Coloring the Mu transpososome

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Darcy, Isabel K ^a   Chang, Jeff ^b   Druivenga, Nathan ^c   McKinney, Colin ^a   Medikonduri, Ram K ^a   Mills, Stacy ^d   Navarra Madsen, Junalyn ^e   Ponnusamy, Arun ^f   Sweet, Jesse ^b   Thompson, Travis ^a  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c INDIANA UNIVERSITY   (United States)

^d FLORIDA STATE UNIVERSITY   (United States)

^e TEXAS WOMAN'S UNIVERSITY   (United States)

^f Credit Suisse USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COLORABILITY; DNA CONFORMATIONS; EXPERIMENTAL TECHNIQUES; KNOT THEORY; PROTEIN COMPLEXES; PROTEIN-DNA COMPLEXES; TRANSPOSASE; TRANSPOSOSOME;

CONFORMATIONS; PLANTS (BOTANY); PROTEINS; TOPOLOGY;

DNA;

CIRCULAR DNA; CRE RECOMBINASE; TRANSPOSASE; DNA BINDING PROTEIN; DNA SUPERCOILING; INTEGRASE; MU TRANSPOSASE; PROTEIN BINDING; TRANSPOSON; VIRUS DNA;

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA CONFORMATION; DNA PROTEIN COMPLEX; DNA TRANSPOSITION; EXPERIMENTAL DESIGN; GENETIC ALGORITHM; GENETIC CODE; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PROTEIN DNA BINDING; PROTEIN LOCALIZATION; ALGORITHM; BINDING SITE; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DNA SUPERCOILING; ENTEROBACTERIA PHAGE MU; GENETICS; METABOLISM; PROTEIN CONFORMATION; TRANSPOSON;

ALGORITHMS; BACTERIOPHAGE MU; BINDING SITES; DNA TRANSPOSABLE ELEMENTS; DNA, SUPERHELICAL; DNA, VIRAL; DNA-BINDING PROTEINS; INTEGRASES; MODELS, CHEMICAL; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; SOFTWARE; TRANSPOSASES;

EID: 33751163463     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-435     Document Type: Article

References (42)

