Single-molecule sorting of DNA helicases

Methods

Volumn 108, Issue , 2016, Pages 14-23

  Bain, Fletcher E ^a   Wu, Colin G ^a   Spies, Maria ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

BRCA1; DNA helicase; FANCJ; FBH1; F rster resonance energy transfer (FRET); Phosphorylation; Single molecule; Total internal reflection fluorescence microscopy; Ubiquitylation

Indexed keywords

BIOTIN; DNA HELICASE; F BOX CONTAINING HELICASE 1; PROTEIN FBH1; UNCLASSIFIED DRUG; ADENOSINE TRIPHOSPHATE; DNA; DNA BINDING PROTEIN; OLIGONUCLEOTIDE;

ANALYTIC METHOD; ARTICLE; CELL GROWTH; CONTROLLED STUDY; EXPRESSION VECTOR; FLUORESCENCE MICROSCOPY; GENETIC TRANSFECTION; HEK293 CELL LINE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROCESSING; SCAVENGING SYSTEM; SINGLE MOLECULE SORTING; CHEMISTRY; FLOW CYTOMETRY; GENETICS; ISOLATION AND PURIFICATION; PROCEDURES; SINGLE MOLECULE IMAGING; SYNTHESIS;

ADENOSINE TRIPHOSPHATE; DNA; DNA HELICASES; DNA-BINDING PROTEINS; FLOW CYTOMETRY; OLIGONUCLEOTIDES; SINGLE MOLECULE IMAGING;

EID: 84969508595     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.05.009     Document Type: Article

References (34)

