Hostname: page-component-cd9895bd7-fscjk Total loading time: 0 Render date: 2024-12-29T19:32:13.520Z Has data issue: false hasContentIssue false

Connect sum of lens spaces surgeries: application to Hin recombination

Published online by Cambridge University Press:  09 March 2011

DOROTHY BUCK
Affiliation:
Department of Mathematics, Imperial College London, 180 Queen's Gate, London SW7 2AZ
MAURO MAURICIO
Affiliation:
Department of Mathematics, Imperial College London, 180 Queen's Gate, London SW7 2AZ

Abstract

We extend the tangle model, originally developed by Ernst and Sumners [18], to include composite knots. We show that, for any prime tangle, there are no rational tangle attachments of distance greater than one that first yield a 4-plat and then a connected sum of 4-plats. This is done by studying the corresponding Dehn filling problem via double branched covers. In particular, we build on results on exceptional Dehn fillings at maximal distance to show that if Dehn filling on an irreducible manifold gives a lens space and then a connect sum of lens spaces, the distance between the slopes must be one. We then apply our results to the action of the Hin recombinase on mutated sites. In particular, after solving the tangle equations for processive recombination, we use our work to give a complete set of solutions to the tangle equations modelling distributive recombination.

Type
Research Article
Copyright
Copyright © Cambridge Philosophical Society 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

