DNA bending and its relation to nucleosome positioning

Drew, Horace R.; Travers, Andrew

doi:10.1016/0022-2836(85)90396-1

Cited by 685 publications

(537 citation statements)

References 53 publications

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“…In the absence of a discernible sequence motif or a secondary structure that could be the recognition signal, other features must be sought. Among tentative possibilities, the CS could bind proteins to a few appropriately spaced flexible regions (Drew and Travers, 1986) or be shaped into a high-affinity conformation after binding of factors, such as IHF or HU (Rice, 1997). Some of the deletions studied here might disturb the local architecture and indirectly reduce the ability of integrase to bind.…”

Section: Discussionmentioning

confidence: 99%

Non‐palindromic attI sites of integrons are capable of site‐specific recombination with one another and with secondary targets

Hansson

Sköld

Sundström

1997

Molecular Microbiology

108

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SummaryGenes borne on cassettes are mobile owing to sitespecific recombination systems called integrons, which have created various combinations of antibiotic resistance genes in R-plasmids. In these processes, the palindromic site, attC (59-base element), at cassette junctions has been proposed as being essential. Excised and circularized cassettes have been found to integrate with preference for an attI site at one end of the conserved sequence in integrons. In this work, we give evidence that recombination is possible in the absence of the highly organized attC sites between the more simply organized attI sites. Furthermore, at a very low frequency representing the background in our recombination assay, we observed cross-overs between attI and secondary sites. To characterize recombination excluding the attC sites, we have used naturally occurring attI variants and constructed mutants. The cross-over point was identified between a guanine and a thymine in attI using point mutations. Progressive deletions showed the extent of attI and identified two important regions in the conserved sequence 5Ј of the cross-over point. A region 27-36 bp 5Ј of attI influenced recombination with attC sites only, whereas a sequence 9-14 bp 5Ј of the cross-over point in attI was important for recombination with both attI and attC. Recombination between attI and secondary sites could allow fusion of the conserved sequence encoding the integron site-specific recombinase to new sequences.

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Section: Discussionmentioning

confidence: 99%

Non‐palindromic attI sites of integrons are capable of site‐specific recombination with one another and with secondary targets

Hansson

Sköld

Sundström

1997

Molecular Microbiology

108

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“…In eukaryotes, the first level of compaction of the DNA molecule consists in the solenoidal folding of the DNA molecule around the histone octamer, which is favoured by the distribution of DNA bending sites allowing a proper rotational orientation of the double helix relatively to the histone protein surface [7,8]. Accordingly, previous works have determined sequencedependent preferences for the bending of the DNA double helix around the core histones [18,19,20,21,140,141]. These allowed to set up a table of the bending values (roll angles) associated to all tri-nucleotides [51], the PNuc table that we used to establish a 'bending profile' of the DNA sequence (see Materials and Methods).…”

Section: To What Mechanisms Of the Eukaryotic Cells Are Related The Smentioning

confidence: 99%

“…So far, such constraints have been evidenced to favour the formation and positioning of nucleosomes [15,16,17,18,19]. These structural properties depend upon the local nucleotides composition and therefore can be seen as statistical features of the DNA primary structure [20,21,22,23,24,25,26]. The actual challenge is thus to find a way to extract these structural informations from an appropriate reading of the DNA text.…”

Section: Introductionmentioning

confidence: 99%

“…This positive supercoiling is mainly seen in the distribution of some dinucleotides such as AA(= TT), GC, and GG(= CC) to some lower extent. Most of these dinucleotides are known to contribute to the intrinsic bending and flexibility properties of the DNA double helix [15,21,50,51,52]. The periodic positioning of these dinucleotides with a rather definite phase shift between them (e.g., about 5 bases between AA and TT as well as in between AA and GC) contributes in a coherent manner to a global curvature of DNA which is likely to amplify the affinity for the histone octamer and therefore to favour the wrapping of DNA on the histone surface [6,18].…”

Section: Introductionmentioning

confidence: 99%

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Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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“…The plasmid pKMp27 [14,15] containing the EcoRI-EcoRI 169 bp tyrT fragment was obtained by courtesy of Dr. A.A. Travers (MRC Laboratory of Molecular Biology, Cambridge, UK). The plasmid was isolated from E. coli by a standard SDS-NaOH lysis procedure and purified by banding in CsCl-ethidium bromide gradients.…”

Section: Purification and Labelling Of The Tyrt Fragmentmentioning

confidence: 99%

A simple ligation assay to detect effects of drugs on the curvature/flexibility of DNA

1996

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Circular DNA molecules can readily be formed from the 169 bp tyrT fragment in the presence of T4 DNA ligase. We have analyzed the formation of DNA circles in the presence of the clinically important antitumour drugs amsacrine, mitoxantrone and daunomycin. All three are intercalating agents but they affect the closure reaction differently: daunomycin and mitoxantrone progressively inhibit the formation of circles whereas at low concentrations amsacrine strongly enhances the yield of circles suggesting that this drug can increase the flexibility and/ or curvature of DNA. The ligation assay described here may prove useful and widely applicable for investigating the effects of small molecules on the secondary structure of DNA.Key words. Anticancer drug; DNA binding; DNA structure can interfere with the biological functions of DNA by inhibiting protein-induced bending or by mimicking an intrinsic or protein-induced curvature. These considerations have prompted us to develop a simple assay to evaluate the effects of DNA-binding ligands on secondary structure and DNA curvature/flexibility in particular. The assay described in this paper is based on the circularisation of the 169 base pair tyrT DNA fragment in the presence of DNA ligase and depends upon measuring the extent to which small molecules interfere with the formation of circular DNA molecules. Results obtained with the antitumour drugs daunomycin, mitoxantrone and amsacrine are reported. Materials and methods

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DNA bending and its relation to nucleosome positioning

Cited by 685 publications

References 53 publications

Non‐palindromic attI sites of integrons are capable of site‐specific recombination with one another and with secondary targets

Non‐palindromic attI sites of integrons are capable of site‐specific recombination with one another and with secondary targets

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

A simple ligation assay to detect effects of drugs on the curvature/flexibility of DNA

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