Search Pubmed for publications from the Trakselis Laboratory. MyNCBI
From Trakselis Lab:
69) Blue, A., Rodriguez-Escalante, M., Villacob, R.A., Bannon, M., Carpenter, G.W., Gallagher, E.S., and Trakselis, M.A.* Response factor correction for quantitative determination of homooligomeric protein binding to DNA by native protein mass spectrometry. submitted. ChemRxiv
68) Baragama Arachchi, R.Y., Okafor, D.C, Snyder, A.J., and Trakselis, M.A.* MCM8/9 and FANCD2 interact within a shared pathway in response to replication stress caused by DNA crosslinks. DNA Repair in press. 10.1016/j.dnarep.2025.103909 or BioRxiv
67) Welikala, M.U., Butterworth, L.J., Baragamaarachchi, R., and Trakselis, M.A.* (2025) Mechanistic coupling of enzymatic activities at the replisome. J. Biol Chem. In press. 10.1016/j.jbc.2025.110761 PMID: 41005479
66) Disha, S.S., Punchipatabendi, T., Kaszubowski, J.D., Liang, B., Pata, J.D., and Trakselis, M.A.* (2025) Residues in the Y-family Dpo4 DNA polymerase communicate to restrict downstream synthesis past 8-oxoguanine lesions. Nuc. Acids. Res. Volume 53, Issue 18, 14 October, gkaf950, https://doi.org/10.1093/nar/gkaf950 PMID: 41002026
65) Butterworth, L.J., Welikala, M.U., Klatt, C.W., Rheney, K.E., and Trakselis, M.A.* (2025) Replisomal coupling between the α-Pol III core and the τ-subunit of the clamp loader complex (CLC) are essential for genomic integrity in E. coli, J Biol Chem. 2024 Aug 28:107726. doi: 10.1016/j.jbc.2025.108177. PMID: 39798872.
64) Welikala, M.U., Butterworth, L.J., Behrmann, M.S., and Trakselis, M.A.* (2024) Tau mediated coupling between Pol III synthesis and DnaB helicase unwinding helps maintain genomic stability, J Biol Chem. 2024 Aug 28:107726. doi: 10.1016/j.jbc.2024.107726. PMID: 39214305.
63) Behrmann, M.S., Perera, H.M., Welikala, M.U., Matthews, J.E, and Trakselis, M.A.* (2024) Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization, NAR, 52 (12), 6977-6993. PMID: 38808668.
62) Edwards, A.N., Blue, A.J., Conforti, J.M., Cordes, M.S., Trakselis, M.A., Gallagher, E.S.* (2023) Gas-phase stability and thermodynamics of ligand-bound, binary complexes of chloramphenicol acetyltransferase reveal negative cooperativity, Analy. Bioanaly. Chem., 415 (25), 6201-6212. DOI:10.1007/s00216-023-04891-5. PMID: 37542535.
61) McKinzey, D., Li, C., Gao, Y., and and Trakselis, M.A.* (2023) Activity, Substrate Preference, and Structure of the HsMCM8/9 Helicase, NAR, Jun 13:gkad508. doi: 10.1093/nar/gkad508. PMID: 37309874.
60) Griffin, W.C., McKinzey, D., Klinzing, K.A., Baratam, R., and Eliyapura, A., and Trakselis, M.A.* (2022) A multi-functional role for the MCM8/9 helicase complex in maintaining fork integrity during replication stress, Nat. Commun. 13, 5090. doi.org/10.1038/s41467-022-32583-8
61) Trakselis, M.A. (ed) (2022) Helicase Enzymes Part B Methods in Enzymology. Vol 673
60) Trakselis, M.A. (ed) (2022) Helicase Enzymes Part A, Methods in Enzymology. Vol 672
59) Behrmann, M.S. and Trakselis, M.A.* (2022) In vivo fluorescent TUNEL detection of single stranded DNA gaps and breaks induced by dnaB helicase mutants in Escherichia coli. Methods in Enzymology. Vol 672, 125-142.
