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Maria Spies, PhD

Professor of Radiation Oncology
Professor of Biochemistry

Contact Information

4-532 Bowen Science Building (BSB)
Iowa City, IA 52242


BS, Physics/Biophysics, Peter the Great St. Petersburg Polytechnic University (aka Kalinin Leningrad Polytechnic Institute, Leningrad, Russia)
MS, Physics/Biophysics, Peter the Great St. Petersburg Polytechnic University
PhD, Biological Sciences/Structural Biology, Graduate School of Science, Osaka University

Education/Training Program Affiliations

Department of Biochemistry PhD, Interdisciplinary Graduate Program in Translational Biomedicine, Medical Scientist Training Program

Research Summary

Work in my lab focuses on genome caretakers at the intersection of the 3Rs of DNA maintenance, Replication, Recombination and DNA Repair. Understanding the molecular bases and regulation of these processes is fundamentally important because accumulation or incomplete repair of DNA lesions can lead to genetic instability and chromosomal rearrangements causing cancer and cell senescence, while erroneous attempts to reestablish stalled or collapsed replication forks may result in diseases associated with progressive expansion of repeated sequences (such as myotonic dystrophy and Fragile X, syndrome among many others). We study DNA repair at the most fundamental level by first deconstructing the macromolecular ensembles orchestrating distinct DNA repair events down to the level of individual proteins. By combining physical and single-molecule biochemistry, we then investigate molecular mechanisms of the key players in these DNA repair pathways and how other protein partners and posttranslational modifications affect their action. We are also developing novel experimental approaches allowing us to sort and interrogate individual macromolecular complexes extracted from human cells and tissue samples. The resulting integrated in vivo – in vitro – in singulo approach is aimed at identifying features of genome caretaker proteins that can be exploited in designing the new therapeutics. Current projects in our lab focus on regulation of RAD51 protein, which orchestrates the central step of homologous genetic recombination, on deciphering the molecular mechanisms and regulation of several motor proteins (FBH1, FANCJ, RTEL, CHLR1 and XPD) involved in control of RAD51-mediated recombination, replication fork progression and chromosome segregation, as well as on interplay between recombination and mismatch repair.


Stekas, B., Yeo, S., Troitskaia, A., Honda, M., Sho, S., Spies, M. & Chemla, Y. R. (2021). Switch-like Control of Helicase Processivity by Single-Stranded DNA Binding Protein. Elife, 10. PMID: 33739282.

Tibbs, J., Ghoneim, M., Caldwell, C. C., Buzynski, T., Bowie, W., Boehm, E. M., Washington, M. T., Tabei, S. M. & Spies, M. (2021). KERA: analysis tool for multi-process, multi-state single-molecule data. Nucleic Acids Res.. PMID: 33660771.

Hefel, A., Honda, M., Cronin, N., Harrell, K., Patel, P., Spies, M. & Smolikove, S. (2021). RPA complexes in Caenorhabditis elegans meiosis; unique roles in replication, meiotic recombination and apoptosis. Nucleic Acids Res., 49(4), 2005-2026. PMID: 33476370.

Caldwell, C. C., Spies, M. (2020). Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol., 55(5), 482-507. PMID: 32856505.

Subramanyam, S., Spies, M. (2020). RAD51 discrimination between single- and double-strand DNA: a matter of flexibility and enthalpy. EMBO J., 39(7), e104547. PMID: 32090346.

Malacaria, E., Honda, M., Franchitto, A., Spies, M. & Pichierri, P. (2020). Physiological and Pathological Roles of RAD52 at DNA Replication Forks. Cancers (Basel), 12(2). PMID: 32050645.

Malacaria, E., Pugliese, G. M., Honda, M., Marabitti, V., Aiello, F. A., Spies, M., Franchitto, A. & Pichierri, P. (2019). Rad52 prevents excessive replication fork reversal and protects from nascent strand degradation. (Vols. 10). (1), pp. 1412. Nature Communications. PMID: 30926821.

Pokhrel, N., Caldwell, C. C., Corless, E. I., Tillison, E. A., Tibbs, J., Jocic, N., Tabei, S. M., Wold, M. S., Spies, M. & Antony, E. (2019). Dynamics and selective remodeling of the DNA-binding domains of RPA. (Vols. 26). (2), pp. 129-136. Nature Structural & Molecular Biology. PMID: 30723326.

