Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models.

Muzard, Gabriel; Théveny, B; Révet, Bernard

doi:10.1002/j.1460-2075.1990.tb08238.x

Cited by 80 publications

(64 citation statements)

References 52 publications

(47 reference statements)

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“…6b). As previously observed (Muzard et al, 1990), the magnitude of the theoretical curvature is lower than that obtained from the experimental analysis. When superimposed two at a time, these curvature maps show many similarities.…”

Section: Experimental Curvature Maps Obtained From Electron Microscopsupporting

confidence: 68%

“…The algorithm calculates the reference frame transformations from one base pair to the adjacent one along the DNA sequence. Local curvature is calculated by the SD parameter, the ratio of the curvilinear (S) to endto-end (D) lengths for a 60 bp window moving along the DNA by 10 bp steps (Muzard et al, 1990). This ratio gives the w parameter, mean dinucleotide wedge angle per bp.…”

Section: Relocation Of the Uas/das Downstream From Rocamentioning

confidence: 99%

“…The co-ordinates (x, y) of each molecular pathway were smoothed and iso-segmented according to the real base-pair number of the DNA. Using the DNA ResCue program (Larquet et al, 1995), the curvature was quantified by the SD parameter, ratio of the curvilinear (S) to end-to-end (D) lengths of the fragment within a 60 bp window moving along the DNA by 10 bp (Muzard et al, 1990). This ratio gives the w parameter, mean dinucleotide wedge angle per base pair, which is an intrinsic parameter for DNA curvature, independent of the fragment length.…”

mentioning

confidence: 99%

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Specificity of the interaction of RocR with the rocG–rocA intergenic region in Bacillus subtilis

et al. 2003

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In Bacillus subtilis, expression of the rocG gene, encoding glutamate dehydrogenase, and the rocABC operon, involved in arginine catabolism, requires SigL (s 54 )-containing RNA polymerase as well as RocR, a positive regulator of the NtrC/NifA family. The RocR protein was purified and shown to bind specifically to the intergenic region located between rocG and the rocABC operon. DNaseI footprinting experiments were used to define the RocR-binding site as an 8 bp inverted repeat, separated by one base pair, forming an imperfect palindrome which is present twice within the rocG-rocABC intergenic region, acting as both a downstream activating sequence (DAS) and an upstream activating sequence (UAS). Point mutations in either of these two sequences significantly lowered expression of both rocG and rocABC. This bidirectional enhancer element retained partial activity even when moved 9 kb downstream of the rocA promoter. Electron microscopy experiments indicated that an intrinsically curved region is located between the UAS/DAS region and the promoter of the rocABC operon. This curvature could facilitate interaction of RocR with s 54-RNA polymerase at the rocABC promoter.

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Section: Experimental Curvature Maps Obtained From Electron Microscopsupporting

confidence: 68%

Section: Relocation Of the Uas/das Downstream From Rocamentioning

confidence: 99%

mentioning

confidence: 99%

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Specificity of the interaction of RocR with the rocG–rocA intergenic region in Bacillus subtilis

et al. 2003

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“…We have compared the STM experimental curvature map to those previously reported from electron microscopy analysis and theoretical calculations for pBR322. Electron microscopy data and three out of the four theoretical models give strikingly similar results [25]. It is worthwhile to mention that the overall path of the STM imaged DNA fragment, as well as the position of bending elements along the molecule (Fig.…”

supporting

confidence: 60%

Scanning tunneling microscopy study of a DNA fragment of known size and sequence

Marilley¹,

Pasero²,

Alain³

et al. 1994

Microsc. Microanal. Microstruct.

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“…A precise quantitative knowledge of the local curvature and the local flexibility has become crucial to understand the molecular biology of DNA-protein interactions. Many different techniques, such as x-ray crystallography (5, 6), electron microscopy (7,8), scanning force microscopy (SFM) (9, 10), gel retardation, and circularization kinetics (11,12) have been used thus far to study these effects. The parameters measured in these studies were global statistical parameters of the double helix such as the persistence length or the end-to-end distance; electron microscopy and SFM are unique techniques that provide information on both the contour of individual molecules and a population of such contours (7,13).…”

Section: Biochemistry For the Article ''Functional Transitions In Mymentioning

confidence: 99%

Mapping the intrinsic curvature and flexibility along the DNA chain

Zuccheri

Scipioni

Cavaliere

et al. 2001

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

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The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a “natural” DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.

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Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models.

Cited by 80 publications

References 52 publications

Specificity of the interaction of RocR with the rocG–rocA intergenic region in Bacillus subtilis

Specificity of the interaction of RocR with the rocG–rocA intergenic region in Bacillus subtilis

Scanning tunneling microscopy study of a DNA fragment of known size and sequence

Mapping the intrinsic curvature and flexibility along the DNA chain

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