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Wang H, Milstein JN. Simulation Assisted Analysis of the Intrinsic Stiffness for Short DNA Molecules Imaged with Scanning Atomic Force Microscopy. PLoS One 2015; 10:e0142277. [PMID: 26535902 PMCID: PMC4633100 DOI: 10.1371/journal.pone.0142277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
Studying the mechanical properties of short segments of dsDNA can provide insight into various biophysical phenomena, from DNA looping to the organization of nucleosomes. Scanning atomic force microscopy (AFM) is able to acquire images of single DNA molecules with near-basepair resolution. From many images, one may use equilibrium statistical mechanics to quantify the intrinsic stiffness (or persistence length) of the DNA. However, this approach is highly dependent upon both the correct microscopic polymer model and a correct image analysis of DNA contours. These complications have led to significant debate over the flexibility of dsDNA at short length scales. We first show how to extract accurate measures of DNA contour lengths by calibrating to DNA traces of simulated AFM data. After this calibration, we show that DNA adsorbed on an aminopropyl-mica surface behaves as a worm-like chain (WLC) for contour lengths as small as ~20 nm. We also show that a DNA binding protein can modify the mechanics of the DNA from that of a WLC.
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Affiliation(s)
- Haowei Wang
- Department of Optics and Optical Engineering, University of Science and Technology of China, Heifei, Anhui, China
- Heifi National Laboratory for Physical Sciences at the Microscale, Heifi, Anhui, China
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joshua N. Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Buzio R, Repetto L, Giacopelli F, Ravazzolo R, Valbusa U. Label-free, atomic force microscopy-based mapping of DNA intrinsic curvature for the nanoscale comparative analysis of bent duplexes. Nucleic Acids Res 2012; 40:e84. [PMID: 22402493 PMCID: PMC3367213 DOI: 10.1093/nar/gks210] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We propose a method for the characterization of the local intrinsic curvature of adsorbed DNA molecules. It relies on a novel statistical chain descriptor, namely the ensemble averaged product of curvatures for two nanosized segments, symmetrically placed on the contour of atomic force microscopy imaged chains. We demonstrate by theoretical arguments and experimental investigation of representative samples that the fine mapping of the average product along the molecular backbone generates a characteristic pattern of variation that effectively highlights all pairs of DNA tracts with large intrinsic curvature. The centrosymmetric character of the chain descriptor enables targetting strands with unknown orientation. This overcomes a remarkable limitation of the current experimental strategies that estimate curvature maps solely from the trajectories of end-labeled molecules or palindromes. As a consequence our approach paves the way for a reliable, unbiased, label-free comparative analysis of bent duplexes, aimed to detect local conformational changes of physical or biological relevance in large sample numbers. Notably, such an assay is virtually inaccessible to the automated intrinsic curvature computation algorithms proposed so far. We foresee several challenging applications, including the validation of DNA adsorption and bending models by experiments and the discrimination of specimens for genetic screening purposes.
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Affiliation(s)
- Renato Buzio
- S.C. Nanobiotecnologie, National Institute for Cancer Research IST, Genova, Italy
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Moukhtar J, Faivre-Moskalenko C, Milani P, Audit B, Vaillant C, Fontaine E, Mongelard F, Lavorel G, St-Jean P, Bouvet P, Argoul F, Arneodo A. Effect of Genomic Long-Range Correlations on DNA Persistence Length: From Theory to Single Molecule Experiments. J Phys Chem B 2010; 114:5125-43. [DOI: 10.1021/jp911031y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julien Moukhtar
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Cendrine Faivre-Moskalenko
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Pascale Milani
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Cedric Vaillant
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Emeline Fontaine
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Fabien Mongelard
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Guillaume Lavorel
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Philippe St-Jean
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Philippe Bouvet
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France, Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France, and Laboratoire Joliot-Curie and Laboratoire de Biologie Moléculaire de la Cellule, CNRS/Ecole Normale Supérieure de Lyon, 46 allée d’Italie, F-69007 Lyon, France
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Zhou Z, Joós B. Disordered, stretched, and semiflexible biopolymers in two dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061911. [PMID: 20365194 DOI: 10.1103/physreve.80.061911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 09/18/2009] [Indexed: 05/29/2023]
Abstract
We study the effects of intrinsic sequence-dependent curvature for a two-dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system." Moreover, under a strong stretching force and for a long biopolymer, the sequence disorder is immaterial for elasticity. Finally, the effect of sequence disorder may depend upon the quantity considered.
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Affiliation(s)
- Zicong Zhou
- Department of Physics, Tamkang University, 151 Ying-chuan, Tamsui 25137, Taiwan, Republic of China.
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Heddi B, Oguey C, Lavelle C, Foloppe N, Hartmann B. Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res 2009; 38:1034-47. [PMID: 19920127 PMCID: PMC2817485 DOI: 10.1093/nar/gkp962] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
B-DNA flexibility, crucial for DNA–protein recognition, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR 31P chemical shifts in solution. These measurements reflect the BI ↔ BII equilibrium in DNA, intimately correlated to helicoidal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacement). Applying the TRX scale to DNA sequences optimized for nucleosome formation reveals a 10 base-pair periodic alternation of stiff and flexible regions. Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition.