Stefanovie, B., Hengel, S. R., Mlcouskova, J., Lin, Y., Prochazkova, J., Spirek, M., nikulenkov, F., Nemecek, D., Koch, B. G., Bain, F. E., Yu, L., Pasero, P., Spies, M. & Krejci, L. (In Press). DSS1 Interacts and Stimulates RAD52 to Promote DSB Repair and Fork Stability. NAR.

Yates, L. A., Aramayo, R. J., Pokhrel, N., Caldwell, C. C., Kaplan, J. A., Perera, R. L., Spies, M., Antony, E. & Zhang, X. (2018). A structural and dynamic model for the assembly of Replication Protein A on single-stranded DNA. (Vols. 9). (1) Nature Communications. DOI: 10.1038/s41467-018-07883-7.

Spies, M., Malkova, A. (Eds.) (2018). Mechanisms of Homologous Recombination and Genome Rearrangements - Part 1. (Vols. 600). Elsevier, Academic Press.

Spies, M., Malkova, A. (Eds.) (2018). Mechanisms of Homologous Recombination and Genome Rearrangements - Part 2. (Vols. 601). Elsevier, Academic Press.

Caldwell, C. C., Spies, M. (2017). Helicase SPRNTing through the nanopore. (Vols. 114). (45), pp. 11809-11811. Proceedings of the National Academy of Sciences of the United States of America. PMID: 29078420.

Spies, M. (2017). Single-Molecule Sorting of Human DNA Repair Enzymes. Biophysical Journal, 112(3), 5a-6a. DOI: 10.1016/j.bpj.2016.11.052.

Spies, M., Chemla, Y. (Eds.) (2017). Single-molecule enzymology: Nanomechanical Manipulation and Hybrid Methods. (Vols. 582). Methods in Enzymology, Elsevier, Academic Press.

Spies, M. (2017). A Time for Promiscuity in a Eukaryotic Recombinase. (Vols. 292). (26), pp. 11136-11137. JBC. PMID: 27793278.

Spies, M., Smith, B. (2017). Protein-Nucleic Acids Interactions: New Ways of Connecting Structure, Dynamics and Function. (Vols. 9). (4), pp. 289-291. Biophys. Rev.. PMID: 28776257.

Hengel, S., Spies, M. & Spies, M. (In Press). Small Molecule Inhibitors Targeting DNA Repair and DNA Repair Deficiency in Research and Cancer Therapy. Cell Chemical Biology.

Spies, M., Chemla, Y. R. (2017). Preface. In Methods in Enzymology. (Vols. 582). pp. xv-xvi. DOI: 10.1016/S0076-6879(16)30443-8.

Spies, M., Chemla, Y. R. (2016). Single-molecule enzymology: Fluorescence-based and high-throughput methods. In Methods in enzymology. (Vols. 581). Elsevier, Academic Press ISSN 9781128092675.

Spies, M. (Eds.) (2016). Preface (2016) Methods in Enzymology, 581, Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods, Methods in Enzymology, 582, Single-Molecule Enzymology: Nanomechanical Manipulation and Hybrid Methods.

Bain, F. E., Wu, C. G. & Spies, M. (2016). Single-molecule sorting of posttranslationally modified DNA helicases. (Vols. S1046-2023). (16), pp. 30132-3. Methods (San Diego, Calif.). PMID: 27223403.

Bain, F. E., Wu, C. G. & Spies, M. (2016). Single-molecule sorting of DNA helicases. Methods, 108, 14-23. DOI: 10.1016/j.ymeth.2016.05.009.

Subramanyam, S., Ismail, M., Bhattacharya, I. & Spies, M. (2016). Tyrosine phosphorylation stimulates activity of human RAD51 recombinase through altered nucleoprotein filament dynamics. (Vols. 113). (41), pp. E6045-E6054. Proc Natl Acad Sci U S A. PMID: 27671650.

Hengel, S. R., Malacaria, E., da Folly Silva Constantino, L., Bain, F. E., Diaz, A., Koch, B. G., Yu, L., Wu, M., Pichierri, P., Spies, M. A. & Spies, M. (2016). Small-molecule inhibitors identify the RAD52-ssDNA interaction as critical for recovery from replication stress and for survival of BRCA2 deficient cells. (Vols. 5). pp. e14740. eLife. PMID: 27434671.