58) Kaszubowski, J.D. and Trakselis, M.A.* (2022) Beyond the lesion: Back to high fidelity DNA synthesis. Front. Mol. Biosci., Vol 8, 811540. link.
57) Behrmann, M.S., Perera, H.M., Hoang, J.M., Venkat, T.A., Visser, B.J., Bates, D. and
56) Perera, H.M. and
55) 
54) A Unifying Framework for Understanding Biological Structures and Functions Across Levels of Biological Organization. Integr. Comp. Biol. icab167. link
53) McKinzey, D.R., Gomathinayagam, S., Griffin, W.C., Klinzing, K.N., Jeffries, E.P., Rajkovic, A. and Trakselis, M.A. (2021) Motifs of the C-terminal domain of MCM9 direct localization to sites of mitomycin-C damage for RAD51 recruitment. JBC, 296, 100355. link bioRxiv
52) Cranford, M.T., Kaszubowski, J.D., and Trakselis, M.A. (2020) A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine. NAR, 48(19) 10986-97. link
51) Perera, H.M. and Trakselis, M.A. (2020) Site-specific DNA mapping using azidophenacyl bromide (APB) to map the binding orientation of proteins. Bio-protocol, 10(12): e3649. link
50) Perera, H.M. and Trakselis, M.A. (2019) Amidst multiple binding orientations on fork DNA, Saccharolobus MCM helicase proceeds N-first for unwinding. Elife, 8. pii: e46096. link
49) Perera, H.M., Behrmann, M.S., Hoang, J.M., Griffin, W.C., Trakselis, M.A. (2019) Contacts and context that regulate DNA helicase unwinding and replisome progression. The Enzymes, 45:183-223. link
48) Brosh, R.M. and Trakselis, M.A. (2019) Fine-tuning of the replisome: Mcm10 regulates fork progression and regression. Cell Cycle, 18(10):1047-1055. link
47) Griffin, W.C. and Trakselis, M.A. (2019) The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance. DNA Repair, 76:1-10. link
46) Graham, B.W., Perera, H., Bougoulias, M.E., Dodge, K.L., Thaxton, C.T., Olaso, D., Young, Tao, Y., N.L., Marshall, A.G., and Trakselis, M.A. (2018) Control of hexamerization, assembly, and excluded strand specificity for the Sulfolobus solfataricus MCM helicase., Biochemistry, 57, 5672-5682. link
45) van Dongen, S. F. M., Clerx, J., van den Boomen, O. I., Pervaiz, M., Trakselis, M. A.
Ritschel, T., Schoonen, L., Schoenmakers, D. C. and Nolte, R. J. M. (2018) Synthetic polymers as substrates for a DNA-sliding clamp protein, Biopolymers, e23119 link
44) Carney, S.M., Gomathinayagam, S., Leuba, S.H., and Trakselis, M.A. (2017) Bacterial DnaB Helicase Interacts with the Excluded Strand to Regulate Unwinding, J. Biol. Chem., 292(46):19001-19012. doi: 10.1074/jbc.M117.814178.
43) Trakselis, M.A., Cranford, M.T., Chu, A.M. (2017) Coordination and Substitution of DNA Polymerases in Response to Genomic Obstacles, ACS Chem. Res. Tox., 30(11):1956-1971. doi: 10.1021/acs.chemrestox.7b00190.
