. J.K. Grohman, R.J. Gorelick, S. Kottegoda, N.L. Allbritton, A. Rein and K.M. Weeks, An immature retroviral RNA genome resembles a kinetically trapped intermediate state. J. Virol. 88, 6061–6068 (2014). pdf
92. G.M. Rice, C.W. Leonard and K.M. Weeks, RNA secondary structure modeling at consistent high accuracy using differential SHAPE. RNA 20, 846-854 (2014). pdf | data | software
2013
91. J. Tyrrell, J.L. McGinnis, K.M. Weeks and G.J. Pielak, The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry 52, 8777-8785 (2013). pdf
90. S. Busan and K.M. Weeks, The role of context in RNA structure: flanking sequences reconfigure CAG motif folding in huntingtin exon 1 transcripts. Biochemistry 52, 8219-8225 (2013). pdf
89. E.J. Archer, M.A. Simpson, N.J. Watts, R. O’Kane, B. Wang, D.A. Erie, A. McPherson and K.M. Weeks, Long-range architecture in a viral RNA genome. Biochemistry 52, 3182-3190 (2013). pdf | data
88. E. Pollom, K.K. Dang, E.L. Potter, R.J. Gorelick, C.L. Burch, K.M. Weeks and R. Swanstrom, Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs. PLoS Path. 9, e1003294 (2013). pdf
87. D.M. Mauger, N.A. Siegfried and K.M. Weeks, The genetic code as expressed through relationships between mRNA structure and protein function. FEBS Lett. 587, 1180-1188 (2013). pdf
86. C.E. Hajdin, S. Bellaousov, W. Huggins, C.W. Leonard, D.H. Mathews and K.M. Weeks, Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc. Natl. Acad. Sci. USA 110, 5498-5503 (2013). pdf | data
85. J.K. Grohman, R.J. Gorelick, C.R. Lickwar, J.D. Lieb, B.D. Bower, B.M. Znosko and K.M. Weeks, A guanosine-centric mechanism for RNA chaperone function. Science 340, 190-195 (2013). pdf
84. S. Ramachandran, F. Ding, K.M. Weeks and N.V. Dokholyan, Statistical analysis of SHAPE-directed RNA secondary structure modeling. Biochemistry 52, 596-599 (2013). pdf
83. C.W. Leonard, C.E. Hajdin, F. Karabiber, D.H. Mathews, O.V. Favorov, N.V. Dokholyan and K.M. Weeks, Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry 52, 588-595 (2013). pdf | data
82. F. Karabiber, J.L. McGinnis, O.V. Favorov and K.M. Weeks, QuShape: Rapid, accurate and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA 19, 63–73 (2013). pdf
2012
81. K.-A. Steen, G.M. Rice and K.M. Weeks, Fingerprinting non-canonical and tertiary RNA structures by differential SHAPE reactivity. J. Am. Chem. Soc. 134, 13160-13163 (2012). pdf
80. F. Ding, C.A. Lavender, K.M. Weeks and N.V. Dokholyan, Three-dimensional RNA structure refinement by hydroxyl radical probing. Nature Meths. 9, 603-608 (2012). pdf
79. J.L. McGinnis, J.A. Dunkle, J.H.D. Cate and K.M. Weeks, The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617-6624 (2012). pdf
78. J.T. Low, S.A. Knoepfel, J.M. Watts, O. ter Brake, B. Berkhout and K.M. Weeks, SHAPE-directed discovery of highly potent shRNA inhibitors of HIV-1. Mol. Ther. 20, 820-828 (2012). pdf
77. J.A. Cruz et al. [C.A. Lavender, K.M. Weeks, and 29 others] and E. Westhof, RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18, 610-625 (2012). pdf
2011
76. J.K. Grohman, S. Kottegoda, R.J. Gorelick, N.L. Allbritton and K.M. Weeks, Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome. J. Am. Chem. Soc. 133, 20326–20334 (2011). pdf
75. K.-A. Steen, N.A. Siegfried and K.M. Weeks, Selective 2ʹ-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA. Nature Protoc. 6, 1683-1694 (2011). pdf
74. K.M. Weeks and D.M. Mauger, Exploring RNA structural codes with SHAPE chemistry. Acc. Chem. Res. 44, 1280-1291 (2011). pdf
73. K.M. Weeks, RNA structure probing dash seq. Proc. Natl. Acad. Sci. USA 108, 10933-10934 (2011). pdf
