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1
C Alén , D
Sherratt , S Colloms , Direct interaction
of aminopeptidase A with recombination site DNA in Xer
site-specific recombination , EMBO J. 16 (1997)
5188
2
J Arsuaga , Y
Diao , M Vazquez , Mathematical methods in DNA
topology : Applications
to chromosome organization and site-specific recombination ,
from: "Mathematics of DNA Structure, Function, and
Interactions" (editors C J Benham, S Harvey, W K
Olson, D W Sumners), IMA Vol. Math. Appl. 150, Springer
(2009) 7
3
T Baker , K
Mizuuchi , DNA-promoted assembly
of the active tetramer of the Mu transposase , Genes
Dev. 6 (1992) 2221
4
A Bates , A
Maxwell , DNA Topology , Oxford Univ. Press (2005)
220
5
W Bauer , F
Crick , J White , Supercoiled DNA , Sci. Am. 243
(1980) 100
6
S A Bleiler ,
R A Litherland , Lens spaces and Dehn
surgery , Proc. Amer. Math. Soc. 107 (1989) 1127
MR984783
7
D Buck , C Verjovsky
Marcotte , Tangle solutions
for a family of DNA-rearranging proteins , Math. Proc.
Cambridge Philos. Soc. 139 (2005) 59 MR2155505
8
H Cabrera-Ibarra ,
On the
classification of rational 3 –tangles , J. Knot Theory Ramifications
12 (2003) 921 MR2017963
9
H Cabrera-Ibarra ,
Results on the
classification of rational 3 –tangles , J. Knot Theory Ramifications
13 (2004) 175 MR2047467
10
C Calladine , H
Drew , B Luisi , A Travers , Understanding
DNA , Academic Press (2004)
11
A J Casson ,
C M Gordon , Reducing
Heegaard splittings , Topology Appl. 27 (1987) 275
MR918537
12
G Chaconas , R
Harshey , Transposition of phage Mu DNA , from: "In
Mobile DNA II" (editors H Craig, R Craigie, M Gellert, A
Lambowitz), Amer. Soc. Microbiology (2002) 384
13
S Colloms , J
Bath , D Sherrat , Topological
selectivity in Xer site-specific recombination , Cell 88
(1997) 855
14
I K Darcy ,
Biological
distances on DNA knots and links : applications to XER
recombination , from: "Knots in Hellas ’98, Vol. 2
(Delphi)", J. Knot Theory Ramifications 10 (2001) 269 MR1822492
15
I K Darcy ,
Modeling
protein-DNA complexes with tangles , Comput. Math. Appl.
55 (2008) 924 MR2389822
16
I K Darcy , J
Chang , N Druivenga , C McKinney , R
Medikonduri , S Mills , J Navarra-Madsen , A
Ponnusamy , J Sweet , T Thompson , Coloring the Mu
transpososome , BMC Bioinformatics 7 (2006) 435
17
I K Darcy ,
R G Scharein , TopoICE-R :
3D visualization modelling the topology of DNA
recombination , Bioinformatics 22 (2006) 1790
18
P L Deininger ,
J V Moran , M A Batzer , H H
Kazazian, Jr. , Mobile elements
and mammalian genome evolution , Curr. Opin. Genet. Dev.
13 (2003) 651
19
J Emert , C
Ernst , N –string tangles , J. Knot Theory
Ramifications 9 (2000) 987 MR1807603
20
C Ernst , D W
Sumners , A calculus for
rational tangles :
applications to DNA recombination , Math. Proc.
Cambridge Philos. Soc. 108 (1990) 489 MR1068451
21
C Ernst , D W
Sumners , Solving tangle
equations arising in a DNA recombination model , Math.
