Department of Biochemistry
and
Molecular Biophysics
Columbia University
College of
Physicians and Surgeons
650 West 168th Street
Black Building Room 536
New York, NY 10032
Map (PDF)
Map (Google)
Phone: 212-342-2944 (office)
Phone: 212-342-2943 (lab)
Fax: 212-305-7932
Email: ecg2108@columbia.edu
© September 2008
Eric C. Greene.
All Rights Reserved.
|
Current Members |
|
Eric C. Greene
|
|
Principal Investigator
|
|
|
|
Ilya Finkelstein
|
|
Postdoctoral Fellow
|
| Email: | ifinkelstein@columbia.edu |
| Interests: | Our cells are constantly subjected to intracellular and extracellular stresses that threaten genomic fidelity. Double strand breaks (DSB) in DNA are a form of damage that may arise spontaneously during DNA replication or as a result of external factors such as ionizing radiation or chemical damaging agents. Upon sensing DSB, the cell initiates a host of responses that identify, encapsulate, and ultimately process the damaged site. The goal of my work is to directly visualize the behavior of several key proteins that participate in DSB repair. Fluorescence and biochemical assays will probe the mechanism of protein-DNA association and observed nuclease activity of the complex in the context of DNA binding. |
| Webpage: | There's more!
|
|
|
Dana Moses
|
|
Postdoctoral Fellow
|
| Email: | dm2563@columbia.edu |
| Interests: | DNA damage in a cell must be quickly located and repaired in a vast excess of intact DNA. Rad51 is a crucial protein that participates in the cell's response to damaged DNA. I am studying the mechanism by which Rad51 locates damaged DNA by directly imaging Rad51 presynaptic complexes interacting with DNA in TIRFM. I will also study the mechanism of this interaction in the context of other proteins involved in recombination, such as Hop2-Mnd1, Rad54, and Rdh54, and proteins present on DNA in cells, such as nucleosomes. |
|
|
Tuschar Kanti Mukherjee
|
|
Postdoctoral Scientist
|
| Email: | tkm2106@columbia.edu |
| Interests: | It is well known that the primary cellular target of anticancer drug cis- diamminedichloroplatinum(II) (cisplatin) is DNA. It forms a number of different types of coordination complex with the N7 position of guanine base. These types of crosslinks results in distortions of the DNA double helix, such as unwinding, shortening of the duplex and loss of helix stability. It has been observed that some proteins bind specifically to the damaged DNA and recognize the DNA lesion caused by cisplatin. My research plan includes modification of lambda-DNA by cisplatin, its characterization by various techniques and the visualization of the interaction of damaged DNA with the mismatch repair (MMR) protein MSH2-MSH6 heterodimer by using Total Internal Reflection Fluorescent Microscopy (TIRFM) as a tool. The goal is to see how the mismatch repair protein MSH2-MSH6 heterodimer identifies the cisplatin induced DNA lesion and how the interaction differs from the normal undamaged DNA. |
|
|
Feng Wang
|
|
Postdoctoral Scientist
|
| Email: | fw2181@columbia.edu |
| Interests: | DNA mismatch repair corrects DNA biosynthetic errors, ensures the fidelity of genome. In E. coli, MutS is responsible for mismatch recognition and MutL serves to interface mismatch recognition to activation of downstream activities. In eukaryotes, heterodimers of MutS homologues (MSH? and MSH?) recognize the mismatch site and interactions with heterodimers of MutL homologues (MLH?, MLH?, and MLH?) assist in coordinating downstream events in the repair pathway that lead to new stand synthesis. Using TIRF microscopy, specially designed flow cells and nano-patterned surfaces, my research focus on the interaction between DNA, MSH?, and MLH?: how they move along the DNA and how the movement changes upon mismatch binding, and in the presence of nucleotides and other factors. |
|
|
Ja Yil Lee
|
|
Postdoctoral Scientist
|
| Email: | jl3337@columbia.edu |