72. P. Rocca-Serra et al. [C.D. Duncan, K.M. Weeks, and 13 others] and A. Laederach, Sharing and archiving nucleic acid structure mapping data. RNA 17, 1204-1212 (2011). pdf
2010
71. D.M. Mauger and K.M. Weeks, Toward global RNA structure analysis. Nature Biotech. 28, 1178-1179 (2010). pdf
70. C. Gherghe, T. Lombo, C.W. Leonard, S.A.K. Datta, J.W. Bess, R.J. Gorelick, A. Rein and K.M. Weeks, Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome. Proc. Natl. Acad. Sci. USA 107, 19248-19253 (2010). pdf
69. E. Simon-Loriere, D.P. Martin, K.M. Weeks and M. Negroni, RNA structures facilitate recombination-mediated gene swapping in HIV-1. J. Virol. 84, 12675-12682 (2010). pdf
68. K.-A. Steen, A. Malhotra and K.M. Weeks, Selective 2ʹ-hydroxyl acylation analyzed by protection from exoribonuclease. J. Am. Chem. Soc. 132, 9940-9943 (2010). pdf
67. C.D.S. Duncan and K.M. Weeks, Non-hierarchical ribonucleoprotein assembly suggests a strain-propagation model for protein-facilitated RNA folding. Biochemistry 49, 5418-5425 (2010). pdf
66. J.T. Low and K.M. Weeks, SHAPE-directed RNA secondary structure prediction. Methods 52, 150-158 (2010). pdf
65. C.A. Lavender, F. Ding, N.V. Dokholyan and K.M. Weeks, Robust and generic RNA modeling using inferred constraints: A structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry 49, 4931-4933 (2010). pdf
64. C.E. Hajdin, F. Ding, N.V. Dokholyan and K.M. Weeks, On the significance of an RNA tertiary structure prediction. RNA 16, 1340-1349 (2010). pdf
63. K.M. Weeks, Advances in RNA structure analysis by chemical probing. Curr. Opin. Struct. Biol. 20, 295-304 (2010). pdf
62. C.D.S. Duncan and K.M. Weeks, The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One 5, e8983 (2010). pdf
61. C. Gherghe, C.W. Leonard, R.J. Gorelick and K.M. Weeks, Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain. J. Virol. 84, 898-906 (2010). pdf
2009
60. J.L. McGinnis, C.D.S. Duncan and K.M. Weeks, High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol. 468, 67-89 (2009). pdf
59. S.A. Mortimer and K.M. Weeks, Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one second snapshots and at single nucleotide resolution. Nature Protoc. 4, 1413-1421 (2009). pdf
58. S.A. Mortimer and K.M. Weeks, C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain. Proc. Natl. Acad. Sci. USA 106, 15622-15627 (2009). pdf
57. J.M. Watts, K.K. Dang, R.J. Gorelick, C.W. Leonard, J.W. Bess, R. Swanstrom, C.L. Burch and K.M. Weeks, Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460, 711-716 (2009). pdf | data
56. K.A. Wilkinson, S.M. Vasa, K.E. Deigan, S.A. Mortimer, M.C. Giddings and K.M. Weeks, Influence of nucleotide identity on ribose 2′-hydroxyl reactivity in RNA. RNA 15, 1314-1321 (2009). pdf
55. S.A. Mortimer, J.S. Johnson and K.M. Weeks, Quantitative analysis of RNA solvent accessibility by N-silylation of guanosine. Biochemistry 48, 2109-2114 (2009). pdf
54. C.M. Gherghe, C.W. Leonard, F. Ding, N.V. Dokholan and K.M. Weeks, Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J. Am. Chem. Soc. 131, 2541-2546 (2009). pdf
53. K.E. Deigan, T.W. Li, D.H. Mathews and K.M. Weeks, Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA 106, 97-102 (2009). pdf | data
2008
52. S.A. Mortimer and K.M. Weeks, Time-resolved RNA SHAPE chemistry. J. Am. Chem. Soc. 130, 16178-16180 (2008). pdf
51. T.S. Maity, H.M. Fried and K.M. Weeks, Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle. Biochem. J. 415, 429-437 (2008). pdf
50. S.M. Vasa, N. Guex, K.A. Wilkinson, K.M. Weeks and M.C. Giddings, ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979-1990 (2008). pdf
49. C.M. Gherghe, Z. Shajani, K.A. Wilkinson, G. Varani and K.M. Weeks, Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J. Am. Chem. Soc. 130, 12244-12245 (2008). pdf
