Search Pubmed for publications from the Trakselis Laboratory. MyNCBI

From Trakselis Lab:

63) Behrmann, M.S., Perera, H.M., Welikala, M.U., Matthews, J.E, and Trakselis, M.A.* (2023) Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization, under review.

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., in press.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.

Previous preprint bioRxiv

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 Trakselis, M.A. (2021)  Targeted chromosomal Escherichia coli:dnaB exterior surface residues regulate DNA helicase behavior to maintain genomic stability and organismal fitness. PLoS Genetics, Nov 12;17(11):e1009886.. linkbioRxiv

56) Perera, H.M. and Trakselis, M.A. (2021) Determining Translocation Orientations of Nucleic Acid Helicases. Methods. in press. link.

55) Beuning, P.J. and Trakselis, M.A. (2021) Division of Chemical Toxicology Program at the American Chemical Society National Meeting: Celebrating 25 years! Chem. Res. Tox. 34, 10, 2167–2168. link54) Herman, M.A., Aiello, B.R., DeLong, J.D., Garcia-Ruiz, H., González , A.L., Hwang, W., McBeth, C.,  Stojković, E.A., Trakselis, M.A., Yakoby, N. (2021) 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

Figure thumbnail gr9

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                                     Access the recommendation on F1000PrimeTwinkle_Hist_ExPRT_Traces_Unwinding_SMC_050516sm

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. linkSE vs SEW Model graphical abstract38) 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
Figure 5 MCM vs MCM 3'5'tails struct only 040616sm37) 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

Figure 1 Hex Helicase Structure 500px36) 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.  linkBarnes Graham Mol Cell 201535) 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.  link2015 MCM8 JCI34) 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 2014 MCM9 AJHG33) Nucleic Acid Polymerases, Murakami, K. and Trakselis, M.A. (Eds.), Nucleic Acids and Molecular Biology Vol. 30, Berlin, Germany, Springer. 2014. link

978-3-642-39795-032) 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

Archaeal DNA pol domains4

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

Bauer 2013 JMB

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

Basic RGB

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

biohybrid clampCommentary 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

MCM DnaG Primisome CartoonD

25) Trakselis, M.A. and Graham, B.W. (2012) Biochemisty: Molecular Hurdles Cleared with Ease, Nature, 492, 195-197. link

2012 Nature N&V

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

2012 Dpo1 MultiEq Biochem Lin23) 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

2012 Shroom MoB22) 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

TOC Rate Fidelity Dpo134D21) 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

Zuo et al TOC GraphicB20) 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

MCM Spool FRET419) 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

Figure 2 Enz Conditions18) 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

2009 Dpo1 trimer Mikheikin17) 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

2007 MCM smFRET Rothenberg

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