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Center Directors

Lynne Maquat, Ph.D.

Director

David H.. Mathews, M.D., Ph.D.

Associate Director

Publications

The following list was auto-generated 6 days ago.

• 1. Bellaousov S
  2. Reuter JS
  3. Seetin MG
  4. Mathews DH
  (2013 Apr 24). RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. In press.
• 1. Liberman JA
  2. Salim M
  3. Krucinska J
  4. Wedekind JE
  (2013 Apr 14). Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat Chem Biol. In press.
• 1. Grant TD
  2. Luft JR
  3. Wolfley JR
  4. Snell ME
  5. Tsuruta H
  6. Corretore S
  7. Quartley E
  8. Phizicky EM
  9. Grayhack EJ
  10. Snell EH
  (2013 Apr 10). The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA. J Mol Biol. In press.
• 1. Gleghorn ML
  2. Gong C
  3. Kielkopf CL
  4. Maquat LE
  (2013 Apr 01). Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat Struct Mol Biol. 20, 515-24.
• 1. Jenkins JL
  2. Agrawal AA
  3. Gupta A
  4. Green MR
  5. Kielkopf CL
  (2013 Apr 01). U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res. 41, 3859-73.
• 1. Wang J
  2. Gong C
  3. Maquat LE
  (2013 Apr 01). Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev. 27, 793-804.
• 1. Blasinski H
  2. Bulan O
  3. Sharma G
  (2013 Apr 01). Per-colorant-channel color barcodes for mobile applications: an interference cancellation framework. IEEE Trans Image Process. 22, 1498-511.
• 1. Huang C
  2. Yu YT
  (2013 Apr 01). Synthesis and labeling of RNA in vitro. Curr Protoc Mol Biol. Chapter 4, Unit4.15.
• 1. Ge J
  2. Yu YT
  (2013 Apr 01). RNA pseudouridylation: new insights into an old modification. Trends Biochem Sci. 38, 210-8.
• 1. Wang J
  2. Li D
  3. Bambara RA
  4. Yang H
  5. Dykes C
  (2013 Mar 27). L74V increases the reverse transcriptase content of HIV-1 virions with non-nucleoside reverse transcriptase drug-resistant mutations L100I+K103N and K101E+G190S, which results in increased fitness. J Gen Virol. In press.
• 1. Trcek T
  2. Sato H
  3. Singer RH
  4. Maquat LE
  (2013 Mar 01). Temporal and spatial characterization of nonsense-mediated mRNA decay. Genes Dev. 27, 541-51.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 28). Flap Endonuclease 1. Annu Rev Biochem. In press.
• 1. Kurosaki T
  2. Maquat LE
  (2013 Feb 26). Rules that govern UPF1 binding to mRNA 3' UTRs. Proc Natl Acad Sci U S A. 110, 3357-62.
• 1. Schmidt K
  2. Butler JS
  (2013 Feb 20). Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity. Wiley Interdiscip Rev RNA. 4, 217-31.
• 1. Tubbs JD
  2. Condon DE
  3. Kennedy SD
  4. Hauser M
  5. Bevilacqua PC
  6. Turner DH
  (2013 Feb 12). The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry. 52, 996-1010.
• 1. Wang W
  2. Maucuer A
  3. Gupta A
  4. Manceau V
  5. Thickman KR
  6. Bauer WJ
  7. Kennedy SD
  8. Wedekind JE
  9. Green MR
  10. Kielkopf CL
  (2013 Feb 05). Structure of phosphorylated SF1 bound to U2AF⁶⁵ in an essential splicing factor complex. Structure. 21, 197-208.
• 1. Balakrishnan L
  2. Bambara RA
  (2013 Feb 01). Okazaki fragment metabolism. Cold Spring Harb Perspect Biol. 5, .
• 1. Ermolenko DN