48. C.D.S. Duncan and K.M. Weeks, SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry 47, 8504-8513 (2008). pdf
47. C.M. Gherghe, S.A. Mortimer, J.M. Krahn, N.L. Thompson and K.M. Weeks, Slow conformational dynamics at C2′-endo nucleotides in RNA. J. Am. Chem. Soc. 130, 8884-8885 (2008). pdf
46. K.A. Wilkinson, R.J. Gorelick, S.M. Vasa, N. Guex, A. Rein, D.H. Mathews, M.C. Giddings and K.M. Weeks, High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biology 6, e96 (2008). pdf | data
45. C.N. Jones, K.A. Wilkinson, K.T. Hung, K.M. Weeks and L.L. Spremulli, Lack of secondary structure characterizes the 5′ ends of mammalian mitochondrial mRNAs. RNA 14, 862-871 (2008). pdf
44. B. Wang, K.A. Wilkinson and K.M. Weeks, Complex ligand-induced conformational changes in tRNAAsp revealed by single nucleotide resolution SHAPE chemistry. Biochemistry 47, 3454-3461 (2008). pdf
2007
43. T.S. Maity and K.M. Weeks, A three-fold RNA-protein interface in the signal recognition particle gates native complex assembly. J. Mol. Biol. 369, 512-524 (2007). pdf
42. S.A. Mortimer and K.M. Weeks, A fast acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc. 129, 4144-4145 (2007). pdf
2006
41. C. Gherghe and K.M. Weeks, The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J. Biol. Chem. 281, 37952-37961 (2006). pdf
40. T.S. Maity, C.W. Leonard, M.A. Rose, H.M. Fried and K.M. Weeks, Compartmentalization directs assembly of the signal recognition particle. Biochemistry 45, 14955-14964 (2006). pdf
39. K.A. Wilkinson, E.J. Merino and K.M. Weeks, Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nature Protoc. 1, 1610-1616 (2006). pdf
38. C.S. Badorrek and K.M. Weeks, Architecture of a gamma retroviral genomic RNA dimer. Biochemistry 45, 12664-12672 (2006). pdf
37. C.S. Badorrek, C.M. Gherghe and K.M. Weeks, Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc. Natl. Acad. Sci. USA 103, 13640-13645 (2006). pdf
36. G. Bokinsky, L.G. Nivon, S. Liu, G. Chai, M. Hong, K.M. Weeks and X. Zhuang, Two distinct binding modes of a protein cofactor with its target RNA. J. Mol. Biol. 361, 771-784 (2006). pdf
35. T.W. Li and K.M. Weeks, Structure-independent and quantitative ligation of single-stranded DNA. Anal. Biochem. 349, 242-246 (2006). pdf
2005
34. C.M. Gherghe, J.M. Krahn and K.M. Weeks, Crystal structures, reactivity and inferred acylation transition states for 2′-amine substituted RNA. J. Am. Chem. Soc. 127, 13622-13628 (2005). Supplementary Movie | pdf
33. E.J. Merino and K.M. Weeks, Facile conversion of aptamers into sensors using a 2′-ribose linked fluorophore. J. Am. Chem. Soc. 127, 12766-12767 (2005). pdf
32. A. Longo, C.W. Leonard, G.S. Bassi, D. Berndt, J.M. Krahn, T.M.T. Hall and K.M. Weeks, Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nature Struct. Mol. Biol. 12, 779-787 (2005). pdf
31. C.L. Badorrek and K.M. Weeks, RNA flexibility in the dimerization domain of a gamma retrovirus. Nature Chem. Biol. 1, 104-111 (2005). pdf
30. K.A. Wilkinson, E.J. Merino and K.M. Weeks, RNA SHAPE chemistry reveals non-hierarchical interactions dominate equilibrium structural transitions in tRNAAsp transcripts. J. Am. Chem. Soc. 127, 4659-4667 (2005). pdf
29. E.J. Merino, K.A. Wilkinson, J.L. Coughlan and K.M. Weeks, RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE). J. Am. Chem. Soc. 127, 4223-4231 (2005). pdf
2004
28. K.L. Buchmueller and K.M. Weeks, Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies. Nucl. Acids Res. 32, e184 (6 pp.) (2004).
27. I. Garcia and K.M. Weeks, Structural basis for the self-chaperoning function of an RNA collapsed state. Biochemistry 43, 15179-15186 (2004).