[1]Bleiler, S. Prime tangles and composite knots. Knot Theory and Manifolds. Proceedings 1983 (Springer-Verlag, 1985).Google Scholar
[2]Boyer, S. and Zhang, X.On Culler-Shalen seminorms and Dehn filling. Ann. Math. 148 (1998), 737801.CrossRefGoogle Scholar
[3]Boyer, S.Dehn surgery on knots. Chaos Solitons Fractals 9 (1998), 657670.CrossRefGoogle Scholar
[4]Brin, M. Seifert Fibered Spaces (lecture notes). ftp://ftp.math.binghamton.edu/pub/matt/seifert.pdf (1993).Google Scholar
[5]Buck, D. and Verjosvky Marcotte, C.Tangle solutions for a family of DNA rearranging proteins. Math. Proc. Camb. Phil. Soc. 139 1 (2005), 5980.CrossRefGoogle Scholar
[6]Buck, D. and Verjosvky Marcotte, C.Classification of tangle solutions for integrases, a protein family that changes DNA topology. J. Knot Theory Ramifications 16 (2007).CrossRefGoogle Scholar
[7]Burde, G. and Zieschang, H.Knots (de Gruyter Studies in Mathematics, 2003).CrossRefGoogle Scholar
[8]Cabrera Ibarra, H.On the classification of rational 3-tangles. J. Knot Theory Ramifications 12 (7) (2003), 921946.CrossRefGoogle Scholar
[9]Cabrera Ibarra, H. Braid solutions to the action of the Gin enzyme. J. Knot Theory Ramifications (in press).Google Scholar
[10]Cabrera Ibarra, H.An algorithm based on 3-braids to solve tangle equations arising in the action of Gin DNA invertase. Appl. Math. Comput. 216 (1) (2010), 95106.Google Scholar
[11]Conway, J. An enumeration of knots and links, and some of their algebraic properties, in Computational Problems in Abstract Algebra (Pergamon Press 1969), 329358.Google Scholar
[12]Cozzarelli, N. and Wasserman, S.Biochemical topology: applications to DNA recombination and replication, Science 232 (4753) (1986), 951960.Google Scholar
[13]Crisona, N., Weinberg, R., Peter, B. and Sumners, D.W.The topological mechanism of phage lambda integrase. J. Mol. Biology 289 no. 4 (1999), 747775.CrossRefGoogle ScholarPubMed
[14]Culler, M., Gordon, C. McA., Luecke, J. and Shalen, P. Dehn surgery on knots. Bull. Amer. Math. Soc. (1985).CrossRefGoogle Scholar
[15]Darcy, I.Biological distances on DNA knots and links: applications to XER recombination. J. knot theory ramifications 2 (2001), 269294.CrossRefGoogle Scholar
[16]Darcy, I., Luecke, J. and Vazquez, M.Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex. Algebr. Geom. Topol. 9 (2009), 22472309.CrossRefGoogle Scholar
[17]Ernst, C. PhD dissertation. Florida State University (1989).CrossRefGoogle Scholar
[18]Ernst, C. and Sumners, D.W.A calculus for rational tangles: applications to DNA recombination. Math. Proc. Camb. Phil. Soc. 108 (1990), 409.CrossRefGoogle Scholar
[19]Ernst, C.Solving tangle equations. J. Knot Theory Ramifications 2 (1996), 145159.CrossRefGoogle Scholar
[20]Ernst, C.Solving tangle equations II. J. Knot Theory Ramifications 1 (1997), 111.CrossRefGoogle Scholar
[21]Gordon, C. McA. and Luecke, J.Reducible manifolds and Dehn Surgery. Topology 35 (1996), 385409.CrossRefGoogle Scholar
[22]Gordon, C. McA. Dehn surgery. Unpublished course notes (2006).Google Scholar
[23]Gordon, C. McA.Small surfaces and Dehn filling. Geom. Topol. Monogr. 2 (1998), 177199.Google Scholar
[24]Gordon, C. McA.Dehn surgery and satellite knots. Trans. Amer. Math. Soc. 275 (2) (1983).CrossRefGoogle Scholar
[25]Grindley, N., Whiteson, K. and Rice, P.Mechanisms of Site-Specific Recombination. Ann. Rev. Biochem. 75 (2006), 567605.CrossRefGoogle ScholarPubMed
[26]Hatcher, A. Notes on Basic 3-Manifold Topology. http://www.math.cornell.edu/~hatcher/3M/3Mdownloads.html (2003).Google Scholar
[27]Heichman, K. et al. Configuration of DNA strands and mechanism of strand exchange in the Hin invertasome as revealed by analysis of recombinant knots. Genes and Development 5 (1991), 16221634.CrossRefGoogle ScholarPubMed
[28]Johnson, R. Bacterial site-specific DNA inversion systems. In Mobile DNA II, edited by Craig, N. et al. (AMS press, 2002).Google Scholar
[29]Kanaar, R. et al. Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange. Proc. natl. Acad. Sci. USA 85 (1990), 752756.CrossRefGoogle Scholar
[30]Kutsukake, K. et al. Two DNA invertases contribute to flagellar phase variation in salmonella enterica Serovar Typhimurium strain LT2. J. Bacteriology 188 no. 3 (2006) 950957.CrossRefGoogle ScholarPubMed
[31]Kronheimer, P., Mrowka, T., Ozsváth, P. and Szabó, Z.Monopoles and lens space surgeries. Ann. Math. 165 (2004), 457546.CrossRefGoogle Scholar
[32]Lickorish, R.Prime knots and tangles. Trans. Amer. Math. Soc. 267 (1981).CrossRefGoogle Scholar
[33]Montesinos, J.Variedades de Seifert que son recubridores ciclicos ramificados de dos hojas. Bol. Soc. Mat. Mexicana 18 (1973), 132.Google Scholar
[34]Moser, L.Elementary surgery on a torus knot. Pacific J. Math. 38 no. 3 (1971).CrossRefGoogle Scholar
[35]Rolfsen, D., Knots and Links (Publish or Perish, 1975).Google Scholar
[36]Sumners, D.W., Ernst, C., Spengler, S. and Cozzarelli, N. Analysis of the mechanism of DNA recombination using tangles. Quart. Rev. Biophysics (1995), 254–313.CrossRefGoogle Scholar
[37]Sumners, D.W.Lifting the curtain: using topology to probe the hidden action of protein. Notices Amer. Math. Soc. 42 no. 5 (1995).Google Scholar
[38]Vazquez, M. and Sumners, D.W.Tangle analysis of Gin site-specific recombination. Math. Proc. Camb. Phil. Soc. 136 (2004).CrossRefGoogle Scholar
[39]Vazquez, M., Colloms, S. D. and Sumners, D. W.Tangle analysis of Xer recombination yields only three solutions, all consistent with a single three dimensional topological pathway. J. Mol. Biology 346 no. 2 (2005), 493504.CrossRefGoogle Scholar
[40]Wu, Y. Q.Incompressibility of surfaces in surgered 3-manifolds. Topology 31 (1992), 271289.CrossRefGoogle Scholar