Proc. Cambridge Philos. Soc. 126 (1999) 23 MR1681651
22
C M Gordon ,
On
primitive sets of loops in the boundary of a
handlebody , Topology Appl. 27 (1987) 285 MR918538
23
I Grainge , M
Bregu , M Vasquez , V Sibanathan , S Ip ,
D Sherrat , Unlinking
chromosome catenates in
vivo by site-specific
recombination , EMBO J. 26 (2007) 4228
24
I Grainge , D
Buck , M Jayaram , Geometry of site
alignment during Int family recombination : antiparallel synapsis by the Flp
recombinase , J. Mol. Biol. 298 (2000) 749
25
F Guo , D
Gopaul , G van Duyne , Structure of Cre recombinase
complexed with DNA in a site-specific recombination
synapse , Nature 389 (1997) 40
26
R Harshey , M
Jayaram , The Mu
transpososome through a topological lens , Crit. Rev.
Biochem. Mol. Biol. 41 (2006) 387
27
M Hirasawa , K
Shimokawa , Dehn
surgeries on strongly invertible knots which yield lens
spaces , Proc. Amer. Math. Soc. 128 (2000) 3445 MR1676336
28
H Hoess , M
Ziese , N Sternberg , P1
site-specific recombination : Nucleotide sequence of the
recombining sites (dyad symmetry/lox site/BAL-31
deletion/plasmid recombination) , Proc. Natl. Acad. Sci.
USA 79 (1982) 3398
29
W Jaco , Adding a 2 –handle to a 3 –manifold : an application to property
R , Proc. Amer. Math. Soc.
92 (1984) 288 MR754723
30
M Jayaram , R
Harshey , Difference topology : Analysis of high-order
DNA-protein assemblies , from: "Mathematics of DNA
Structure, Function, and Interactions" (editors C J
Benham, S Harvey, W K Olson, D W Sumners, D Swigon),
IMA Vol. Math. Appl. 150, Springer (2009) 139
31
E Kilbride , M
Boocock , W Stark , Topological
selectivity of a hybrid site-specific recombination system with
elements from Tn3 res/resolvase and bacteriophase PL lox
P/Cre , J. Mol. Biol. 289 (1999) 1219
32
S Kim , K Darcy
Isabel , Topological analysis of DNA-protein
complexes , from: "Mathematics of DNA Structure, Function,
and Interactions" (editors C J Benham, S Harvey, W K
Olson, D W Sumners, D Swigon), IMA Vol. Math. Appl. 150,
Springer (2009) 177
33
P Kronheimer , T
Mrowka , P Ozsváth , Z Szabó , Monopoles and
lens space surgeries , Ann. of Math. (2) 165 (2007) 457
MR2299739
34
W Li , S
Kamtekar , Y Xiong , G Sarkis , N
Grindley , T Steitz , Structure of a
synaptic γδ resolvase tetramer
covalently linked to two cleaved DNAs , Science 209
(2005) 1210
35
W B R
Lickorish , Prime knots and
tangles , Trans. Amer. Math. Soc. 267 (1981) 321
MR621991
36
M Miziuuchi , T
Baker , K Mizuuchi , Assembly of
the active form of the transposase-Mu DNA complex : a critical control point in Mu
transposition , Cell 70 (1992) 303
37
K Mouw , S
Rowland , M Gajjar , M Boocock , W Stark ,
P Rice , Architecture
of a serine recombinase-DNA regulatory complex ,
Molecular Cell 30 (2008) 145
38
S Pathania , M
Jayaram , R Harshey , Path of DNA
within the Mu Transpososome : Transposase interaction bridging
two Mu ends and the enhancer trap five five DNA
supercoils , Cell 109 (2002) 425
39
S Pathania , M
Jayaram , R Harshey , A unique right
end-enhancer complex precedes synapsis of Mu ends : the enhancer is sequestered
within the transpososome throughout transposition , EMBO
J. 22 (2003) 3725
40
N Robertson ,
P D Seymour , R Thomas , Linkless
embeddings of graphs in 3 –space , Bull. Amer. Math. Soc. (N.S.)
