Coloring the Mu transpososome

Darcy, Isabel K.; Chang, Jeff H.; Druivenga, Nathan; McKinney, Colin; Medikonduri, Ram K.; Mills, Stacy; Navarra-Madsen, Junalyn; Ponnusamy, Arun; Sweet, J. Eric F.; Thompson, Travis

doi:10.1186/1471-2105-7-435

Cited by 21 publications

(16 citation statements)

References 38 publications

(33 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5B) (62). A mathematical tangle analysis of the difference topology experiments concludes that the experimentally observed three-branched, five-crossing topological architecture of the Mu transpososome is the simplest solution, and thus biologically most likely (73, 74). …”

Section: Enhancer and Transpososome Topologymentioning

confidence: 97%

Transposable Phage Mu

Harshey

2014

Microbiol Spectr

View full text Add to dashboard Cite

Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.

show abstract

Section: Enhancer and Transpososome Topologymentioning

confidence: 97%

Transposable Phage Mu

Harshey

2014

Microbiol Spectr

View full text Add to dashboard Cite

show abstract

“…A cohomology theory of quandles have been developed, and their cocycles have been used as state-sum invariants of knots and knotted surfaces [4]. Quandles are used to investigate tangles also in [6,17].…”

Section: Introductionmentioning

confidence: 99%

Tangle Embeddings and Quandle Cocycle Invariants

Ameur

Elhamdadi

Rose

et al. 2008

Experimental Mathematics

View full text Add to dashboard Cite

show abstract

“…For example, recombination can be modeled using tangle equations [23,24]. In [1], a computational method is presented for solving tangle equations using the coloring invariant, which is then applied to analyze the topology of protein-bound DNA. In this case the motivation for generating a list of tangles was to solve tangle equations.…”

Section: Applications To Biologymentioning

confidence: 99%

“…Chapter 4 discusses tangle tabulation, and we present an algorithm for tabulating tangles by crossing number through a program developed in C/C++. This program is an extension of the algorithm developed in [1] for solving tangle equations, which was extended and modified over time in collaboration with a number of undergraduates including Danielle Washburn, Guanyu Wang, Fengfeng Xia, Timothy…”

Section: Organization Of Thesismentioning

confidence: 99%

“…The algorithm for determining whether a tangle projection is realizable uses the Dowker code to embed the crossings in order while maintaining the orientation of the string, eventually determining whether all crossings can be drawn and the arcs can reach the boundary of the ball. This algorithm is described in detail in [36] and [1], and an example of a non-drawable tangle can be seen below in figure 4.4.…”

Section: Dowker Codementioning

confidence: 99%

See 1 more Smart Citation

Classifying 2-string tangles within families and tangle tabulation

Caples¹

View full text Add to dashboard Cite

Coloring the Mu transpososome

Abstract: Background: Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA complex.

Cited by 21 publications

References 38 publications

Transposable Phage Mu

Transposable Phage Mu

Tangle Embeddings and Quandle Cocycle Invariants

Classifying 2-string tangles within families and tangle tabulation

Contact Info

Product

Resources

About