42) Cranford, M.T., Chu, A.M., Baguley, J., Bauer, R.J., and Trakselis, M.A. (2017) Characterization of a Coupled DNA Replication and Translesion Synthesis Polymerase Supraholoenzyme, Nuc. Acids Res., 45, 8329-40. link
41) Trakselis, M.A., Siedman, M.M., Brosh, R.M. Jr. (2017) Mechanistic Insights Into How CMG Helicase Facilitates Replication Past DNA Roadblocks. DNA Repair, 108, 79-91. link
40) Khan, I., Crouch, J.D., Bharti, S.K., Sommers, J.A., Carney, S.M., Yakubovskaya, E., Garcia-Diaz, M., Trakselis, M.A., Brosh, R.M. Jr. (2016) Biochemical characterization of the human mitochondrial replicative Twinkle helicase: Substrate specificity, DNA branch-migration, and ability to overcome blockades to DNA unwinding. J. Biol. Chem., 291, 14324-39. link 
39) Carney, S.M. and Trakselis, M.A. (2016) The Excluded DNA Strand is SEW Important for Hexameric Helicase Unwinding, Methods, 108, 79-91. doi:10.1016/j.ymeth.2016.04.008 in press. link
38) Graham, B.W., Tao, Y., Dodge, K.L., Zhang, Q., Thaxton, C.T., Olaso, D., Young, N.L., Marshal, A.G., and Trakselis, M.A. (2016) DNA Interactions probed by H/D exchange FT-ICR mass spectrometry confirm external surface binding sites on the MCM helicase. J. Biol. Chem., 291, 12467-80. link
37) Trakselis, M.A., (2016) Structural mechanisms of hexameric helicase loading, assembly, and unwinding. F1000Research, 5(F1000 Faculty Rev):111 (doi: 10.12688/f1000research.7509.1). link
36) Barnes, C.O.,Calero, M.,Malik, I.,Graham, B.W., Spahr, H.,Lin, G.,Cohen, A.E., Brown, I.S.,Zhang, Q., Pullara, F., Trakselis, M.A., Kaplan, C.D., Calero, G. (2015) Crystal structure of a transcribing RNA polymerase II complex reveals a complete transcription bubble. Mol. Cell, 59 (2), 258-69. link
35) AlAsiri, S., Basit, S., Wood-Trageser, M.A., Yatsenko, S.A., Jeffries, E.P., Surti, U., Ketterer, D.M., Afzal, S., Ramzan, R., Faiyaz-Ul Haque, M., Jiang, H, Trakselis, M.A., Rajkovic, A. (2015) Exome sequencing reveals MCM8 mutation underlies ovarian failure and chromosomal instability. J. Clin. Invest., 125 (1), 754-62. link
34) Wood-Trageser, M.A., Gurbuz, F., Yatsenko, S.A., Jeffries, E.P., Kotan, L.D., Surti, U., Ketterer, D.M., Matic, J., Chipkin, J., Jiang, H, Trakselis, M.A., Topaloglu, A.K., Rajkovic, A. (2014) Exome sequencing identifies MCM9 mutations in ovarian failure, short stature and chromosomal instability. Am. J. Hum. Genetics, 95 (6), 754-762. link 
33) Nucleic Acid Polymerases, Murakami, K. and Trakselis, M.A. (Eds.), Nucleic Acids and Molecular Biology Vol. 30, Berlin, Germany, Springer. 2014. link
32) Trakselis, M.A. and Murakami, K. Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms, (Chapter 1), Nucleic Acid Polymerases, Murakami, K. and Trakselis, M.A. (Eds.), Nucleic Acids and Molecular Biology Vol. 30, Berlin, Germany, Springer. 2014. link
31) Trakselis, M.A. and Bauer, R.J. Archaeal DNA Polymerases: Enzymatic Abilities, Coordination, and Unique Properties, (Chapter 6), Nucleic Acid Polymerases, Murakami, K. and Trakselis, M.A. (Eds.), Nucleic Acids and Molecular Biology Vol. 30, Berlin, Germany, Springer. 2014. link
30) Bauer, R.J., Wolff, I.D., Zuo, X., Lin, H-K., Trakselis, M.A. (2013) Assembly and Distributive Action of an Archaeal DNA Polymerase Holoenzyme. Special Issue of J. Mol. Biol. entitled “DNA replication & Genomic instability – Replicon Theory”, 425 (230), 4820-36. link
29) Mohan S., Das, D., Bauer R.J., Heroux A., Zalewski, J.K., Heber, S., Dosunmu-Oqunbi, A.M., Trakselis, M.A., Hildebrand J.D., and VanDemark A.P (2013) Structure of a Highly Conserved Domain of Rock1 Required for Shroom-mediated Regulation of Cell Morphology. PLOS One, 8(12), e81075. link
28) van Dongen, S.F.M., Clerx, J., Nørgaard, K., Bloemberg. T.G., Cornelissen, J.J.L.M., Trakselis, M.A., Nelson, S.W., Benkovic, S.J., Rowan, A.E., Nolte, R.J.M. A Clamp-Shaped Bio-Hybrid Catalyst for DNA Oxidation. Nature Chem., 5(11), 946-51. link
Commentary by: Prins, L.J. & Scrimin, S. Processive Catalysis: Tread and Cut, News and Views, Nature Chem., 5, 899-900.