  2. Cornish PV
  3. Ha T
  4. Noller HF
  (2013 Feb 01). Antibiotics that bind to the A site of the large ribosomal subunit can induce mRNA translocation. RNA. 19, 158-66.
• 1. Preston MA
  2. D'Silva S
  3. Kon Y
  4. Phizicky EM
  (2013 Feb 01). tRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae. RNA. 19, 243-56.
• 1. Sobczak K
  2. Wheeler TM
  3. Wang W
  4. Thornton CA
  (2013 Feb 01). RNA interference targeting CUG repeats in a mouse model of myotonic dystrophy. Mol Ther. 21, 380-7.
• 1. Park E
  2. Gleghorn ML
  3. Maquat LE
  (2013 Jan 08). Staufen2 functions in Staufen1-mediated mRNA decay by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity. Proc Natl Acad Sci U S A. 110, 405-12.
• 1. Childs-Disney JL
  2. Parkesh R
  3. Nakamori M
  4. Thornton CA
  5. Disney MD
  (2012 Dec 21). Rational design of bioactive, modularly assembled aminoglycosides targeting the RNA that causes myotonic dystrophy type 1. ACS Chem Biol. 7, 1984-93.
• 1. Dean KM
  2. Grayhack EJ
  (2012 Dec 01). RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay. RNA. 18, 2335-44.
• 1. Kennedy SD
  2. Kierzek R
  3. Turner DH
  (2012 Nov 20). Novel conformation of an RNA structural switch. Biochemistry. 51, 9257-9.
• 1. Salter JD
  2. Lippa GM
  3. Belashov IA
  4. Wedekind JE
  (2012 Nov 06). Core-binding factor β increases the affinity between human Cullin 5 and HIV-1 Vif within an E3 ligase complex. Biochemistry. 51, 8702-4.
• 1. Moss WN
  2. Dela-Moss LI
  3. Priore SF
  4. Turner DH
  (2012 Nov 01). The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family. RNA Biol. 9, 1305-10.
• 1. Banáš P
  2. Sklenovský P
  3. Wedekind JE
  4. Šponer J
  5. Otyepka M
  (2012 Oct 25). Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B. 116, 12721-34.
• 1. Liberman JA
  2. Guo M
  3. Jenkins JL
  4. Krucinska J
  5. Chen Y
  6. Carey PR
  7. Wedekind JE
  (2012 Oct 17). A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis. J Am Chem Soc. 134, 16933-6.
• 1. Schmidt K
  2. Xu Z
  3. Mathews DH
  4. Butler JS
  (2012 Oct 01). Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance. RNA. 18, 1934-45.
• 1. Gong C
  2. Popp MW
  3. Maquat LE
  (2012 Oct 01). Biochemical analysis of long non-coding RNA-containing ribonucleoprotein complexes. Methods. 58, 88-93.
• 1. Guy MP
  2. Podyma BM
  3. Preston MA
  4. Shaheen HH
  5. Krivos KL
  6. Limbach PA
  7. Hopper AK
  8. Phizicky EM
  (2012 Oct 01). Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA. 18, 1921-33.
• 1. Dewe JM
  2. Whipple JM
  3. Chernyakov I
  4. Jaramillo LN
  5. Phizicky EM
  (2012 Oct 01). The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications. RNA. 18, 1886-96.
• 1. Moss WN
  2. Eickbush DG
  3. Lopez MJ
  4. Eickbush TH
  5. Turner DH
  (2012 Sep 06). The R2 retrotransposon RNA families. RNA Biol. 8, 714-8.
• 1. Kantartzis A
  2. Williams GM
  3. Balakrishnan L
  4. Roberts RL
  5. Surtees JA
  6. Bambara RA
  (2012 Aug 30). Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions. Cell Rep. 2, 216-22.
• 1. Wheeler TM
  2. Leger AJ
  3. Pandey SK
  4. MacLeod AR
  5. Nakamori M
  6. Cheng SH
  7. Wentworth BM