| Interests: | MMR (Mismatch repair) is one DNA repair mechanisms, which corrects mispaired bases that result as errors during replication or recombination, and hence enhances the genomic fidelity. Among various MMR proteins, Msh2-Msh6, a human homologue of MutS in E.coli, plays the first role in MMR pathway. The enzyme must scan DNA during its search for mismatched bases. When Msh2-Msh6 locates a mismatch, it binds to the lesion and recruits the other MMR proteins. My research interest is the behavior of Msh2-Msh6 on DNA. By using a combined technique of dual-trap optical tweezers and TIRF microscopy, I will investigate the physical basis of the motion of Msh2-Msh6 on single DNA molecules. The technique enables us to observe the motion of the proteins under various tensions, excluding the interaction of the proteins and the flowcell surface. Finally, I will provide detailed mechanisms that Msh2-Msh6 recognizes the mismatches on DNAs, and how recognition is related to structural transitions in the protein-DNA complex. |
|
 |
Jason Gorman
|
|
Graduate Student
|
| Email: | jg2307@columbia.edu |
| Interests: | Post-replicative mismatch repair (MMR) corrects errors introduced during DNA synthesis before they lead to genomic instability. Mutations in MMR proteins result in a dramatically increased frequency of spontaneous mutation and have been implicated in the onset of various cancers. In S. cerevisiae and humans, the MMR complex Msh2-Msh6 is responsible for recognition of mispaired bases and recruitment of downstream repair factors responsible for excision of the flawed daughter strand. Steps involved in this process include surveying the genome for replication errors, recognition of DNA lesions, identification of strand discrimination signals, and initiation of downstream repair steps. Our hypothesis is that Msh2-Msh6 scans DNA passively through one-dimensional diffusion and becomes energetically trapped upon binding mismatched DNA. Nucleotide exchange then promotes a conformational change releasing Msh2-Msh6 from the site of the lesion and leaves the complex primed for recruitment of downstream repair factors. We will use total internal reflection fluorescent microscopy (TIRFM) to identify the mechanisms involved in these processes and determine the progression of recruitment events in the MMR pathway at a single molecule level. Also, I like candy. |
|
|
Mari-Liis Visnapuu
|
|
Graduate Student
|
| Email: | mv2192@columbia.edu |
| Interests: | The accessibility of DNA to factors that control essential processes such as DNA replication, gene expression, DNA-damage repair and maintenance must be carefully regulated. The compaction of eukaryotic DNA into chromatin and the formation of other nucleoprotein complexes often necessitate specialized enzymes, such as the Snf2 family proteins, to control the accessibility of DNA. However, the details of these reactions remain elusive. I am interested in revealing the dynamic aspects of the mechanisms that Rdh54 and other Snf2 proteins use to translocate along DNA molecules helping to determine how these essential proteins influence the accessibility of DNA in chromatin structures and nucleoprotein complexes. We will visualize the Snf2 protein Rdh54 in real time as it interacts with naked DNA, chromatin substrates, Rad51 nucleoprotein filaments and other nucleoprotein complexes and study the dynamic aspects of these reactions. I also like candy.
|
|
|
Brett Alcott
|
|
Graduate Student
|
| Email: | bea2111@columbia.edu |
| Interests: | The packaging of eukaryotic DNA - which starts at the molecular level of the DNA/histone octamer and "beads-on-a-string" nucleoprotein complex and progresses in magnitude from chromatin to micrometer-sized chromosomes, is the result of highly dynamic, yet tightly controlled set of processes, with genetic calamity the usual result of de-regulation. In the last decade, enzymatic modifications of the histone proteins, primarily at residues in their N- and C- terminal tails, has been shown to influence the physical state - closed or open - of chromatin. My research interests lie in visualizing chromatin dynamics via single-molecule TIRF microscopy - at present, I am working to elucidate the biophysical mechanisms of chromatin compaction and understand how compaction is influenced by various factors.
|
|
|
Teresa Fazio
|
|
Graduate Student in Applied Physics/Applied Math (affiliated member)
|
| Email: | taf2102@columbia.edu |
| Interests: | Engineering active surfaces at the nanoscale revolutionizes the way biologists observe protein-DNA interactions. For the Greene Group, I pattern < 100nm features to tether DNA strands for observation, integrating state-of-the-art lithography and nanopatterning techniques into single-molecule biology experiments.