27) Jeffries, E.P., Denq, W.I., Bartko, J.C., and Trakselis, M.A. (2013) Identification, Quantification, and Evolutionary Analysis of a Novel Isoform of MCM9, Gene, 519, 41-49. link
26) Bauer, R.J., Graham, B.W., and Trakselis, M.A. (2013) Novel Interaction of the Bacterial-like DnaG Primase with the MCM Helicase in Archaea, J. Mol. Biol., 8(26), 1259-1273. link
25) Trakselis, M.A. and Graham, B.W. (2012) Biochemisty: Molecular Hurdles Cleared with Ease, Nature, 492, 195-197. link
24) Lin, H-K., Chase, S.F., Laue, T.M., Jen-Jacobsen, L., and Trakselis, M.A. (2012) Differential Temperature Dependent Multimeric Assemblies of Replication and Repair Polymerases on DNA Increase Processivity. Biochemistry,51, 7367-7382. link
23) Mohan, S., Rizaldy, R., Das D., Bauer R.J., Heroux A., Trakselis, M.A., Hildebrand J.D., Vandemark, A.P. (2012) Structure of the shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, rock binding, and apical constriction, Mol. Biol. Cell, 23, 2131-2142. link
22) Bauer, R.J., Begley M.T., and Trakselis, M.A. (2012) Kinetics and fidelity of polymerization by DNA polymerase III from Sulfolobus solfataricus, Biochemistry, 51, 1996-2007. link
21) Zuo, Z., Lin, H-K, and Trakselis, M.A. (2011) Strand annealing and terminal transferase activities of a B-family DNA Polymerase, Biochemistry, 50, 5379-5370. link
20) Graham, B.W., Schauer, G.D., Leuba, S.H. and Trakselis, M.A. (2011) Steric Exclusion and Wrapping of the Excluded DNA Strand Occurs Along Discrete External Binding Paths During MCM Helicase Unwinding, NAR, 39, 6585. link
19) Zuo, Z., Rodgers, C., Mikheikin, A.L., and Trakselis, M.A. (2010) Characterization of a functional DnaG-type primase in Archaea: Implications for a dual primase system, J. Mol. Biol., 397, 664-676. link
18) Mikheikin A.L., Lin, H-K, Mehta, P., Jen-Jacobson, L., and Trakselis, M.A. (2009) The DNA replication polymerase from Sulfolobus solfataricus forms a multimer when bound to DNA, NAR, 37, 7194-205. link
17) Rothenberg, E., Trakselis, M.A., Bell, S.D., and Ha, T. (2007) MCM Forked substrate specificity involves dynamic interaction with the 5′-tail. JBC, 282, 34229-34. link
From Gradute and Postdoc Work:
16) McGeoch, A.T., Trakselis, M.A., Laskey, R.A., and Bell, S.D. (2005) Organization of the Archaeal MCM Complex on DNA and Implications for a Helicase Mechanism. Nat Struc. Mol. Biol., 12, 756-762. (Cover) link
15) Trakselis, M.A., Alley, S.C., and Ishmael, F.T. (2005) Identification of Protein-Protein Interactions Using Novel Crosslinking Reagents. Bioconjugate Techniques, 16, 741-750. (Cover) link
