The stereostructure of knots and catenanes produced by phage λ integrative recombination: implications for mechanism and DNA structure

Spengler, Sylvia J.; Stasiak, Andrzej; Cozzarelli, Nicholas R.

doi:10.1016/s0092-8674(85)80128-8

Cited by 166 publications

(89 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Because the electrophoretic migration of knots formed on the same-size DNA molecules is related to the average crossing number of the ideal representation of the corresponding knot (37) and this relation is approximately linear up to knots with 10 crossings (38), populations of knots with 3, 4, 5, 6, 7, 8, 9, and 10 crossings were assigned to the distinguishable gel bands in Fig. 2 A. Although it is known that some knots might deviate from this linear relation (39,40), a continuous correlation between electrophoretic migration and the number of knot crossings also applies to more complex knots (41). Therefore, as a first approximation we used linear extrap- olation to estimate the number of crossings of the more complex knot populations (Fig.…”

Section: Resultsmentioning

confidence: 92%

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

Arsuaga

Vázquez

Trigueros

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

243

305

View full text Add to dashboard Cite

When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled. Nevertheless, when DNA is extracted from a tailless mutant of the P4 phage, DNA is found to be cyclic and knotted (probability of 0.95). The knot spectrum is very complex, and most of the knots have a large number of crossings. We quantified the frequency and crossing numbers of these knots and concluded that, for the P4 tailless mutant, at least half the knotted molecules are formed while the DNA is still inside the viral capsid rather than during extraction. To analyze the origin of the knots formed inside the capsid, we compared our experimental results to Monte Carlo simulations of random knotting of equilateral polygons in confined volumes. These simulations showed that confinement of closed chains to tightly restricted volumes results in high knotting probabilities and the formation of knots with large crossing numbers. We conclude that the formation of the knots inside the viral capsid is driven mainly by the effects of confinement.

show abstract

Section: Resultsmentioning

confidence: 92%

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

Arsuaga

Vázquez

Trigueros

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

243

305

View full text Add to dashboard Cite

show abstract

“…In these counterion-induced, tightly supercoiled DNA molecules, the opposing segments of interwound superhelix appeared to be in close proximity longitudinally with small terminal loops called apexes at both ends of the molecules (Bednar et al 1994). This tightly supercoiled DNA is not static, but rather has a very dynamic structure that allows aligned segments to move freely with respect to each other (Brady et al 1983;Spengler et al 1985). Such a feature is unique to supercoiled DNA because neither nicked circular nor linear DNA molecules under the same conditions exhibit signs of intersegmental attraction, suggesting that the free energy of supercoiling is needed to induce the formation of tightly supercoiled DNA.…”

Section: Tightly Compacted Supercoiled Dna Is the Preferred Substratementioning

confidence: 99%

RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription

Sukhodolets¹,

Cabrera²,

Zhi³

et al. 2001

Genes Dev.

122

View full text Add to dashboard Cite

We report that RapA, an Escherichia coli RNA polymerase (RNAP)-associated homolog of SWI2/SNF2, is capable of dramatic activation of RNA synthesis. The RapA-mediated transcriptional activation in vitro depends on supercoiled DNA and high salt concentrations, a condition that is likely to render the DNA superhelix tightly compacted. Moreover, RapA activates transcription by stimulating RNAP recycling. Mutational analyses indicate that the ATPase activity of RapA is essential for its function as a transcriptional activator, and a rapA null mutant exhibits a growth defect on nutrient plates containing high salt concentrations in vivo. Thus, RapA acts as a general transcription factor and an integral component of the transcription machinery. The mode of action of RapA in remodeling posttranscription or posttermination complexes is discussed.

show abstract

“…It also carries two directly repeated complete res sites for ISXc5 resolvase. Recombination of pABI411 by Int, (i) generates DNA knots (Spengler et al 1985;Craigie & Mizuuchi 1986) and (ii) inverts the two ISXc5 res sites. The inverted orientation of gd res sites will remain unchanged by Int recombination, however.…”

Section: Test For Recombination On Inverted Isxc5 Res Sitesmentioning

confidence: 99%

The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases

Liu

Hühne

et al. 1998

Genes to Cells

View full text Add to dashboard Cite

Background: Conservative site-specific recombination is responsible for the resolution of cointegrates which result during the transposition of class II transposable elements. Resolution is catalysed by a transposonencoded recombinase, resolvase, that belongs to a large family of recombinases, including DNA invertases. Resolvases and the related invertases are likely to employ similar reaction mechanisms during recombination. There are important differences, however. Resolvases require two accessory DNA binding sites within each of the two directly repeated recombination sites. Invertases instead need a host factor, Fis, and an enhancer type DNA sequence, in addition to two inversely orientated recombination sites.

show abstract

The stereostructure of knots and catenanes produced by phage λ integrative recombination: implications for mechanism and DNA structure

Cited by 166 publications

References 34 publications

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids

RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription

The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases

Contact Info

Product

Resources

About