Chen, R., Subramanyam, S., Elcock, A. H., Spies, M. & Wold, M. S. (2016). Dynamic binding of replication protein a is required for DNA repair. (Vols. 44). (12), pp. 5758-72. NAR. PMID: 27131385.

Wu, C. G., Spies, M. (2016). G-quadruplex recognition and remodeling by the FANCJ helicase. (Vols. 44). (18), pp. 8742-8753. NAR. PMID: 27342280.

Boehm, E. M., Spies, M. & Washington, M. T. (2016). PCNA tool belts and polymerase bridges form during translesion synthesis. (Vols. 44). (17), pp. 8250-60. NAR. PMID: 27325737.

Boehm, E. M., Powers, K. T., Kondratick, C. M., Spies, M., Houtman, J. C. & Washington, M. T. (2016). The Proliferating Cell Nuclear Antigen (PCNA)-interacting Protein (PIP) Motif of DNA Polymerase ? Mediates Its Interaction with the C-terminal Domain of Rev1. (Vols. 291). (16), pp. 8735-44. JBC. PMID: 26903512.

Xu, Z., Gakhar, L., Boehm, E., Washington, T., Spies, M. & Fuentes, E. J. (2016). Insights into the Autoinhibition Mechanism of the Tiam1 Guanine Nucleotide Exchange Factor. Biophysical Journal, 110(3), 206a. DOI: 10.1016/j.bpj.2015.11.1149.

Boehm, E. M., Subramanyam, S., Ghoneim, M., Washington, M. T. & Spies, M. (2016). Chapter 5-Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. pp. 105-145. Methods in Enzymology, 581, Single-Molecule Enzymology: Fluorescent-Based and High-Throughput Methods. PMID: 27793278.

Spies, M., Chemla, Y. R. (2016). Preface. In Methods in Enzymology. (Vols. 581). pp. xvii-xviii. DOI: 10.1016/S0076-6879(16)30407-4.

Spies, M., Fishel, R. (2015). Mismatch repair during homologous and homeologous recombination. (Vols. 7). pp. a022657. Cold Spring Harbor Perspectives in Biology. PMID: 25731766.

Honda, M., Okuno, Y., Hengel, S. R., Martin-Lopez, J. V., Cook, C. P., Amunugama, R., Soukup, R. J., Subramanyam, S., Fishel, R. & Spies, M. (2014). hMSH2-hMSH6 recognizes mismatches and forms sliding clamps within a D-loop recombination intermediate. (Vols. 111). (3), pp. E316-25. PNAS. PMID: 24395779.

Ghoneim, M., Spies, M. (2014). Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. (Vols. 14). (10), pp. 5920-31. Nano Lett. PMID: 25204359.

Spies, M. (2014). Fulfilling the dream of a perfect genome editing tool. (Vols. 111). (28), pp. 10029-30. PNAS. PMID: 24989506.

Spies, M. (2014). Two steps forward, one step back: determining XPD helicase mechanism by single-molecule fluorescence and high-resolution optical tweezers. (Vols. 20). pp. 58-70. DNA Repair (Amst). PMID: 24560558.

(2014). Sliding Clamps within D-loop Recombination Intermediate. Proc Natl Acad Sci USA, 111(3), E316-325. PMID: 24395779.

Haghighat Jahromi, A., Honda, M., Zimmerman, S. C. & Spies, M. (2013). Single-molecule study of the CUG repeat-MBNL1 interaction and its inhibition by small molecules. Nucleic acids research. PMID: 23661680.

Spies, M. (2013). There and back again: new single-molecule insights in the motion of DNA repair proteins. (Vols. 23). (1), pp. 154-60. Current opinion in structural biology. PMID: 23260129.

Subramanyam, S., Jones, W. T., Spies, M. & Spies, M. A. (2013). Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction. (Vols. 41). (19), pp. 9020-9032. NAR. PMID: 23935068.

Spies, M. (2013). DNA repair: trust but verify. (23), pp. R115-7. Curr Biol. PMID: 23391386.

Wu, C. G., Spies, M. (2013). Overview: What are helicases?. In , M. Spies (Eds.) DNA Helicases. (Vols. 767). pp. 47-73. Adv Exp Med Biol.. PMID: 23161004.

Qi, Z., Pugh, R. A., Spies, M. & Chemla, Y. R. (2013). Sequence-dependent base pair stepping dynamics in XPD helicase unwinding. (Vols. 2). pp. e00334. eLife. PMID: 23741615.

