Melike Caglayan,

Laboratory of Genome Stability and DNA Repair

The integrity of one’s genetic material is constantly being threatened by a variety of endogenous sources and exogenous factors such as UV-light and environmental agents. Unintended changes to DNA have the potential to lead to permanent alterations in the coding property of the genome or to drive adverse molecular events, such as transcriptional blockage or replication fork collapse.

Fortunately, cells have evolved a suite of mechanisms, known as DNA repair, that aim to recognize and resolve harmful damage, preserving genome integrity and averting disease development. Of the DNA repair pathways that operate to avoid pathogenic outcomes, base excision repair (BER) is often considered the workhorse system, responsible for resolving numerous spontaneous and oxidative forms of DNA damage.

Base Excision Repair (BER)

BER is the most important process for preventing the mutagenic and lethal consequences of DNA damage, namely base lesions, e.g., 8-oxo-2′-deoxyguanine (8-oxodG), abasic (AP) sites, and single-strand breaks. Inherited or sporadic defects in BER have been demonstrated to result in increased cancer predisposition, immunological dysfunction, and many degenerative diseases, including those of the brain. BER pathway involves the removal of the damaged base and subsequent processing by a multi-protein complex that protects the cell from toxic DNA intermediates.

CAGLAYAN LAB

The Caglayan lab focuses on the molecular basis of BER to elucidate the mechanism of the repair pathway coordination at the downstream steps involving gap filling (or DNA synthesis) by DNA polymerase β and subsequent nick sealing (or DNA ligation) by DNA ligase 1 and 3α using a combined approach including biochemical, biophysical, structural, and single-molecule studies.

Using biochemical and DNA repair assays in vitro, Caglayan’s lab study how polβ and LIG1/LIG3α coordinate to execute DNA damage processing for faithful BER.

Using X-ray crystallography, Caglayan’s lab gains an atomic insight into nick sealing by LIG1 and LIG3α that finalize BER repair pathway to elucidate how BER ligases ensure fidelity at the final step.

By employing a three-color total internal reflection fluorescence (TIRF) microscopy, her laboratory monitors the sequential multi-step process of BER coordination at single-molecule level, and the dynamics of nick sealing by DNA ligases in real-time.

Dr. Caglayan’s research program has been continuously funded by R00 from NIEHS, UF Health Cancer Center, Thomas Maren Award from UF/COM, R35 MIRA ESI from NIGMS. Her laboratory’s work has been recognized by the scientific community via invitations for review articles, talks at national/international conferences, and requests to serve on grant review committees for NIH and NSF.

Key publications:

Published at Nature

1. Tang Q., Gulkis M., McKenna R., Çağlayan M. (2022) Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair. Nature Communications 13: 3860.

2. Çağlayan M*. and Wilson S.H. (2018) Pol μ dGTP mismatch insertion opposite T coupled with ligation reveals a promutagenic DNA intermediate during double strand break repair. Nature Communications 9: 4213. *Co-corresponding author

3. Çağlayan M., Horton J.K., Da-Peng D., Stefanick D.F., Wilson S.H. (2017) Oxidized nucleotide insertion by pol β confounds ligation during base excision repair. Nature Communications 8: 14045.

4. Çağlayan M., Batra V.K., Sassa A., Prasad R., Wilson S.H. (2014) Role of polymerase β in complementing aprataxin deficiency during abasic-site base excision repair. Nature Structural and Molecular Biology 21: 497-499.

Published at Nucleic Acids Research

1. Chatterjee S., Chaubet L., Berg A., Mukhortava A., Almohdar D., Ratcliffe J., Gulkis M., Çağlayan M. (2024) Probing nick DNA binding by LIG1 at the single-molecule level. Nucleic Acids Research. gkae865

2. Gulkis M., Martinez E., Almohdar D., Çağlayan M. (2024) Unfilled gaps by polβ leads to aberrant ligation by LIG1 at the downstream steps of base excision repair. Nucleic Acids Research. 52: 3810-3822.

3. Çağlayan M. (2020) The ligation of polβ mismatch insertion products governs the formation of promutagenic base excision DNA repair intermediates. Nucleic Acids Research 8: 3708-3721.

4. Çağlayan M., Prasad R., Krasich R., Longley M.J., Kadoda K., Tsuda M., Sasanuma H., Takeda S., Tano K., Copeland W.C., Wilson S.H. (2017) Complementation of aprataxin deficiency by base excision repair enzymes in mitochondrial extracts. Nucleic Acids Research 17: 10079-10088.

5. Çağlayan M., Horton J.K., Prasad R., Wilson S.H. (2015) Complementation of aprataxin deficiency by base excision repair enzymes. Nucleic Acids Research 43: 2271-2281.

Published at Journal of Biological Chemistry

1. Balu K., Almohdar D., Tang, Q., Ratcliffe J., Kalaycioglu, M., Çağlayan M. (2024) Structures of LIG1 uncover the mechanism of sugar discrimination against 5′-RNA-DNA junctions during ribonucleotide excision repair. Journal of Biological Chemistry – in press. PMID: 39159820

2. Almohdar D., Murcia M., Tang Q., Ortiz A., Martinez E., Parwal, T., Kamble P., Çağlayan M. (2024) Impact of DNA ligase 1 and IIIα interactions with APE1 and polβ on the efficiency of base excision repair pathway at the downstream steps. Journal of Biological Chemistry. 300: 107355.

3. Balu K., Gulkis M., Almohdar D., Çağlayan M. (2024) Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3′-end of nick DNA. Journal of Biological Chemistry. 300: 107216.

4. Tang Q. and Çağlayan M. (2021) The scaffold protein XRCC1 stabilizes the formation of polβ/gap DNA and ligase IIIα/nick DNA complexes in base excision repair. Journal of Biological Chemistry 297: 101025.

5. Kamble P., Hall K., Chandak M., Tang Q., Çağlayan M. (2021) DNA ligase I fidelity the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair. Journal of Biological Chemistry 296: 100427.

0000-0003-1107-1042

• Biochemistry
• DNA Repair
• DNA Replication
• DNA damage
• Genome Stability
• Oxidative stress
• Protein biochemistry
• X-ray crystallography
• single molecule biophysics