Effect of ethidium binding and superhelix density on the apparent supercoiling free energy and torsion constant of pBR322 DNA

Naimushin, Alexei N.; Clendenning, James B.; Kim, Ug-Sung; Lu, Song; Fujimoto, Bryant S.; Stewart, D. W.; Schurr, J. Michael

doi:10.1016/0301-4622(94)00037-k

Cited by 29 publications

(59 citation statements)

References 14 publications

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“…Due to this additivity, and the central limiting theorem of the probability theory, various experimental data converge to the WLC model regardless of the local DNA properties, with only a few concatenated bps being sufficient for the apparent statistical equivalence with a harmonic elastic rod [53]. This effect shadows the true mechanical properties of the DNA double helix which remain elusive.The present study evidences that, under normal temperature, the local DNA elasticity is strongly anharmonic, in agreement with the early hypotheses [78] and some experimental data [22][23][24]. The results of computations using empirical forcefields certainly require further verification.…”

supporting

confidence: 78%

“…In contrast, for TA 6 an opposite trend is observed under small torques, but l t passes via a minimum under positive torques. A qualitatively similar behavior was experimentally observed for one natural DNA sequence [22,24].The growth of rigidity with torques of both signs agrees with simple physical intuition for a twist energy profile resembling a flat-bottomed basin with vertical walls. In this case the system cannot go very far even with strong energy fluctuations.…”

supporting

confidence: 71%

“…For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results shed light upon the earlier experimental observations [22][23][24] and have important implications for the possible mechanisms of allosteric gene regulation [7,8,55]. …”

mentioning

confidence: 80%

“…Alternatively, the action of the torsional stress may be conveyed through a property other than the structure of the double helix. For instance, the untwisting may change the elastic parameters of DNA [22][23][24]. The supercoiled DNA is governed by the interplay between the local bending and twisting fluctuations.…”

mentioning

confidence: 99%

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Local elasticity of strained DNA studied by all-atom simulations

Mazur

2011

Phys. Rev. E

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Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT-and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light upon earlier experimental observations. PACS numbers: 87.14.gk 87.15.H-87.15.ap 87.15.ak IntroductionInternal mechanical stress is ubiquitous in the biologically active state of double helical DNA. In eucaryotic cells, DNA is densely packed in chromosomes and forced to bend, twist and stretch by numerous protein factors involved in genome regulation [1,2]. In procaryotes, DNA is subjected to a constitutive unwinding torque maintained by special enzymes, which leads to supercoiling, as in a long rope with bending and twisting elasticity [3,4]. The supercoiling and, more generally, stressinduced DNA forms are key factors in a variety of cellular processes [5]. For instance, the degree of supercoiling in bacteria changes systematically during the cell cycle and in response to environmental conditions, which is accompanied by activation or suppression of certain genes [6]. The promoter sensitivity to supercoiling stems from the recognition of short promoter elements by RNA polymerase [7]. Detailed studies indicate that it probably does not require DNA melting nor transitions to alternative forms [6]. In E. coli, relaxation of the superhelical stress simultaneously alters the activity of 306 genes (7% of the genome), with 106 genes activated and others deactivated [8]. The genes concerned are functionally diverse and widely dispersed throughout the chromosome, and the effect is dose-dependent.The physical mechanisms of such effects are understood only partially. Long DNA is well described by the coarse-grained worm-like chain (WLC) model [9,10] supplemented with harmonic twisting and stretching elasticity [11][12][13][14][15][16]. This model nicely explains the stressmodulated probability of looping, wrapping around proteins, and juxtaposition of distant protein binding sites [17]. However, it cannot account for the promoter sen- * Electronic address: alexey@ibpc.fr sitivity to supercoiling, for instance, because in this and many other cases the gene regulation has a strong local...

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supporting

confidence: 78%

supporting

confidence: 71%

mentioning

confidence: 80%

mentioning

confidence: 99%

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Local elasticity of strained DNA studied by all-atom simulations

Mazur

2011

Phys. Rev. E

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“…A group of closely spaced bands in the region of 2600-3100 bp appeared first, followed at still higher Hi/DNA ratios by a pair of distinct bands of =2150 and -2250 bp and a band of =4000 bp. These bands were never seen when plasmid with low (or zero) Hi In general, the changes observed with Si were very similar to those with P1, with only minor differences in band intensities, most probably due to slight differences in the superhelical density of the plasmid preparations (25), to differences in incubation and digestion conditions, or to slight differences in enzyme specificity of cutting (11 (pGCP-36AT). This sequence could potentially be extruded into a stable cruciform; alternatively, it has been reported to adopt an altered conformation that is different from A-, B-, or Z-DNA and is susceptible to a number of reagents and enzymes, including mung bean and SI nucleases (27,28).…”

Section: Methodsmentioning

confidence: 56%

Linker histones affect patterns of digestion of supercoiled plasmids by single-strand-specific nucleases.

Ivanchenko

Zlatanova²,

Varga‐Weisz³

et al. 1996

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

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The effect of histone H1 binding on the cleavage of superhelical plasmids by single-strand-specific nucleases was investigated. Mapping of P1 cleavage sites in pBR322, achieved by EcoRI digestion after the original P1 attack, showed an intriguing phenomenon: preexisting susceptible sites became "protected," whereas some new sites appeared at high levels of H1. Similar results were obtained with another single-strand-specific nuclease, S1. Disappearance of cutting at preexisting sites and appearance of new sites was also observed in a derivative plasmid that contains a 36-bp stretch of alternating d(AT) sequence that is known to adopt an altered P1-sensitive conformation. On the other hand, H1 titration of a dimerized version of the d(AT)18-containing plasmid led to protection of all preexisting sites except the d(AT)18 inserts, which were still cut even at high H1 levels; in this plasmid no new sites appeared. The protection of preexisting sites is best explained by long-range effects of histone H1 binding on the superhelical torsion of the plasmid. The appearance of new sites, on the other hand, probably also involves a local effect of stabilization of specific sequences in Pl-sensitive conformation, due to direct H1 binding to such sequences. That such binding involves linker histone N- and/or C-terminal tails is indicated by the fact that titration with the globular domain of H5, while causing disappearance of preexisting sites, does not lead to the appearance of any new sites.

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