28 (1993) 84 MR1164063
41
S Rowland , W
Stark , M Boocock , Sin
recombinase from Staphylococcus
aureus : synaptic complex architecture and
transposon targeting , Mol. Microbiol. 44 (2002)
607
42
Y Saka , M
Vazquez ,
Topological analysis of site-specific recombination ,
Bioinformatics 18 (2002) 1011
43
D Sankoff , Rearrangements
and chromosomal evolution , Curr. Opin. Genet. Dev. 13
(2003) 583
44
M Scharlemann ,
Outermost forks and a theorem of Jaco , from:
"Combinatorial methods in topology and algebraic geometry
(Rochester, N.Y., 1982)" (editors J R Harper, R Richard
Mandelbaum), Contemp. Math. 44, Amer. Math. Soc. (1985) 189
MR813113
45
M Scharlemann , A
Thompson , Detecting
unknotted graphs in 3 –space , J. Differential Geom. 34
(1991) 539 MR1131443
46
W Stark , D
Sherratt , M Boocock , Site-specific recombination
by Tn3 resolvase :
topological changes in the forward and reverse reactions ,
Cell 58 (1989) 779
47
D Sumners , Lifting
the curtain: using topology to probe the hidden action of
enzymes , Notices Amer. Math. Soc. 42 (1995) 528 MR1324733
48
D Sumners , C
Ernst , N Cozzarelli , S Spengler ,
Mathematical analysis of the mechanisms of DNA recombination
using tangles , Quarterly Reviews of Biophysics 28 (1995)
253
49
A Thompson ,
A
polynomial invariant of graphs in 3 –manifolds , Topology 31 (1992) 657
MR1174264
50
M Vazquez , S
Colloms , D Sumners , Tangle analysis
of Xer recombination reveals only three solutions, all
consistent with a single three-dimensional topological
pathway , J. Mol. Biol. 346 (2005) 493
51
M Vazquez , D
Sumners , Tangle analysis
of Gin site-specific recombination , Math. Proc.
Cambridge Philos. Soc. 136 (2004) 565 MR2055047
52
A Vetcher , A
Lushnikov , J Navarra-Madsen , R Scharein , Y
Lyubchenko , I K Darcy , S Levene ,
DNA
topology and geometry in Flp and Cre recombination , J.
Mol. Biol. 357 (2006) 1089
53
C Wang , Helical
repeat of DNA in Solution , Proc. Natl. Acad. Sci. USA 76
(1979) 200
54
S Wasserman , J
Dungan , N Cozzarelli , Discovery of a predicted
DNA knot substantiates a model for site-specific
recombination , Science 229 (1985) 171
55
J Watson , F
Crick , The structure of DNA , Cold Spring Harb. Symp.
Quant. Biol. 18 (1953) 123
56
Y Q Wu ,
A generalization
of the handle addition theorem , Proc. Amer. Math. Soc.
114 (1992) 237 MR1070535
57
Y Q Wu ,
On planarity
of graphs in 3 –manifolds ,
Comment. Math. Helv. 67 (1992) 635 MR1185812
58
Y Q Wu ,
The
classification of nonsimple algebraic tangles , Math.
Ann. 304 (1996) 457 MR1375620
59
Z Yin , M
Jayaram , S Pathania , R Harshey , The Mu
transposase interwraps distant DNA sites within a functional
transposome in the absence of DNA supercoiling , J.
Biol. Chem. 280 (2005) 6149
60
Z Yin , A
Suzuki , Z Lou , M Jayaram , Interactions of
phage Mu enhancer and termini that specify the assembly of a
topologically unique interwrapped transpososome , J.
Mol. Biol. 372 (2007) 382
61
W Zheng , C
Galloy , B Hallet , M Vasquez , The tangle
model for site-specific recombination : a computer interface and the
TnpI-IRS recombination system , from: "Knot Theory for
Scientific Objects (Proc. of Intl. Workshop, Osaka, 2006)"
(editor K Kawauchi), Ocami Studies 1, Osaka Municipal Univ.
Press (2007) 251