26. D.M. John, E.J. Merino and K.M. Weeks, Mechanics of DNA flexibility visualized by selective 2′-amine acylation at nucleotide bulges. J. Mol. Biol. 337, 611-619 (2004).
2003
25. K.L. Buchmueller and K.M. Weeks, Near native structure in an RNA collapsed state. Biochemistry 42, 13869-13878 (2003).
24. E.J. Merino and K.M. Weeks, Fluorogenic resolution of ligand binding by a nucleic acid aptamer. J. Am. Chem. Soc. 125, 12370-12371 (2003).
23. K.L. Buchmueller, B.T. Hill, M.S. Platz and K.M. Weeks, RNA-tethered phenylazide photocrosslinking via a short-lived indiscriminant electrophile. J. Am. Chem. Soc. 125, 10850-10861 (2003).
22. G.S. Bassi and K.M. Weeks, A kinetic and thermodynamic framework for assembly of the six-component bI3 group I intron ribonucleoprotein catalyst. Biochemistry 42, 9980-9988 (2003).
21. I. Garcia and K.M. Weeks, Small structural costs for evolution from RNA to RNP-based catalysis. J. Mol. Biol. 331, 57-73 (2003).
20. S.I. Chamberlin and K.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 42, 901-909 (2003).
2002
19. S.I. Chamberlin, E.J. Merino and K.M. Weeks, Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups. Proc. Natl. Acad. Sci. USA 99, 14688-14693 (2002).
18. D.M. John and K.M. Weeks, Chemical interrogation of mismatches in DNA-DNA and DNA-RNA duplexes under non-stringent conditions by selective 2′-amine acylation. Biochemistry 41, 6866-6874 (2002).
17. G.S. Bassi, D.M. de Oliviera, M.F. White and K.M. Weeks, Recruitment of intron encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proc. Natl. Acad. Sci. USA 99, 128-133 (2002).
2001
16. A.E. Webb, M.A. Rose, E. Westhof and K.M. Weeks, Protein-dependent transition states for ribonucleoprotein assembly. J. Mol. Biol. 309, 1087-1100 (2001).
15. M.A. Rose and K.M. Weeks, Visualizing induced fit in early assembly of the human signal recognition particle. Nature Struct. Biol. 8, 515-520 (2001).
14. A.E. Webb and K.M. Weeks, A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nature Struct. Biol. 8, 135-140 (2001).
2000
13. D.M. John and K.M. Weeks, van’t Hoff enthalpies without baselines. Protein Sci. 9, 1416-1419 (2000).
12. D.M. John and K.M. Weeks, Tagging DNA mismatches by selective 2′-amine acylation. Chem. Biol. 7, 405-410 (2000).
11. K.L. Buchmueller, A.E. Webb, D.A. Richardson and K.M. Weeks, A collapsed, non-native RNA folding state. Nature Struct. Biol. 7, 362-366 (2000).
10. S.I. Chamberlin and K.M. Weeks, Mapping local nucleotide flexibility by selective acylation of 2′-amine substituted RNA. J. Am. Chem. Soc. 122, 216-224 (2000).
Pre-2000
9. K.M. Weeks, Protein-facilitated RNA folding. Curr. Opin. Struct. Biol. 7, 336-342 (1997).
8. K.M. Weeks and T.R. Cech, Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271, 345-348 (1996).
7. K.M. Weeks and T.R. Cech, Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5′ splice site domain. Cell 82, 221-230 (1995).
6. K.M. Weeks and T.R. Cech, Efficient protein-facilitated splicing of the yeast mitochondrial bI5 intron. Biochemistry 34, 7728-7738 (1995).
5. K.M. Weeks and D.M. Crothers, Major groove accessibility of RNA. Science 261, 1574-1577 (1993).
4. K.M. Weeks and D.M. Crothers, RNA Targeting by the HIV-1 Tat Protein. Persp. in Drug Discovery and Design 1, 225-234 (1993).
3. K.M. Weeks and D.M. Crothers, RNA binding assays for Tat-derived peptides: implications for specificity. Biochemistry 31, 10281-10287 (1992).
2. K.M. Weeks and D.M. Crothers, RNA recognition by Tat-derived peptides: interaction in the major groove? Cell 66, 577-588 (1991); 70, 1069.
1. K.M. Weeks, C. Ampe, S.C. Schultz, T.A. Steitz and D.M. Crothers, Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science 249, 1281-1285 (1990).