14) Norcum, M.T., Warrington, A., Spiering, M.M., Ishmael, F.T., Trakselis, M.A., and Benkovic, S.J. (2005) Architecture of the Bacteriophage T4 Primosome: Electron Microscopy Studies of gp41 and gp61. PNAS, 102, 3623-3626. link
13) Zhang, Z, Spiering, M.M., Trakselis, M.A., Ishmael, F.T., Xi, J., Benkovic, S.J., and Hammes, G.G. (2005) Assembly of the Bacteriophage T4 Primosome: Single Molecule and Ensemble Studies. PNAS, 102, 3254-3259. link
12) Millar, D., Trakselis, M.A., and Benkovic, S.J. (2004) On the Solution of T4 Sliding Clamp (gp45). Biochemistry, 43, 12723-7. link
11) Zhang, Z., Spiering, M.M., Berdis, A.J., Trakselis, M.A., and Benkovic, S.J. (2004) ‘Screw-cap’ Clamp Loader Proteins that Thread. Nat. Struc. Biol. 11, 580-581. link
10) Trakselis, M.A. and Bell, S.D. (2004) Loader of the Rings. Nature, 249, 798-799. link
9) Yang, J., Zhuang, Z., Roccasecca, R., Trakselis, M.A., and Benkovic, S.J. (2004) The Dynamic Processivity of the T4 Polymerase during Replication. PNAS, 101, 8289-8294. link
8) Trakselis, M.A., Roccasecca, R., Yang, J., Valentine, A., and Benkovic, S.J. (2003) Dissociative Properties of the Proteins within the Bacteriophage T4 Replisome. JBC, 278, 49839-49849. link
7) Yang, J., Trakselis, M.A., Roccasecca, R., and Benkovic, S.J. (2003) The Application of a Minicircle Substrate in the Study of the Coordinated T4 DNA Replication. JBC, 278, 49828-49838. link
6) Ishmael, F.T. Trakselis, M.A., and Benkovic, S.J. (2003) Protein-Protein Interactions in the Bacteriophage T4 Replisome: The Leading Strand Holoenzyme is Physically Linked to the Lagging Strand Holoenzyme and Primosome. JBC, 278, 3145-3152. link
5) Trakselis, M.A., Berdis, A.J., Benkovic, S.J. (2003) Examination of the Role of the Clamp-Loader and ATP Hydrolysis in the Formation of the Bacteriophage T4 Polymerase Holoenzyme. J. Mol. Biol., 326, 435-451. link
4) Trakselis, M.A. and Benkovic, S.J. (2001) Intricacies in ATP Dependent Clamp Loading: Variations Across Replication Systems. Structure, 9, 999-1004. link
3) Alley, S.C., Trakselis, M.A., Mayer, M.U., Ishmael, F.T., Jones, A.D., Benkovic, S.J. (2001) Building a Replisome Solution Structure by Elucidation of Protein-Protein Interactions in the Bacteriophage T4 DNA Polymerase Holoenzyme. J. Biol. Chem., 276, 39340-39349. link
2) Trakselis, M.A., Mayer, M.U., Ishmael, F.T., Roccasecca R., and Benkovic, S.J. (2001) Use of Small Molecules to Determine Dynamic Protein-Protein Interactions in the Multi-Protein Bacteriophage T4 Replication Complex. TIBS, 26, 566-572. link
1) Trakselis, M.A., Alley, S.C., Abel-Santos, E., Benkovic, S.J. (2001) Creating a Dynamic Picture of the Sliding Clamp During T4 DNA Polymerase Holoenzyme Assembly Using Fluorescence Resonance Energy Transfer. PNAS, 98, 8368-8375. link