Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 51, 2012, Pages 20871-20876

  Pinkney, Justin N M ^a   Zawadzki, Pawel ^b   Mazuryk, Jaroslaw ^c   Arciszewsk, Lidia K ^b   Sherratt, David J ^b   Kapanidis, Achillefs N ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

Alternating laser excitation; Holliday junction dynamics; Protein DNA interactions; Site specific DNA recombination; Tethered fluorophore motion

Indexed keywords

CRE RECOMBINASE;

ARTICLE; CONFORMATIONAL TRANSITION; DNA RECOMBINATION; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; ISOMERIZATION; LOXP SITE; PRIORITY JOURNAL;

BINDING SITES; BIOCHEMISTRY; DNA; DNA NUCLEOTIDYLTRANSFERASES; DNA, CRUCIFORM; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; INTEGRASES; KINETICS; MODELS, CHEMICAL; PROTEIN BINDING; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; RECOMBINATION, GENETIC;

EID: 84871394004     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1211922109     Document Type: Article

References (31)

1. Grindley NDF, Whiteson KL, Rice PA (2006) Mechanisms of site-specific recombination. Annu Rev Biochem 75:567-605.
2. Van Duyne GD (2001) A structural view of cre-loxp site-specific recombination. Annu Rev Biophys Biomol Struct 30:87-104.
3. Grainge I, Lesterlin C, Sherratt DJ (2011) Activation of XerCD-dif recombination by the FtsK DNA translocase. Nucleic Acids Res 39(12):5140-5148.
4. Mumm JP, Landy A, Gelles J (2006) Viewing single lambda site-specific recombination events from start to finish. EMBO J 25(19):4586-4595.
5. Sauer B (1993) Manipulation of transgenes by site-specific recombination: use of Cre recombinase. Guide to Techniques in Mouse Development, eds Wassarman PM, DePamphilis ML (Academic Press, Waltham, MA), Vol 225, pp 890-900.
6. Ghosh K, Lau C-K, Gupta K, Van Duyne GD (2005) Preferential synapsis of loxP sites drives ordered strand exchange in Cre-loxP site-specific recombination. Nat Chem Biol 1(5):275-282.
7. Hoess R, Wierzbicki A, Abremski K (1987) Isolation and characterization of intermediates in site-specific recombination. Proc Natl Acad Sci USA 84(19):6840-6844.
8. Lee L, Sadowski PD (2003) Sequence of the loxP site determines the order of strand exchange by the Cre recombinase. J Mol Biol 326(2):397-412.
9. Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation. Nucleic Acids Res 31(18):5449-5460.
10. Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin EP (2002) The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex. J Mol Biol 319(1):107-127.
11. Vetcher AA, et al. (2006) DNA topology and geometry in Flp and Cre recombination. J Mol Biol 357(4):1089-1104.
12. Fan H-F (2012) Real-time single-molecule tethered particle motion experiments reveal the kinetics and mechanisms of Cre-mediated site-specific recombination. Nucleic Acids Res 40(13):6208-6222.
13. Bai H, et al. (2011) Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proc Natl Acad Sci USA 108(18):7419-7424.
14. Kapanidis AN, et al. (2004) Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci USA 101(24):8936-8941.
15. Kapanidis AN (2008) Alternating-laser excitation of single molecules. Single Molecule Techniques: A Laboratory Manual, eds Selvin PR, Ha T (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), 1st Ed, pp 85-119.
16. Nelson PC, et al. (2006) Tethered particle motion as a diagnostic of DNA tether length. J Phys Chem B 110(34):17260-17267.
17. Axelrod D (1981) Cell-substrate contacts illuminated by total internal reflection fluorescence. J Cell Biol 89(1):141-145.
18. Ringrose L, et al. (1998) Comparative kinetic analysis of FLP and cre recombinases: Mathematical models for DNA binding and recombination. J Mol Biol 284(2):363-384.
19. Lee L, Sadowski PD (2001) Directional resolution of synthetic Holliday structures by the Cre recombinase. J Biol Chem 276(33):31092-31098.
20. Lee NK, et al. (2005) Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J 88(4):2939-2953.
21. Ghosh K, Guo F, Van Duyne GD (2007) Synapsis of loxP sites by Cre recombinase. J Biol Chem 282(33):24004-24016.
22. Lee L, Sadowski PD (2003) Identification of Cre residues involved in synapsis, isomerization, and catalysis. J Biol Chem 278(38):36905-36915.
23. Holden SJ, et al. (2010) Defining the limits of single-molecule FRET resolution in TIRF microscopy. Biophys J 99(9):3102-3111.
24. Santoso Y, et al. (2010) Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proc Natl Acad Sci USA 107(2):715-720.
25. Arciszewska LK, Baker RA, Hallet B, Sherratt DJ (2000) Coordinated control of XerC and XerD catalytic activities during Holliday junction resolution. J Mol Biol 299(2):391-403.
26. Hamilton DL, Abremski K (1984) Site-specific recombination by the bacteriophage P1 lox-Cre system. Cre-mediated synapsis of two lox sites. J Mol Biol 178(2):481-486.
27. Shoura MJ, et al. (2012) Measurements of DNA-loop formation via Cre-mediated recombination. Nucleic Acids Res 40(15):7452-7464.
28. Schafer DA, Gelles J, Sheetz MP, Landick R (1991) Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352(6334):444-448.
29. Segall DE, Nelson PC, Phillips R (2006) Volume-exclusion effects in tethered-particle experiments: Bead size matters. Phys Rev Lett 96(8):088306-088310.
30. McKinney SA, Déclais A-C, Lilley DMJ, Ha T (2003) Structural dynamics of individual Holliday junctions. Nat Struct Biol 10(2):93-97.
31. Gopaul DN, Guo F, Van Duyne GD (1998) Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J 17(14):4175-4187.