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Daniel Semlow

Research Summary
DNA replication and repair; nucleic acid chemistry
Profile

Assistant: Ann Mao

The Semlow lab uses complementary biochemical, genetic, and analytical approaches to understand the mechanisms that allow cells to tolerate and repair DNA damage during replication. Furthermore, the lab develops tools to identify novel forms of chemical DNA damage and elucidate the origin of these lesions. Beyond advancing current understanding of critical DNA repair pathways, these studies may form the basis of therapeutic interventions that sensitize cancer cells to chemotherapy or mitigate the effects of disease-causing DNA repair deficiencies.

Publications

DR Semlow†, VA MacKrell, and JC Walter† (2022) The HMCES DNA-protein cross-link functions as an intermediate in DNA interstrand cross-link repair. Nat. Struct. Mol. Biol. doi:10.1038/s41594-022-00764-0.

DR Semlow and JC Walter (2021) Mechanisms of Vertebrate DNA Interstrand Cross-Link Repair. Annu. Rev. Biochem. doi:10.1146/annurev-biochem-080320-112510.

RA Wu*, DR Semlow*, AN Kamimae-Lanning, OV Kochenova, G Chistol, MR Hodskinson, R Amunugama, JL Sparks, M Wang, L Deng, CA Mimoso, E Low, KJ Patel, and JC Walter, J.C. (2019). TRAIP is a master regulator of DNA interstrand crosslink repair. Nature. doi:10.1038/s41586-019-1002-0.

DR Semlow*, J Zhang*, M Budzowska, AC Drohat, and JC Walter (2016). Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase. Cell. doi:10.1016/j.cell.2016.09.008.

D.R. Semlow, M.R. Blanco, N.G. Walter, and JP Staley, J.P. (2016). Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites. Cell. doi:10.1016/j.cell.2016.01.025.

D.R. Semlow and J.P. Staley (2012). Staying on message: ensuring fidelity in pre-mRNA splicing. Trends Biochem. Sci. doi:10.1016/j.tibs.2012.04.001.

R.M. Mayas*, H. Maita*, D.R. Semlow*, and J.P. Staley (2010). Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc. Natl. Acad. Sci U.S.A. doi:10.1073/pnas.0906022107.

D.R. Semlow and S.K. Silverman (2005). Parallel selections in vitro reveal a preference for 2'-5' RNA ligation upon deoxyribozyme-mediated opening of a 2',3'-cyclic phosphate. J. Mol. Evol. doi:10.1007/s00239-004-0326-y.

T. K. Prior, D.R. Semlow, A. Flynn-Charlebois, I. Rashid, and S.K. Silverman (2004). Structure-function correlations derived from faster variants of a RNA ligase deoxyribozyme. Nucleic Acids Res. doi:10.1093/nar/gkh263.

(† corresponding author; * equal contribution)

2025-26
Ch/Bi 111. Biochemistry of Gene Expression. 12 units (4-0-8); second term, 2025-26. Prerequisites: Ch/Bi 110 ab; Bi 8 and Bi 122 recommended. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and chromatin structure.
Instructors: Parker, Semlow
BMB/Bi/Ch 174. Macromolecular Machines of the Central Dogma. 6 units (3-0-3); first term, 2025-26. Prerequisites: Ch/Bi 110 ab or equivalent. The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein. Each step in this process depends on different macromolecular machines that copy, transcribe, and decode the information stored in DNA. This course will focus on the function of such assemblies, including the replisome, RNA Pol II, the spliceosome, the ribosome, and translocons. The course will be taught through a combination of lectures and student-led discussions of the primary literature that has shaped our understanding of how macromolecular machines operate. Students will also prepare a short research proposal that will be peer reviewed and discussed at the end of the term at a mock NIH-style study section.
Instructor: Semlow
2023-24
BMB/Bi/Ch 174. Advanced Topics in Biochemistry and Molecular Biophysics. 6 units (3-0-3); first term, 2023-24. Prerequisites: Ch/Bi 110 or equivalent. Discussion of research fields in biochemistry and molecular biophysics at Caltech. Development of skills in literature analysis and information synthesis.
Instructors: Chong, Semlow, and guest lecturers
2022-23
Ch/Bi 111. Biochemistry of Gene Expression. 12 units (4-0-8); third term, 2022-23. Prerequisites: Ch/Bi 110 ab; Bi 8 and Bi 122 recommended. Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and chromatin structure.
Instructors: Parker, Semlow
BMB/Bi/Ch 174. Advanced Topics in Biochemistry and Molecular Biophysics. 6 units (3-0-3); first term, 2022-23. Prerequisites: Ch/Bi 110 or equivalent. Discussion of research fields in biochemistry and molecular biophysics at Caltech. Development of skills in literature analysis and information synthesis.
Instructors: Chong, Semlow, and guest lecturers