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Marilley M, Milani P, Thimonier J, Rocca-Serra J, Baldacci G. Atomic force microscopy of DNA in solution and DNA modelling show that structural properties specify the eukaryotic replication initiation site. Nucleic Acids Res 2007; 35:6832-45. [PMID: 17933778 PMCID: PMC2175326 DOI: 10.1093/nar/gkm733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The replication origins (ORIs) of Schizosaccharomyces pombe, like those in most eukaryotes, are long chromosomal regions localized within A+T-rich domains. Although there is no consensus sequence, the interacting proteins are strongly conserved, suggesting that DNA structure is important for ORI function. We used atomic force microscopy in solution and DNA modelling to study the structural properties of the Spars1 origin. We show that this segment is the least stable of the surrounding DNA (9 kb), and contains regions of intrinsically bent elements (strongly curved and inherently supercoiled DNAs). The pORC-binding site co-maps with a superhelical DNA region, where the spatial arrangement of adenine/thymine stretches may provide the binding substrate. The replication initiation site (RIP) is located within a strongly curved DNA region. On pORC unwinding, this site shifts towards the apex of the curvature, thus potentiating DNA melting there. Our model is entirely consistent with the sequence variability, large size and A+T-richness of ORIs, and also accounts for the multistep nature of the initiation process, the specificity of pORC-binding site(s), and the specific location of RIP. We show that the particular DNA features and dynamic properties identified in Spars1 are present in other eukaryotic origins.
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Affiliation(s)
- Monique Marilley
- Régulation génique et fonctionnelle & microscopie champ proche, EA 3290, IFR 125, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille cedex 5, France.
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Marilley M, Milani P, Rocca-Serra J. Gradual melting of a replication origin (Schizosaccharomyces pombe ars1): in situ atomic force microscopy (AFM) analysis. Biochimie 2007; 89:534-41. [PMID: 17397989 DOI: 10.1016/j.biochi.2007.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 02/15/2007] [Indexed: 02/02/2023]
Abstract
Local DNA melting is integral to fundamental processes such as replication or transcription. In vivo, these two processes do not occur on molecules free in solution but, instead, involve DNA molecules which are organized into DNA/proteins complexes. Atomic force microscopy imaging offers a possibility to look at individual molecules. It allowed us to follow the progress of local denaturation in liquid, but with the added constraints of DNA lying on a surface. We present a kinetic analysis of the mapping of the temperature-driven melting seen at a replication origin (Schizosaccharomyces pombe ars1). The results indicate an expected base composition dependency, but also a strong extremity effect. Noteworthy, a "structural" effect is clearly occurring - which is shown by the greater susceptibility of the strongly curved region present in the sequence to unwind. DNA melting, at this place, is seen to occur after an increase in the curvature amplitude and a simultaneous shift of the nucleotide sequence positioned at the apex. Because this may determine the position of the Replication Initiation (R.I.) site, the result suggests that eukaryotic replication origins, although described as possessing no consensus sequences, may well have their mechanics sustained by the properties of common structural features. Our analysis may, therefore, provide new information that will give genuine insights on how DNA molecules behave when organized into primosomes, replisomes, promoter initiation complexes, etc. and thus, be essential to better understanding the way genes function.
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Affiliation(s)
- Monique Marilley
- Laboratoire de régulation génique et fonctionnelle & microscopie champ proche (RGFCP), IFR 125, Faculté de Médecine, Réseau AFM, Université de la Méditerranée, 13385 Marseille cedex 5, France.
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Milani P, Marilley M, Rocca-Serra J. TBP binding capacity of the TATA box is associated with specific structural properties: AFM study of the IL-2R alpha gene promoter. Biochimie 2006; 89:528-33. [PMID: 17336441 DOI: 10.1016/j.biochi.2006.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 12/12/2006] [Indexed: 11/27/2022]
Abstract
DNA is not only a nucleotide sequence which allows the binding of regulators but its intrinsic structural properties such as curvature and flexibility are also viewed as playing an active role in the regulation of transcription. Our combination of computer modelling and AFM imaging allow direct access to DNA curvature and flexibility. We have searched for these DNA structural features involved in transcription regulation within the IL-2Ralpha gene promoter. Investigation of these structural characteristics shows concordant results. First, in the core promoter, the region containing the functional TATA box shows intrinsic curvature associated with a peculiar distribution of flexibility. Both these inherent properties are characteristic of this region as compared with the other parts of the promoter. Second, the proximal promoter exhibits two important regions: a first one flexible and curved, followed by a segment of rigid linear DNA, each localised within one of the two Positive Regulatory Regions PRRI and PRRII respectively. Based on these observations, we propose different roles for DNA curvature and/or flexibility in promoter sequences.
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Affiliation(s)
- Pascale Milani
- RGFCP EA 3290, Faculté de Médecine, Université de la Méditerranée, 27, Bvd Jean Moulin, 13385 Marseille cedex 5, France.
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