Static Curvature and Flexibility Measurements of DNA with Microscopy. A Simple Renormalization Method, its Assessment by Experiment and Simulation

Cognet, Jean A. H.; Pakleza, Christophe; Cherny, Dmitry; Delain, Etienne; Cam, Eric Le

doi:10.1006/jmbi.1998.2322

Cited by 34 publications

(41 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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.

View full text Add to dashboard Cite

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.

show abstract

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.

View full text Add to dashboard Cite

show abstract

“…33 The bending of DNA by interaction with MC1 has been measured by dark-field electron microscopy (EM) and electrophoresis and studied by molecular modeling. 7,34,35 Visualization of DNA molecules by EM shows sharp kinks in DNA and using short DNA of 176 bp containing a preferential binding site located in the center of DNA sequence. This allowed a precise determination of a bending angle of 1168 or 0.32 turns.…”

Section: 33mentioning

confidence: 99%

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins

2007

View full text Add to dashboard Cite

Histonelike proteins in prokaryotes and histone octamers in eukaryotes carry large positive charges, which are responsible of strong electrostatic interactions with DNA. As a result, DNA wraps around proteins and genetic information is condensed. We describe a generalized model of these electrostatic interactions mediated by salt that explains the wrapping of DNA around the nucleosome octamer, around remodeling factors in eukaryotes and around histonelike proteins in prokaryotes. It comes out that small changes in protein dimension and charge produce large effects in the supramolecular DNA-protein architecture.

show abstract

“…A value for that significantly exceeds the measured value for free DNA can be explained by a higher flexibility of the complex (42). The mean value of for each pcPNA-DNA complex was found to be 1-3°higher than the corresponding value for free DNA (data not shown), indicating that the complexes may have a higher flexibility.…”

Section: Circular Permutation Assay (Cpa)mentioning

confidence: 80%

“…EM allows visualization of specific DNA complexes and measurement of the extent of DNA bending (39)(40)(41). In addition, a bending angle distribution is readily obtained providing useful information about the flexibility of a specific complex (42). Visualization and angle measurements of a large number of DNA fragment molecules bound centrally with pcPNA I, pcPNAs II͞III, or with all three pcPNAs revealed significant DNA bending in the middle of the fragments, as shown in the histograms and microphotographs in Fig.…”

Section: Circular Permutation Assay (Cpa)mentioning

confidence: 99%

Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids

Kuhn

Cherny

Demidov

et al. 2004

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

View full text Add to dashboard Cite

DNA bending is significant for various DNA functions in the cell. Here, we demonstrate that pseudocomplementary peptide nucleic acids (pcPNAs) represent a class of versatile, sequence-specific DNA-bending agents. The occurrence of anisotropic DNA bends induced by pcPNAs is shown by gel electrophoretic phasing analysis. The magnitude of DNA bending is determined by circular permutation assay and by electron microscopy, with good agreement of calculated mean values between both methods. Binding of a pair of 10-meric pcPNAs to its target DNA sequence results in moderate DNA bending with a mean value of 40 -45°, while binding of one self-pc 8-mer PNA to target DNA yields a somewhat larger average value of the induced DNA bend. Both bends are found to be in phase when the pcPNA target sites are separated by distances of half-integer numbers of helical turns of regular duplex DNA, resulting in an enhanced DNA bend with an average value in the range of 80 -90°. The occurrence of such a sharp bend within the DNA double helix is confirmed and exploited through efficient formation of 170-bp-long DNA minicircles by means of dimerization of two bent DNA fragments. The pcPNAs offer two main advantages over previously designed classes of nonnatural DNAbending agents: they have very mild sequence limitations while targeting duplex DNA and they can easily be designed for a chosen target sequence, because their binding obeys the principle of complementarity. We conclude that pcPNAs are promising tools for inducing bends in DNA at virtually any chosen site.I ntrinsic or induced DNA bending plays an important role in various biological processes such as transcription, replication, recombination, DNA packaging, and repair (1-6). It has therefore been recognized that biological functions relying on DNA bending may be influenced by nonnatural DNA-bending agents (7-11). So far, two classes of artificial DNA-bending agents have been investigated: tethered triple-helix-forming oligonucleotides (7-9) and six-zinc-finger peptides (10, 11). In both classes, two DNA-binding domains are connected by a linker and targeted to two separated sites in double-stranded DNA (dsDNA), thus inducing bending at the intervening region. Whereas tethered triplex-forming oligonucleotides can easily be designed, they suffer from severe sequence limitations because they require the presence of two Ն15-bp-long homopurine-homopyrimidine (hypr) tracts, located not far from each other in the target DNA. On the other hand, the design of artificial DNA-binding peptides such as the reported six-zinc-finger peptides is not straightforward and may require a selection process starting with a pool of peptides for any chosen DNA target sequence (12). Thus, a DNA-binding ligand capable of sequence-specific recognition and bending of DNA, which could easily be designed for a chosen DNA target sequence, would be of great interest.Certain types of peptide nucleic acids (PNAs) are known to bind complementary target sites in dsDNA sequence-specifically through invasion of the ...

show abstract

Static Curvature and Flexibility Measurements of DNA with Microscopy. A Simple Renormalization Method, its Assessment by Experiment and Simulation

Cited by 34 publications

References 45 publications

Mapping the intrinsic curvature and flexibility along the DNA chain

Mapping the intrinsic curvature and flexibility along the DNA chain

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins

Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids

Contact Info

Product

Resources

About