|
|
 |
Pat Gordon |
|
Rotation Student
|
| Email: | pmg2120@columbia.edu |
| Interests: |
Efficient repair of double-stranded DNA breaks (DSBs) is crucial for maintenance of genome integrity. DSBs can be repaired through homologous recombination (HR), in which continuity is restored using homologous DNA as a template. The eukaryotic recombinase Rad51 mediates heteroduplex formation during HR by assembling on ssDNA and catalyzing strand exchange. Although Rad51 functions on ssDNA, it binds equally well to dsDNA. I am interested in the mechanism of Rad51 dissociation from dsDNA, which occurs with the help of Rad54 and Rhd54/Tid1. I will use TIRF microscopy to visualize the interactions between Rad51 and Rad54. |
|
 |
Holly Wolcott
|
|
Rotation Student
|
| Email: | hnw2104@columbia.edu |
| Interests: | In order to survive, cells must replicate DNA and repair breaks that occur as a result of replication errors or other external factors. Molecular motors help proteins processively translocate on DNA. Molecular motor proteins are essential to these processes. A further understanding of these proteins will provide valuable insight into the mechanisms of DNA replication and repair. I am interested in observing molecular motor proteins using single molecule TIRF microscopy. These experiments will allow us to further understand these proteins and their role in key survival mechanisms. |
|
|
Daniel Duzdevich
|
|
Undergraduate Student
|
| Email: | dd2235@columbia.edu |
| Interests: | Visualization of scRdh54 on DNA arrays to better understand its kinetics and function as a motor protein. Interests in general include chromatin remodeling proteins involved in homologous recombination and helping develop novel techniques for TIRFM visualization of DNA. |
|
|
Pamela Y. Chan
|
|
Undergraduate Student
|
| Email: | pyc2104@columbia.edu |
| Interests: | My work focuses on the single molecule analysis of Rad51-DNA interactions.
Oh yes, I am also the webmaster. |
|
|
Luke Kaplan
|
|
Undergraduate Student, Amgen Scholar
|
| Email: | lk2298@columbia.edu |
| Interests: | Visualization of Rdh54 and its properties as a motor protein
|
|
|
Former Members
|
|
Annette Granéli
|
|
Postdoctoral Scientist
|
| Email: | ag2328@columbia.edu |
Interests: | Rad51 sliding, filament assembly and dynamics. Mechanisms of DNA damage recognition. |
|
|
Caitlyn Yeykal
|
|
|
|
Rachel Zeldin
|
|
|
|
|
Cheryl Lee
|
|
High School Student & Intel Science Competition Contestant
|
| Email: | leec4@bxscience.edu |
| Interests: | Effect of common breast cancer mutations on BRCA2 directed assembly of Rad51. |
|
|
Arindam Chowdhury
|
|
|
|
Prasad Tekkatte Krishnamurthy
|
| Email: | tkprasad1975@gmail.com |
| Currently: | Leading Scientist, Cell Line Development Group,
Biologics Development Centre,
Dr. Reddy's Laboratories Ltd.,
Bachupally, Hyderabad 500072 |
|
|
David Morse
|
|
|
|
Ragan B. Robertson
|
|
Graduate Student
|
| Email: | rbr2005@columbia.edu |
| Interests: | Rad51 is a member of the RecA-like family of DNA recombinases and is involved in a DNA repair pathway called Homologous Recombination. The repair pathway mends double stranded breaks and is conserved from bacteria to man. When Rad51 is bound to DNA, it forms a right-handed helical nucleoprotein filament and extends the original length of the DNA by 50%. This form catalyzes the strand invasion reaction in Homologous Recombination and interacts with a variety of proteins throughout the repair pathway. Our goal is to develop an interactive fluorescence-based assay that will allow us to visualize the nucleoprotein filament in real time at the single molecule level. We will then use this assay to probe the interactions between Rad51 and other proteins and other DNA molecules. |
|
|
|