  8. Bennett CF
  9. Thornton CA
  (2012 Aug 02). Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature. 488, 111-5.
• 1. Gloor JW
  2. Balakrishnan L
  3. Campbell JL
  4. Bambara RA
  (2012 Aug 01). Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1. Nucleic Acids Res. 40, 6774-86.
• 1. Van Damme P
  2. Lasa M
  3. Polevoda B
  4. Gazquez C
  5. Elosegui-Artola A
  6. Kim DS
  7. De Juan-Pardo E
  8. Demeyer K
  9. Hole K
  10. Larrea E
  11. Timmerman E
  12. Prieto J
  13. Arnesen T
  14. Sherman F
  15. Gevaert K
  16. Aldabe R
  (2012 Jul 31). N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB. Proc Natl Acad Sci U S A. 109, 12449-54.
• 1. Spasic A
  2. Serafini J
  3. Mathews DH
  (2012 Jul 10). The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. J Chem Theory Comput. 8, 2497-2505.
• 1. Jenkins JL
  2. Laird KM
  3. Kielkopf CL
  (2012 Jul 03). A Broad range of conformations contribute to the solution ensemble of the essential splicing factor U2AF(65). Biochemistry. 51, 5223-5.
• 1. Ofori LO
  2. Hoskins J
  3. Nakamori M
  4. Thornton CA
  5. Miller BL
  (2012 Jul 01). From dynamic combinatorial 'hit' to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy. Nucleic Acids Res. 40, 6380-90.
• 1. Childs-Disney JL
  2. Hoskins J
  3. Rzuczek SG
  4. Thornton CA
  5. Disney MD
  (2012 May 18). Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive. ACS Chem Biol. 7, 856-62.
• 1. Smith HC
  2. Bennett RP
  3. Kizilyer A
  4. McDougall WM
  5. Prohaska KM
  (2012 May 01). Functions and regulation of the APOBEC family of proteins. Semin Cell Dev Biol. 23, 258-68.
• 1. Chen JL
  2. Dishler AL
  3. Kennedy SD
  4. Yildirim I
  5. Liu B
  6. Turner DH
  7. Serra MJ
  (2012 Apr 24). Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters. Biochemistry. 51, 3508-22.
• 1. Kennedy EM
  2. Amie SM
  3. Bambara RA
  4. Kim B
  (2012 Apr 20). Frequent incorporation of ribonucleotides during HIV-1 reverse transcription and their attenuated repair in macrophages. J Biol Chem. 287, 14280-8.
• 1. Liberman JA
  2. Wedekind JE
  (2012 Apr 20). Riboswitch structure in the ligand-free state. Wiley Interdiscip Rev RNA. 3, 369-84.
• 1. Grant TD
  2. Snell EH
  3. Luft JR
  4. Quartley E
  5. Corretore S
  6. Wolfley JR
  7. Snell ME
  8. Hadd A
  9. Perona JJ
  10. Phizicky EM
  11. Grayhack EJ
  (2012 Apr 01). Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic Acids Res. 40, 3723-31.
• 1. Schoenberg DR
  2. Maquat LE
  (2012 Apr 01). Regulation of cytoplasmic mRNA decay. Nat Rev Genet. 13, 246-59.
• 1. Huang C
  2. Wu G
  3. Yu YT
  (2012 Apr 01). Inducing nonsense suppression by targeted pseudouridylation. Nat Protoc. 7, 789-800.
• 1. Seetin MG
  2. Mathews DH
  (2012 Mar 15). TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots. Bioinformatics. 28, 792-8.
• 1. Tang ZZ
  2. Yarotskyy V
  3. Wei L
  4. Sobczak K
  5. Nakamori M
  6. Eichinger K
  7. Moxley RT
  8. Dirksen RT
  9. Thornton CA
  (2012 Mar 15). Muscle weakness in myotonic dystrophy associated with misregulated splicing and altered gating of Ca(V)1.1 calcium channel. Hum Mol Genet. 21, 1312-24.