1. Ernst C, Sumners DW: A calculus for rational tangles: applications to DNA recombination. Math Proc Cambridge Philos Soc 1990, 108(3):489-515.
2. Crisona N, Weinberg R, Peter B, Sumners D, Cozzarelli N: The topological mechanism of phage lambda integrase. J Mol Biol 1999, 289(4):747-75.
3. Vazquez M, Colloms SD, Sumners D: Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway. J Mol Biol 2005, 346(2):493-504.
4. Vetcher AA, Lushnikov AY, Navarra-Madsen J, Scharein RG, Lyubchenko YL, Darcy IK, Levene SD: DNA Topology and Geometry in Flp and Cre Recombination. J Mol Biol 2006, 357(4):1089-1104.
5. Pathania S, Jayaram M, Harshey R: Path of DNA within the Mu transpososome. Transposase interactions bridging two Mu ends and the enhancer trap five DNA supercoils. Cell 2002, 109(4):425-436.
6. Chaconas G, Harshey R: Transposition of phage Mu DNA. In Mobile DNA II Edited by: Craig NL, Craigie R, Gellert M, Lambowitz A. ASM Press; 2002.
7. Grainge I, Buck D, Jayaram M: Geometry of site-alignment during Int family recombination. J Mol Biol 2000, 298:749-764.
8. Kilbride E, Boocock M, Stark W: Topological selectivity of a hybrid site-specific recombination system with elements from Tn3 res/resolvase and bacteriophage PL loxP/Cre. J Mol Biol 1999, 289:1219-1230.
9. Pathania S, Jayaram M, Harshey R: A unique right end-enhancer complex precedes synapsis of Mu ends: the enhancer is sequestered within the transpososome throughout transposition. The EMBO Journal 2003, 22(14):3725-3736.
10. Yin Z, Jayaram M, Pathania S, Harshey R: The Mu transposase interwraps distant DNA sites within a functional transpososome in the absence of DNA supercoiling. J Biol Chem 2005, 280(7):6149-6156.
11. Guo F, Gopaul DN, van Duyne GD: Structure of Cre Recombinase complexed with DNA in a site-specific recombination synapse. Nature 1997, 389:40-46.
12. Fox RH: Metacyclic Invariants of Knots and Links. Canadian Journal Math 1970, 22:193-201.
13. Livingston C: Knot Theory Washington, DC: Math. Assoc. Amer; 1993.
14. Przytycki J: 3-Coloring and other Invariants of Knots. Banach Center Publications 1998, 42:275-295.
15. Navarra-Madsen J, Darcy IK: Colorability and n-String Tangles. [http://lanl.arxiv.org/abs/math.GT/0609587].
16. Dowker CH, Thistlethwaite MB: Classification of Knot Projections. Topol Appl 1983, 16:19-31.
17. Ewing B, Millett KC: Computational algorithms and the complexity of link polynomials. In Progress in knot theory and related topics Volume 56. Travaux en Cours, Paris: Hermann; 1997:51-68.
18. Doll H, Hoste J: A tabulation of oriented links. Math Comp 1991, 57(196):747-761.
19. Yuan JF, Beniac DR, Chaconas G, Ottensmeyer FP: 3D reconstruction of the Mu transposase and the Type 1 transpososome: a structural framework for Mu DNA transposition. Genes & Development 2005, 19:840-852.
20. Kilbride EA, Burke ME, Boocock M, Stark W: Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system. J Mol Biol 2006, 355(2):185-95.
21. Bar-Natan D: The Mathematica Package KnotTheory. [http://katlas.math.toronto.edu/wiki/ The_Mathematica_Package_ KnotTheory].
22. Flammini A, Maritan A, Stasiak A: Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophysical Journal 2004, 87:2968-2975.
23. Hoste J, Thistlethwaite M, Weeks J: The first 1,701,936 knots. Math Intelligencer 1998, 20(4):33-48.
24. Culler M, Gordan C, Luecke J, Shalen P: Dehn surgery on knots. An of Math 1987, 125:237-300.
25. Sumners D, Ernst C, Spengler S, Cozzarelli N: Analysis of the mechanism of DNA recombination using tangles. Quarterly Reviews of Biophysics 1995, 28:253-313.
26. Ernst C: Tangle equations. J Knot Theory Ramifications 1996, 5(2):145-159.
27. Ernst C: Tangle equations. II. J Knot Theory Ramifications 1997, 6:1-11.
28. Ernst C, Sumners DW: Solving tangle equations arising in a DNA recombination model. Math Proc Camb Phil Soc 1999, 126:23-36.
29. Hirasawa M, Shimokawa K: Dehn surgeries on strongly invertible knots which yield lens spaces. Proc Amer Math Soc 2000, 128:3445-3451.
30. Darcy IK: Biological distances on DNA knots and links: applications to XER recombination. J Knot Theory Ramifications 2001, 10(2):269-294. [Knots in Hellas '98, Vol. 2 (Delphi)].
31. Kauffman LH, Lambropoulou S: Classifying and applying rational knots and rational tangles. In Physical knots: knotting, linking, and folding geometric objects in R3 (Las Vegas, NV, 2001), of Contemp. Math Volume 304. Providence, RI: Amer. Math. Soc; 2002:223-259.
32. Vazquez M, Sumners DW: Tangle analysis of Gin site-specific recombination. Math Proc Cambridge Philos Soc 2004, 136(3):565-582.
33. Darcy IK: Solving unoriented tangle equations involving 4-plats. J Knot Theory Ramifications 2005, 14(8):993-1005.
34. Darcy IK: Solving oriented tangle equations involving 4-plats. J Knot Theory Ramifications 2005, 14(8):1007-1027.
35. Buck D, Verjovsky Marcotte C: Tangle solutions for a family of DNA-rearranging proteins. Math Proc Cambridge Philos Soc 2005, 139:59-80.
36. Kronheimer P, Mrowka T, Ozsvath P, Szabo Z: Monopoles and lens space surgeries. [http://lanl.arxiv.org/abs/math.GT/0310164].
37. Saka Y, Vazquez M: TangleSolve: topological analysis of site-specific recombination. Bioinformatics 2002, 18:1011-1012.
38. Darcy IK, Scharein RG: TopoICE-R: 3D visualization modeling the topology of DNA recombination. Bioinformatics 2006, 22(14):1790-1791.
39. Cabrera-Ibarra H: Results on the classification of rational 3-tangles. J Knot Theory Ramifications 2004, 13(2):175-192.
40. Cabrera-Ibarra H: On the classification of rational 3-tangles. J Knot Theory Ramifications 2003, 12(7):921-946.
41. Emert J, Ernst C: N-string tangles. J Knot Theory Ramifications 2000, 9(8):987-1004.
42. Scharlemann M, Thompson A: Detecting unknotted graphs in 3-space. J Differential Geom 1991, 34(2):539-560.