Molecular mechanisms of DNA recombination and repair; single molecule fluorescence microscopy and other biochemical approaches.
Our group uses single-molecule optical microscopy to study fundamental interactions between proteins and nucleic acids - we literally watch individual protein molecules or protein complexes as they interact with their DNA substrates. Our overall goal is to reveal the molecular mechanisms that cells use to repair, maintain, and decode their genetic information. This research combines aspects of biochemistry, physics, and nanoscale technology to answer questions about complex biological problems that simply can not be addressed through traditional biochemical approaches. The primary advantages of our approaches are that we can actually see what proteins are bound to DNA, where they are bound, how they move, and how they influence other components of the system - all in real-time, at the level of a single reaction.
Our research program is focused on studying the regulation and activity of proteins that are involved in repairing damaged chromosomes. We are particularly interested in determining the physical basis for the mechanisms that proteins use to survey DNA molecules for damage and initiate repair processes, and how these initial steps are coordinated with downstream events that lead to completion of repair. As part of our work, we are also actively pursuing the development of novel experimental tools that can be used to facilitate the study of single biochemical reactions. In particular, we are applying techniques derived from nanotechnology to our biological research, and using nano- and micro-scale engineering to facilitate the development of new, robust experimental platforms that enable "high throughput" single molecule imaging.
- A Molecular Take on Aesop's The Oak and the Reeds.
Moevus CJ, Greene EC.
Cell. 2015 Mar 12;160(6):1039-40. doi: 10.1016/j.cell.2015.02.036.
- DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination.
Qi Z, Redding S, Lee JY, Gibb B, Kwon Y, Niu H, Gaines WA, Sung P, Greene EC.
Cell. 2015 Feb 26;160(5):856-69. doi: 10.1016/j.cell.2015.01.029. Epub 2015 Feb 12.
- Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules.
Gibb B, Ye LF, Kwon Y, Niu H, Sung P, Greene EC.
Nat Struct Mol Biol. 2014 Oct;21(10):893-900. doi: 10.1038/nsmb.2886. Epub 2014 Sep 7.
- DNA curtains: novel tools for imaging protein-nucleic acid interactions at the single-molecule level.
Collins BE, Ye LF, Duzdevich D, Greene EC.
Methods Cell Biol. 2014;123:217-34. doi: 10.1016/B978-0-12-420138-5.00012-4. Review.
- Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA.
Lee JY, Finkelstein IJ, Arciszewska LK, Sherratt DJ, Greene EC.
Mol Cell. 2014 Jun 5;54(5):832-43. doi: 10.1016/j.molcel.2014.03.033. Epub 2014 Apr 24.
- RPA antagonizes microhomology-mediated repair of DNA double-strand breaks.
Deng SK, Gibb B, de Almeida MJ, Greene EC, Symington LS.
Nat Struct Mol Biol. 2014 Apr;21(4):405-12. doi: 10.1038/nsmb.2786. Epub 2014 Mar 9.
- Visualizing protein movement on DNA at the single-molecule level using DNA curtains.
Silverstein TD, Gibb B, Greene EC.
DNA Repair (Amst). 2014 Aug;20:94-109. doi: 10.1016/j.dnarep.2014.02.004. Epub 2014 Mar 2.
- Concentration-dependent exchange of replication protein A on single-stranded DNA revealed by single-molecule imaging.
Gibb B, Ye LF, Gergoudis SC, Kwon Y, Niu H, Sung P, Greene EC.
PLoS One. 2014 Feb 3;9(2):e87922. doi: 10.1371/journal.pone.0087922. eCollection 2014.
- DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA.
Nature. 2014 Mar 6;507(7490):62-7. doi: 10.1038/nature13011. Epub 2014 Jan 29.
- DNA dynamics and single-molecule biology.
Duzdevich D, Redding S, Greene EC.
Chem Rev. 2014 Mar 26;114(6):3072-86. doi: 10.1021/cr4004117. Epub 2014 Jan 8. Review. No abstract available.
- How do proteins locate specific targets in DNA?
Redding S, Greene EC.
Chem Phys Lett. 2013 May 10;570. doi: 10.1016/j.cplett.2013.03.035.
- Tension modulates actin filament polymerization mediated by formin and profilin.
Courtemanche N, Lee JY, Pollard TD, Greene EC.
Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9752-7. doi: 10.1073/pnas.1308257110. Epub 2013 May 28.
- Molecular traffic jams on DNA.
Finkelstein IJ, Greene EC.
Annu Rev Biophys. 2013;42:241-63. doi: 10.1146/annurev-biophys-083012-130304. Epub 2013 Feb 28. Review.
- Target search dynamics during post-replicative mismatch repair.
Gorman J, Greene EC.
Cell Cycle. 2013 Feb 15;12(4):537-8. doi: 10.4161/cc.23669. Epub 2013 Jan 23. No abstract available.
- Towards physiological complexity with in vitro single-molecule biophysics.
Duzdevich D, Greene EC.
Philos Trans R Soc Lond B Biol Sci. 2012 Dec 24;368(1611):20120271. doi: 10.1098/rstb.2012.0271. Print 2013 Feb 5. Review.
- The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion.
Wang F, Redding S, Finkelstein IJ, Gorman J, Reichman DR, Greene EC.
Nat Struct Mol Biol. 2013 Feb;20(2):174-81. doi: 10.1038/nsmb.2472. Epub 2012 Dec 23.
- Sliding to the rescue of damaged DNA.
Gibb B, Greene EC.
Elife. 2012 Dec 13;1:e00347. doi: 10.7554/eLife.00347.