1. [1] Bianco, P.R., Brewer, L.R., Corzett, M., Balhorn, R., Yeh, Y., Kowalczykowski, S.C., Baskin, R.J., Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409 (2001), 374–378.
2. [2] Xue, Q., Yeung, E.S., Differences in the chemical reactivity of individual molecules of an enzyme. Nature 373:6516 (1995), 681–683.
3. [3] Seet, B.T., Dikic, I., Zhou, M.M., Pawson, T., Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7:7 (2006), 473–483.
4. [4] Jensen, O.N., Interpreting the protein language using proteomics. Nat. Rev. Mol. Cell Biol. 7:6 (2006), 391–403.
5. [5] Lohman, T.M., Tomko, E.J., Wu, C.G., Non-hexameric DNA helicases and translocases: mechanisms and regulation. Nature reviews. Mol. Cell Biol., 2008.
6. [6] Wu, C.G., Spies, M., Overview: What are helicases?. Adv. Exp. Med. Biol. 973 (2013), 1–16.
7. [7] Brosh, R.M. Jr., DNA helicases involved in DNA repair and their roles in cancer. Nat. Rev. Cancer 13:8 (2013), 542–558.
8. [8] Bohm, S., Bernstein, K.A., The role of post-translational modifications in fine-tuning BLM helicase function during DNA repair. DNA Repair (Amst) 22 (2014), 123–132.
9. [9] Fugger, K., Mistrik, M., Danielsen, J.R., Dinant, C., Falck, J., Bartek, J., Lukas, J., Mailand, N., Human Fbh1 helicase contributes to genome maintenance via pro- and anti-recombinase activities. J. Cell Biol. 186:5 (2009), 655–663.
10. [10] Osman, F., Dixon, J., Barr, A.R., Whitby, M.C., The F-Box DNA helicase Fbh1 prevents Rhp51-dependent recombination without mediator proteins. Mol. Cell. Biol. 25:18 (2005), 8084–8096.
11. [11] Morishita, T., Furukawa, F., Sakaguchi, C., Toda, T., Carr, A.M., Iwasaki, H., Shinagawa, H., Role of the Schizosaccharomyces pombe F-Box DNA helicase in processing recombination intermediates. Mol. Cell. Biol. 25:18 (2005), 8074–8083.
12. [12] Chiolo, I., Saponaro, M., Baryshnikova, A., Kim, J.H., Seo, Y.S., Liberi, G., The human F-Box DNA helicase FBH1 faces Saccharomyces cerevisiae Srs2 and postreplication repair pathway roles. Mol. Cell. Biol. 27:21 (2007), 7439–7450.
13. [13] Lorenz, A., Osman, F., Folkyte, V., Sofueva, S., Whitby, M.C., Fbh1 limits Rad51-dependent recombination at blocked replication forks. Mol. Cell. Biol. 29:17 (2009), 4742–4756.
14. [14] Masuda-Ozawa, T., Hoang, T., Seo, Y.S., Chen, L.F., Spies, M., Single-molecule sorting reveals how ubiquitylation affects substrate recognition and activities of FBH1 helicase. Nucleic Acids Res. 41:6 (2013), 3576–3587.
15. [15] Cantor, S.B., Bell, D.W., Ganesan, S., Kass, E.M., Drapkin, R., Grossman, S., Wahrer, D.C., Sgroi, D.C., Lane, W.S., Haber, D.A., Livingston, D.M., BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 105:1 (2001), 149–160.
16. [16] Botuyan, M.V., Nomine, Y., Yu, X., Juranic, N., Macura, S., Chen, J., Mer, G., Structural basis of BACH1 phosphopeptide recognition by BRCA1 tandem BRCT domains. Structure 12:7 (2004), 1137–1146.
17. [17] Clapperton, J.A., Manke, I.A., Lowery, D.M., Ho, T., Haire, L.F., Yaffe, M.B., Smerdon, S.J., Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat. Struct. Mol. Biol. 11:6 (2004), 512–518.
18. [18] Shiozaki, E.N., Gu, L., Yan, N., Shi, Y., Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling. Mol. Cell 14:3 (2004), 405–412.
19. [19] Rabuka, D., Rush, J.S., deHart, G.W., Wu, P., Bertozzi, C.R., Site-specific chemical protein conjugation using genetically encoded aldehyde tags. Nat. Protoc. 7:6 (2012), 1052–1067.
20. [20] Aggarwal, V., Ha, T., Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts. BioEssays 36:11 (2014), 1109–1119.
21. [21] Jain, A., Liu, R., Xiang, Y.K., Ha, T., Single-molecule pull-down for studying protein interactions. Nat. Protoc. 7:3 (2012), 445–452.
22. [22] Durocher, Y., Perret, S., Kamen, A., High-level and high-throughput recombinant protein production by transient transfection of suspension-growing human 293-EBNA1 cells. Nucleic Acids Res., 30(2), 2002, E9.
23. [23] Kichler, A., Gene transfer with modified polyethylenimines. J. Gene Med. 6:Suppl. 1 (2004), S3–S10.
24. [24] Honda, M., Park, J., Pugh, R.A., Ha, T., Spies, M., Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicase. Mol. Cell 35:5 (2009), 694–703.
25. [25] Rasnik, I., McKinney, S.A., Ha, T., Surfaces and orientations: much to FRET about?. Acc. Chem. Res. 38:7 (2005), 542–548.
26. [26] Roy, R., Hohng, S., Ha, T., A practical guide to single-molecule FRET. Nat. Methods 5:6 (2008), 507–516.
27. [27] L.S. Milescu, C. Nicolai, J. Bannen, QuB Software, 2000–2013.
28. [28] Nicolai, C., Sachs, F., Solving ion channel kinetics with the QuB software. Biophys. Rev. Lett. 8:03n04 (2013), 191–211.
29. [29] Szoszkiewicz, R., Ainavarapu, S.R., Wiita, A.P., Perez-Jimenez, R., Sanchez-Ruiz, J.M., Fernandez, J.M., Dwell time analysis of a single-molecule mechanochemical reaction. Langmuir 24:4 (2008), 1356–1364.
30. [30] Joo, C., Ha, T., Single-molecule FRET with total internal reflection microscopy. Cold Spring Harb. Protoc., 2012(12), 2012.
31. [31] Myong, S., Rasnik, I., Joo, C., Lohman, T.M., Ha, T., Repetitive shuttling of a motor protein on DNA. Nature 437:7063 (2005), 1321–1325.
32. [32] Zhou, R., Zhang, J., Bochman, M.L., Zakian, V.A., Ha, T., Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA.eLife., 3, 2014, e02190.
33. [33] Ghoneim, M., Spies, M., Direct correlation of DNA binding and single protein domain motion via dual illumination fluorescence microscopy. Nano Lett. 14:10 (2014), 5920–5931.
34. [34] Galletto, R., Amitani, I., Baskin, R.J., Kowalczykowski, S.C., Direct observation of individual RecA filaments assembling on single DNA molecules. Nature 443:7113 (2006), 875–878.