Professor of Biochemistry and Biophysics, and Co-director of Graduate Studies
(PhD - University of Toronto)
Ramsden Lab Website
HONORS AND REWARDS
- Leukemia and Lymphoma Society Scholarship, 2006-2011
- Jefferson Pilot fellowship, 2003-2006
- Searle Scholar, 1999-2002
- Cancer Research Institute fellowship, 1996-1998
- Governor General’s Gold Medal, 1994
Double Strand Break Repair
We use diverse molecular biological approaches in an effort to understand both how chromosome double strand breaks are repaired, as well as the consequences of failed or mutagenic repair.
Ku loads on broken ends, and excises abasic site damage at ends
using a well-positioned active site (cyan residues)
We build and rebuild our genomes through excision (nucleases), synthesis (polymerases), and joining (ligases). These processes typically rely on cues specific to a double helix to guide their function, but these cues are missing at double strand breaks. We are thus working to understand how the enzymes implicated in repair of double strand breaks nevertheless remain active. We want to know how they bypass the standard requirements for fundamental DNA transactions, as well as the mechanistic basis for this increased flexibility.
A DSB repair polymerase uses a protein “loop” (magenta) as a surrogate for DNA template (green) when template is missing at a double strand break.
We are also using next generation sequencing to evaluate the consequences of flexibility in double strand break repair - when and how flexibility protects from, or contributes to, mutations. Many agents used in cancer therapies work by introducing chromosome breaks. We are therefore also evaluating how cells vary in the way they repair DNA breaks with a focus on cancer-specific heterogeneity, to see how this impacts the effectiveness and safety of cancer therapies.
- Mohapatra S, Yannone SM, Lee SH, Hromas RA, Akopiants K, Menon V., Ramsden DA, and Povirk LF. Trimming of damaged 3' overhangs of DNA double strand breaks by the Metnase and Artemis endonucleases." DNA repair 12:422-432, 2013.
- Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS. “Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.” Nat. Struc and Mol Biol 19:1363-71 2012.
- Strande NT, Waters CA, and Ramsden DA. "Resolution of complex ends by nonhomologous end joining - better to be lucky than good?" Genome integrity, 3: 10.2012
- Strande, N, Roberts, S.A., Oh, S., Hendrickson, E.A., and Ramsden, D.A. Specificity of Ku’s dRP/AP lyase promotes nonhomologous end joining (NHEJ) fidelity at damaged ends. J. Biol, Chem., 287: 13686-93, 2012.
- Ramsden, DA and Asagoshi, K. " DNA polymerases in Nonhomologous end joining: are there any benefits from standing out from the crowd?". Environ. Mol. Mutagen., 53:741-751, 2012.
- Roberts, S.A., Strande, N, Burkhalter, M.D., Strom, C., Havener, J.M., Hastry, P., and Ramsden, D.A. Ku is a 5’dRP/AP lyase that excises nucleotide damage near broken ends. Nature, 464:1214-7. 2010
- Burkhalter MD, Roberts SA, Havener JM, Ramsden DA. Activity of ribonucleotide reductase helps determine how cells repair DNA double strand breaks. DNA Repair (Amst). 2009 Nov 2;8(11):1258-63. Epub 2009 Aug 26. PubMed PMID: 19713159; PubMed Central PMCID: PMC2763971.
- Garcia-Diaz M, Bebenek K, Larrea AA, Havener JM, Perera L, Krahn JM, Pedersen LC, Ramsden DA, Kunkel TA. Template strand scrunching during DNA gap repair synthesis by human polymerase lambda. Nat Struct Mol Biol. 2009 Sep;16(9):967-72. Epub 2009 Aug 23. PubMed PMID: 19701199; PubMed Central PMCID: PMC2767187.
- Zhou T, Akopiants K, Mohapatra S, Lin PS, Valerie K, Ramsden DA, Lees-Miller SP, Povirk LF. Tyrosyl-DNA phosphodiesterase and the repair of 3'-phosphoglycolate-terminated DNA double-strand breaks. DNA Repair (Amst). 2009 Aug 6;8(8):901-11. Epub 2009 Jun 7. PubMed PMID: 19505854; PubMed Central PMCID: PMC2763370.
- Bukowy Z, Harrigan JA, Ramsden DA, Tudek B, Bohr VA, Stevnsner T. WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand. Nucleic Acids Res. 2008 Sep;36(15):4975-87. Epub 2008 Jul 25. PubMed PMID: 18658245; PubMed Central PMCID: PMC2528166.
- Mueller GA, Moon AF, Derose EF, Havener JM, Ramsden DA, Pedersen LC, London RE. A comparison of BRCT domains involved in nonhomologous end-joining: introducing the solution structure of the BRCT domain of polymerase lambda. DNA Repair (Amst). 2008 Aug 2;7(8):1340-51. Epub 2008 Jun 26. PubMed PMID: 18585102; PubMed Central PMCID: PMC2583787
- Davis BJ, Havener JM, Ramsden DA. End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining. Nucleic Acids Res. 2008 May;36(9):3085-94. Epub 2008 Apr 8. PubMed PMID: 18397950; PubMed Central PMCID: PMC2396419.
- DeRose EF, Clarkson MW, Gilmore SA, Galban CJ, Tripathy A, Havener JM, Mueller GA, Ramsden DA, London RE, Lee AL. Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining. Biochemistry. 2007 Oct 30;46(43):12100-10. Epub 2007 Oct 4. PubMed PMID: 17915942; PubMed Central PMCID: PMC2653216.
- Roberts SA, Ramsden DA. Loading of the nonhomologous end joining factor, Ku, on protein-occluded DNA ends. J Biol Chem. 2007 Apr 6;282(14):10605-13. Epub 2007 Feb 8. PubMed PMID: 17289670.
- Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC. Structural insight into the substrate specificity of DNA Polymerase mu. Nat Struct Mol Biol. 2007 Jan;14(1):45-53. Epub 2006 Dec 10. Erratum in: Nat Struct Mol Biol. 2007 Jul;14(7):680. PubMed PMID: 17159995.
- Povirk LF, Zhou RZ, Ramsden DA, Lees-Miller SP, Valerie K. Phosphorylation in the serine/threonine 2609-2647 cluster promotes but is not essential for DNA-dependent protein kinase-mediated nonhomologous end joining in human whole-cell extracts. Nucleic Acids Res. 2007;35(12):3869-78. Epub 2007 May 25. PubMed PMID: 17526517; PubMed Central PMCID: PMC1919499.
- Reddy YV, Perkins EJ, Ramsden DA. Genomic instability due to V(D)J recombination-associated transposition. Genes Dev. 2006 Jun 15;20(12):1575-82. PubMed PMID: 16778076; PubMed Central PMCID: PMC1482478.
- Nick McElhinny SA, Havener JM, Garcia-Diaz M, Juárez R, Bebenek K, Kee BL, Blanco L, Kunkel TA, Ramsden DA. A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol Cell. 2005 Aug 5;19(3):357-66. PubMed PMID: 16061182.