Publications
2012
78. 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, in press (2012).
77. 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, in press (2012).
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).
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).
74. K.M. Weeks and D.M. Mauger, Exploring RNA structural codes with SHAPE chemistry. Acc. Chem. Res. 44, 1280-1291 (2011). link pdf
73. K.M. Weeks, RNA structure probing dash seq. Proc. Natl. Acad. Sci. USA 108, 10933-10934 (2011). link 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). link
2010
71. D.M. Mauger and K.M. Weeks, Toward global RNA structure analysis. Nature Biotech. 28, 1178-1179 (2010). link 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). link 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). link 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). link 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). link pdf
66. J.T. Low and K.M. Weeks, SHAPE-directed RNA secondary structure prediction. Methods 52, 150-158 (2010). link 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). link 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). link pdf
63. K.M. Weeks, Advances in RNA structure analysis by chemical probing. Curr. Opin. Struct. Biol. 20, 295-304 (2010). link 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). link 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). link 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). link 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). link 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). link pdf
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). link 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). link 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). link 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). link pdf
2008
52. S.A. Mortimer and K.M. Weeks, Time-resolved RNA SHAPE chemistry. J. Am. Chem. Soc. 130, 16178-16180 (2008). link 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). link 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). link 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). link 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). link 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). link 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). open access pdf
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). link 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). link 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). link 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). link 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). link 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). link 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). link 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). link 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). link pdf
35. T.W. Li and K.M. Weeks, Structure-independent and quantitative ligation of single-stranded DNA. Anal. Biochem. 349, 242-246 (2006). link 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). link 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). link 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). link 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). link 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). link 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). link 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). link
27. I. Garcia and K.M. Weeks, Structural basis for the self-chaperoning function of an RNA collapsed state. Biochemistry 43, 15179-15186 (2004). link
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). link
2003
25. K.L. Buchmueller and K.M. Weeks, Near native structure in an RNA collapsed state. Biochemistry 42, 13869-13878 (2003). link
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). link
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). link
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). link
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). link
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). link
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). link
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). link
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). link
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). link
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). link
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). link
2000
13. D.M. John and K.M. Weeks, van't Hoff enthalpies without baselines. Protein Sci. 9, 1416-1419 (2000). link
12. D.M. John and K.M. Weeks, Tagging DNA mismatches by selective 2'-amine acylation. Chem. Biol. 7, 405-410 (2000). link
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). link
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). link
8. K.M. Weeks and T.R. Cech, Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271, 345-348 (1996). link
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). link
6. K.M. Weeks and T.R. Cech, Efficient protein-facilitated splicing of the yeast mitochondrial bI5 intron. Biochemistry 34, 7728-7738 (1995). link
5. K.M. Weeks and D.M. Crothers, Major groove accessibility of RNA. Science 261, 1574-1577 (1993). link
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). link
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. link
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). link
Kevin Weeks, Department of Chemistry, CB-3290, University of North Carolina, Chapel Hill, NC 27599-3290