Affiliation: University of North Carolina
- Direct visualization of asymmetric adenine-nucleotide-induced conformational changes in MutL alphaElizabeth J Sacho
Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Mol Cell 29:112-21. 2008..These data reveal an ATPase cycle in which sequential nucleotide binding, hydrolysis, and release modulate the conformational states of MutL alpha...
- Single molecule studies of DNA mismatch repairDorothy A Erie
Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States Electronic address
DNA Repair (Amst) 20:71-81. 2014..These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair. ..
- Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactionsYong Yang
Department of Chemistry, University of North Carolina at Chapel Hill Chapel Hill, NC 27599 3290, USA
Nucleic Acids Res 33:4322-34. 2005..In conclusion, from a single set of AFM experiments, it is possible to determine the binding affinity, specificity and stoichiometry, as well as the conformational properties of the protein-DNA complexes...
- The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcriptionDorothy A Erie
Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 3290, USA
Biochim Biophys Acta 1577:224-39. 2002..The role of each of the conformational states in elongation is then discussed in detail. Finally, an integrated mechanism of elongation is presented, bringing together the panoply of experiments...
- Four-color single-molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexesVANESSA DEROCCO
Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Biotechniques 49:807-16. 2010....
- Forks, pincers, and triggers: the tools for nucleotide incorporation and translocation in multi-subunit RNA polymerasesDorothy A Erie
Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States
Curr Opin Struct Biol 19:708-14. 2009....
- Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motionShannon F Holmes
Department of Chemistry, The University of North Carolina, Chapel Hill, North Carolina 27599, USA
J Biol Chem 278:35597-608. 2003..This model provides an alternative mechanism for pausing as well as a structural explanation not only for our kinetic data but also for data from elongation studies on yeast RNAP II...
- Kinetics of multisubunit RNA polymerases: experimental methods and data analysisShannon F Holmes
Department of Chemistry, CB 3290, Venable and Kenan Laboratories, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3290, USA
Methods Enzymol 371:71-81. 2003
- Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelityShannon F Holmes
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
J Biol Chem 281:18677-83. 2006..We suggest a mechanism of nucleotide discrimination that is governed both by rotation of the NTP through this pore and subsequent rearrangement or closure of RNAP to align the NTP in the A site...
- DNA bending and unbending by MutS govern mismatch recognition and specificityHong Wang
Department of Chemistry and Curriculum in Applied and Materials Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
Proc Natl Acad Sci U S A 100:14822-7. 2003..Our results provide a structural explanation for the long-standing question of how MutS achieves mismatch repair specificity...
- Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factorsBrian P Hogan
Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 3290, USA
J Biol Chem 277:967-75. 2002..This protein, Gfh1, functions as an anti-GreA factor in vitro by reducing intrinsic cleavage and competing with GreA for a binding site on the polymerase...
- Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexesLauryn E Sass
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
Biochemistry 49:3174-90. 2010..Finally, in addition to revealing these important biological implications of MutS-DNA interactions, this FRET TACKLE method will enable the analysis of the complex dynamics of other biological systems...
- Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopyYong Yang
Department of Chemistry, University of North Carolina at Chapel Hill at Chapel Hill, Chapel Hill, NC 27599, USA
Methods 29:175-87. 2003..These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation...
- Mechanism of MutS searching for DNA mismatches and signaling repairIngrid Tessmer
Department of Chemistry and Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA
J Biol Chem 283:36646-54. 2008..These results provide a structural explanation for the mechanism by which MutS searches for and recognizes mismatches and for the observed phenotypes of mutants with substitutions in the Phe-Xaa-Glu motif...
- Catching RNA polymerase in the act of binding: intermediates in transcription illuminated by synchrotron footprintingMichael Brenowitz
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
Proc Natl Acad Sci U S A 102:4659-60. 2005
- Functional oligomeric state of avian sarcoma virus integraseKogan K Bao
Department of Biochemistry and Biophysics, Oregon State University, Oregon 97331, USA
J Biol Chem 278:1323-7. 2003..These results suggest that tetramer formation may be a requisite step during catalysis with ramifications for antiviral design strategies targeting the structurally homologous human immunodeficiency virus, type 1 (HIV-1) integrase...
- Interconvertible lac repressor-DNA loops revealed by single-molecule experimentsOi Kwan Wong
Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
PLoS Biol 6:e232. 2008..The ability to switch between different loop structures may help to explain how robust transcription regulation is maintained even though the mechanical work required to form a loop may change substantially with metabolic conditions...
- A model for oligomeric regulation of APOBEC3G cytosine deaminase-dependent restriction of HIVLinda Chelico
Department of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089 2910, USA
J Biol Chem 283:13780-91. 2008..We suggest that diverse A3G oligomerization modes contribute to the human immunodeficiency virus, type 1, proviral DNA mutational bias...
- Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNASukhdev S Brar
Laboratory of Molecular Genetics, D3 01, National Institute of Environmental Health Sciences National Institutes of Health, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA
DNA Repair (Amst) 7:77-87. 2008....
- Unactivated PKR exists in an open conformation capable of binding nucleotidesPeter A Lemaire
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
Biochemistry 45:9074-84. 2006..The resolution of the individual domains in the images supports a model in which unactivated PKR exists in an open conformation where the kinase domain is accessible and capable of binding substrate...
- Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavageValerie Lamour
The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
J Mol Biol 356:179-88. 2006..The latter two characteristics suggest that Gfh1 chelates a magnesium ion in the RNA polymerase active site (like GreA) but in a catalytically inactive configuration...
- DNA mismatch repairThomas A Kunkel
Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Annu Rev Biochem 74:681-710. 2005..Emphasis is on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error...
- Structure Function Studies of DNA Mismatch RepairDorothy A Erie; Fiscal Year: 2010....
- BIOPHYSICAL AND SCANNING FORCE MICROSCOPY STUDIESDOROTHY ERIE; Fiscal Year: 2001..3) How do polymorphisms affect the above properties? ..
- 2002 Gordon Research Conference on BiopolymersDOROTHY ERIE; Fiscal Year: 2002..The program encompasses some of the most exciting research in the field of nucleic acid and protein biophysics and promises to generate lively discussions both in and outside of the sessions. ..
- Kinetic Studies of Transcription ElongationDOROTHY ERIE; Fiscal Year: 2005..Accordingly, we will use this information to begin to understand, at the amino acid level, the role of NTP binding and conformational transitions in the regulation of elongation. ..
- Mechanistic studies of DNA repair and damage responseDorothy A Erie; Fiscal Year: 2010..abstract_text> ..