Visualization of the bent helix in kinetoplast DNA by electron microscopy

Griffith, Jack D.; Bleyman, Michael; Rauch, Carol A.; Kitchin, P.; Englund, Paul T.

doi:10.1016/0092-8674(86)90347-8

Cited by 231 publications

(142 citation statements)

References 25 publications

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“…A tract of DNA with very extensive phasing of repeated A-tracts is readily available in the kinetoplast DNA of the Trypanosomatidae protozoan Crithidia fasciculata. This DNA segment is the most highly curved DNA we know of at present (5). The profiles assumed by these curved DNA molecules on deposition on a flat surface can be observed by scanning force microscopy (SFM).…”

mentioning

confidence: 99%

Recognition of the DNA sequence by an inorganic crystal surface

Sampaolese¹,

Bergia²,

Scipioni³

et al. 2002

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

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The sequence-dependent curvature is generally recognized as an important and biologically relevant property of DNA because it is involved in the formation and stability of association complexes with proteins. When a DNA tract, intrinsically curved for the periodical recurrence on the same strand of A-tracts phased with the B-DNA periodicity, is deposited on a flat surface, it exposes to that surface either a T-or an A-rich face. The surface of a freshly cleaved mica crystal recognizes those two faces and preferentially interacts with the former one. Statistical analysis of scanning force microscopy (SFM) images provides evidence of this recognition between an inorganic crystal surface and nanoscale structures of double-stranded DNA. This finding could open the way toward the use of the sequence-dependent adhesion to specific crystal faces for nanotechnological purposes.I t is widely accepted that the local, sequence-dependent curvature and dynamics of the double-stranded DNA chain segments play a crucial and active role in DNA packaging, transcription, replication, recombination, and repair processes, and in nucleosome stability and positioning (1). Thus, a quantitative knowledge of the curvature and the flexibility of doublestranded DNA has become important to understand the determinants of DNA-protein recognition. We have recently described how SFM makes it possible to map sequencedependent curvature and flexibility along the DNA chain (2, 3). In these previous investigations, indications of preferential adsorption involving curved DNA tracts on the surface of mica were obtained. To reach definite evidence of such recognition we have investigated a highly curved DNA fragment to amplify this effect.A periodic recurrence of A-tracts phased with the B-DNA periodicity, like tracts of three to six adenine steps centered approximately every 10.5 base pairs, drives extended intrinsic curvatures along a DNA chain (4). These curved DNA tracts give rise to planar or quasi planar superstructures. It is worth noting that, when these short stretches of adenine steps are positioned on the same strand, the adenine bases tend to be preferentially positioned on one side of the curvature plane, while the complementary thymines will be found on the other side. When deposited on a flat surface, these curved DNA tracts will thus interact with that surface, on average, with either an A-or a T-rich face. A tract of DNA with very extensive phasing of repeated A-tracts is readily available in the kinetoplast DNA of the Trypanosomatidae protozoan Crithidia fasciculata. This DNA segment is the most highly curved DNA we know of at present (5). The profiles assumed by these curved DNA molecules on deposition on a flat surface can be observed by scanning force microscopy (SFM). Only if the sequence orientation for each of the imaged molecules could be known would it be possible to determine the face with which the molecules adsorb on the surface (on average) through the study of the average chain-curvature of the molecule ensemble. To remo...

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mentioning

confidence: 99%

Recognition of the DNA sequence by an inorganic crystal surface

Sampaolese¹,

Bergia²,

Scipioni³

et al. 2002

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

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“…The groups of Englund and Crothers raised the possibility that this seemingly larger size might be caused by a static curvature of the DNA, resulting from the repeating blocks of four to six adenines phased with the helical repeat over the 220-bp length of the DNA. Direct EM visualization, done in with collaboration with Paul, verified this possibility (32). Although there is no question that the elegant phasing experiments of Wu and Crothers (33) had proven the point, images of fields of 223-bp DNA fragments bent into almost perfect circles provided important visual confirmation.…”

Section: Nucleotide Tripletsmentioning

confidence: 69%

Many Ways to Loop DNA

Griffith

2013

Journal of Biological Chemistry

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In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three-and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.

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“…Applying the Fourier transform for SE(3) on both sides of (3), one can obtain a system of linear ordinary differential equations in the form of (5) where B r is a matrix function that is independent of s under the assumption that the stiffness and chirality of the intrinsically straight macromolecular chain are constant along the whole chain. Solving (5), one obtains (6) Then, the desired PDF can be obtained by the inverse transform 51, 61…”

Section: Review Of the General Inextensible Semi-flexible Macromolecumentioning

confidence: 99%

“…First discovered in the early 1980's 1 , intrinsically bent DNAs have been observed and studied experimentally [2][3][4][5][6][7][8] . Local structures, which are more complex than rigid bends, have also been observed from various experiments.…”

Section: Introductionmentioning

confidence: 99%

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

Chirikjian

2006

Macromolecules

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Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semiflexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities.

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Visualization of the bent helix in kinetoplast DNA by electron microscopy

Cited by 231 publications

References 25 publications

Recognition of the DNA sequence by an inorganic crystal surface

Recognition of the DNA sequence by an inorganic crystal surface

Many Ways to Loop DNA

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

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