Masuda-Ozawa, T., Hoang, T., Seo, Y. S., Chen, L. F. & Spies, M. (2013). Single-molecule sorting reveals how ubiquitylation affects substrate recognition and activities of FBH1 helicase. (Vols. 41). (6), pp. 3579-3587. NAR. PMID: 23393192.

Beyer, D. C., Ghoneim, M. K. & Spies, M. (2013). Structure and Mechanisms of SF2 DNA Helicases. In , M. Spies (Eds.) DNA Helicases. (Vols. 767). pp. 47-73. Adv Exp Med Biol.. PMID: 23161006.

Murfuni, I., Basile, G., Subramanyam, S., Malacaria, E., Bignami, M., Spies, M., Franchitto, A. & Pichierri, P. (2013). Survival of the replication checkpoint deficient cells requires MUS81-RAD52 function. PLOS Genetics e100391. PMID: 24204313.

Spies, M. (2013). DNA Helicases and DNA Motor Proteins. In M. Spies (Eds.) Advances in Experimental Medicine and Biology. Springer New York. DOI: 10.1007/978-1-4614-5037-5.

Ghoneim, M. K., Spies, M. (2013). Single-Molecule Analysis of Conformational Transitions in XPD Helicase. Biophysical Journal, 104(2), 61a. DOI: 10.1016/j.bpj.2012.11.375.

Pugh, R. A., Wu, C. G. & Spies, M. (2012). Regulation of translocation polarity by helicase domain 1 in SF2B helicases. (Vols. 31). (2), pp. 503-14. EMBO Journal. PMID: 22081110.

Spies, M. (2012). Single-Molecule Sorting of DNA Repair Machines. Biophysical Journal, 102(3), 233a. DOI: 10.1016/j.bpj.2011.11.1280.

Honda, M., Okuno, Y., Yoo, J., Ha, T. & Spies, M. (2011). Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding. (Vols. 30). (16), pp. 3368-82. EMBO Journal. PMID: 21804533.

Qi, Z., Pugh, R. A., Spies, M. & Chemla, Y. R. (2011). Displaced Strand Regulation of Facxpd Helicase Activity. Biophysical Journal, 100(3), 73a. DOI: 10.1016/j.bpj.2010.12.599.

Grimme, J. M., Spies, M. (2011). FRET-based assays to monitor DNA binding and annealing by Rad52 recombination mediator protein. (Vols. 745). pp. 463-83. Methods in molecular biology (Clifton, N.J.). PMID: 21660711.

Pugh, R. A., Honda, M. & Spies, M. (2010). Ensemble and single-molecule fluorescence-based assays to monitor DNA binding, translocation, and unwinding by FeS-containing helicases. (Vols. 51). (3), pp. 313-21. Methods. PMID: 20167274.

Grimme, J. M., Honda, M., Wright, R., Okuno, Y., Rothenberg, E., Mazin, A. V., Ha, T. & Spies, M. (2010). Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexes. (Vols. NAR, 38). (9), pp. 2917-30. Nucleic acids research. PMID: 20081207.

Spies, M., Ha, T. (2010). Inching over hurdles: how DNA helicases move on crowded lattices. (Vols. 9). (9), pp. 1742-9. Cell cycle (Georgetown, Tex.). PMID: 20436294.

Honda, M., Park, J., Pugh, R. A., Ha, T. & Spies, M. (2009). Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase. (Vols. 35). (5), pp. 694-703. Molecular Cell. PMID: 19748362.

Rothenberg, E., Grimme, J. M., Spies, M. & Ha, T. (2008). Rad52 protein mediates directionally biased homology search and DNA annealing through continuous association of two Rad52-ssDNA complexes. (Vols. PNAS 105). (51), pp. 20274-9. Proceedings of the National Academy of Sciences of the United States of America. PMID: 19074292.

Pugh, R. A., Lin, Y., Eller, C., Leesley, H., Cann, I. K. & Spies, M. (2008). Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase. (Vols. 383). (5), pp. 982-98. Journal of Molecular Biology. PMID: 18801373.

Lin, Y., Lin, L. J., Sriratana, P., Coleman, K., Ha, T., Spies, M. & Cann, I. K. (2008). Engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds. (Vols. 190). (17), pp. 5766-80. Journal of Bacteriology. PMID: 18586938.

Pugh, R. A., Spies, M. (2008). DNA Helicases, Chemistry and Mechanisms of. Wiley Encyclopedia of Chemical Biology.

Pugh, R. A., Honda, M., Leesley, H., Thomas, A., Lin, Y., Nilges, M. J., Cann, I. K. & Spies, M. (2008). The iron-containing domain is essential in Rad3 helicases for coupling of ATP hydrolysis to DNA translocation and for targeting the helicase to the single-stranded DNA-double-stranded DNA junction. (Vols. 283). (3), pp. 1732-43. The Journal of Biological Chemistry. PMID: 18029358.

Spies, M., Amitani, I., Baskin, R. J. & Kowalczykowski, S. C. (2007). RecBCD Enzyme Switches Lead Motor Subunits in Response to ? Recognition. Cell, 131(4), 694-705. DOI: 10.1016/j.cell.2007.09.023.

Grimme, J. M., Spies, M. (2007). "DNA helicases in homologous recombination"(in "Molecular Genetics, Biophysics and Medicine Today" (Bresler Memorial Lectures --II) Editor: Vladislav Lanzov), PNPI Press, 2007, St. Petersburg, Russia., V. Lanzov (Eds.) pp. 123-140.

Spies, M., Amitani, I., Baskin, R. J. & Kowalczykowski, S. C. (2007). Translocation by single-molecules of a RecBCD motor mutant reveals a switch in motor subunit usage at X. pp. 694-705, highlight 651-653. Cell.

Spies, M., Kowalczykowski, S. C. (2006). The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins. (Vols. 21). (4), pp. 573-80. Molecular Cell. PMID: 16483938.

Spies, M., Dillingham, M. S. & Kowalczykowski, S. C. (2005). Translocation by the RecB motor is an absolute requirement for {chi}-recognition and RecA protein loading by RecBCD enzyme. (Vols. 280). (44), pp. 37078-87. The Journal of Biological Chemistry. PMID: 16041060.

Spies, M., Dillingham, M. S. & Kowalczykowski, S. C. (2005). DNA helicases. McGraw-Hill Professional (Eds.) McGraw-Hill Encyclopedia of Science & Technology (McGraw-Hill Professional 2005 edition).

Spies, M., Kowalczykowski, S. C. (2004). "Homologous recombination by RecBCD and RecF Pathways" in "The Bacterial Chromosome"., ASM Press Washington D.C. (Eds.) pp. 389-403. ASM Press, Washington, DC.

Spies, M., Bianco, P. R., Dillingham, M. S., Handa, N., Baskin, R. J. & Kowalczykowski, S. C. (2003). A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. (Vols. 114). (5), pp. 647-54. Cell. PMID: 13678587.

Dillingham, M. S., Spies, M. & Kowalczykowski, S. C. (2003). RecBCD enzyme is a bipolar DNA helicase. (Vols. 423). (6942), pp. 893-7. Nature. PMID: 12815438.

Spies, M., Dillingham, M. S. & Kowalczykowski, S. C. (2003). DNA helicases. McGraw-Hill Professional (Eds.) pp. 95-98. McGraw-Hill 2003 Yearbook of Science & Technology.

Spies, M., Kil, Y., Masui, R., Kato, R., Kujo, C., Ohshima, T., Kuramitsu, S. & Lanzov, V. (2000). The RadA protein from a hyperthermophilic archaeon Pyrobaculum islandicum is a DNA-dependent ATPase that exhibits two disparate catalytic modes, with a transition temperature at 75 degrees C. (Vols. 267). (4), pp. 1125-37. European journal of biochemistry / FEBS. PMID: 10672022.

Mirlina, E. D., Manicheva, O. A., Visnevsky, B. I., Silbergleit Arc, S., Tchernayenko, V. M. & Lanzov, V. A. (1996). PCR-based molecular diagnostics procedure for revealing Mycobacterium tuberculosis complex: visualization of the results using avidinbiotin system. (Vols. 2). pp. 48-55. Biotehnologia (Biotechnology Russ.).

Koudrova, M., Arnold, H. H., Koster, M. & Braun, T. (1996). Regulation and function of SF/HGF during migration of limb muscle precursor cells in chicken. (Vols. 180). (2), pp. 566-578. Developmental Biology.