1
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Wang X, Huang T, Li L, Xu Y. Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation. RSC Adv 2024; 14:17170-17177. [PMID: 38808231 PMCID: PMC11130765 DOI: 10.1039/d4ra02354d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Employing all-atom molecular dynamics simulations, we examined the temperature-dependent behavior of bending elasticity in double-stranded RNA (dsRNA). Specifically, we focused on the bending persistence length and its constituent components, namely, the tilt and roll stiffness. Our results revealed a near-linear decrease in these stiffness components as a function of temperature, thereby highlighting the increased flexibility of dsRNA at elevated temperatures. Furthermore, our data revealed a significant anisotropy in dsRNA bending elasticity, which diminished with increasing temperature, attributable to marked disparities in tilt and roll stiffness components. We delineated the underlying biophysical mechanisms and corroborated our findings with extant literature. These observations offer salient implications for advancing our understanding of nucleic acid elasticity, and are pertinent to potential medical applications.
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Affiliation(s)
- Xianghong Wang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Tingting Huang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Liyun Li
- Department of Physics, Wenzhou University Wenzhou 325035 China
| | - Yanliang Xu
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
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2
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Zhang Z, Mou X, Zhang Y, He L, Li S. Influence of temperature on bend, twist and twist-bend coupling of dsDNA. Phys Chem Chem Phys 2024; 26:8077-8088. [PMID: 38224130 DOI: 10.1039/d3cp04932a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to assess the bend and twist elasticities through their stiffness matrix. Our analysis indicates that the bend and twist stiffnesses decrease as the temperature rises, primarily owing to entropic influences stemming from thermodynamic fluctuations. Furthermore, the couplings between these rotational parameters also exhibit a decline with increasing temperature, although the roll-twist coupling displays greater strength than the tilt-roll and tilt-twist couplings, attributed to its more robust correction component. We elucidated the influence of temperature on bend and twist elasticities based on the comparisons between various models and existing data.
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Affiliation(s)
- Zihao Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Xuankang Mou
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Yahong Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
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3
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Basov A, Dorohova A, Malyshko V, Moiseev A, Svidlov A, Bezhenar M, Nechipurenko Y, Dzhimak S. Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17. Int J Mol Sci 2023; 24:12137. [PMID: 37569512 PMCID: PMC10418495 DOI: 10.3390/ijms241512137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.
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Affiliation(s)
- Alexandr Basov
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
| | - Anna Dorohova
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Vadim Malyshko
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Arkadii Moiseev
- Scientific Department, Kuban State Agrarian University, Krasnodar 350004, Russia;
| | - Alexandr Svidlov
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Maria Bezhenar
- Department of Function Theory, Kuban State University, Krasnodar 350040, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Stepan Dzhimak
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
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4
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Zhang Y, He L, Li S. Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study. J Chem Phys 2023; 158:094902. [PMID: 36889965 DOI: 10.1063/5.0138940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.
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Affiliation(s)
- Yahong Zhang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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5
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Basu M, Mishra PP. Kineto-Mechanistic Investigation of Effect of Macromolecular Crowding on the Breathing of DNA Bubble. J Phys Chem B 2022; 126:1375-1387. [PMID: 35143192 DOI: 10.1021/acs.jpcb.1c08206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macromolecular crowding along with hydrogen bonding or stacking interactions and hydration reportedly has enormous repercussions on elementary biochemical processes, such as the folding of proteins or nucleic acids involving the stability of DNA base pairing. By using the mismatch-induced DNA bubble as a mesoscopic model, the complex interplay of macromolecular crowding on the dynamical fluctuations at the bubble region within the thermodynamic limit has been monitored using single-molecule fluorescence resonance energy transfer (sm-FRET). These single-molecule experimental results have been further corroborated using physical models such as "scaled particle theory" (SPT) and "Gaussian cloud model" (GCM), to predict the biological activity of DNA. The two-state fluctuation of the DNA bubble has been visualized as a function of the nature, size, and concentration of the crowder. The influence of crowders on the DNA conformation has been investigated with the help of the m-factor, the eccentricity, and the kinetic and thermodynamic parameters without any prior assumption. The clear effect of crowding on the dynamics of such a simple biomolecular system emphasizes the power of single-molecule methods and the dependency of the radius of gyration of the co-solute as well as the preferential interaction with the crowder on the distinct conformational states adopted by the bubble. This study provides an idea and hypothesizes the preferential propensity of the DNA bubble to adopt a conformation with the single-stranded domains being far apart, independent of the crowder size, that may be beneficial for efficient recognition by proteins for an uninterrupted procession of the biological process of the central dogma.
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Affiliation(s)
- Manali Basu
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.,Homi Bhaba National Institute, Mumbai, Maharashtra 400094, India
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6
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Yeou S, Lee NK. Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability. Mol Cells 2022; 45:33-40. [PMID: 34470919 PMCID: PMC8819492 DOI: 10.14348/molcells.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022] Open
Abstract
The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.
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Affiliation(s)
- Sanghun Yeou
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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7
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Li K, Carroll M, Vafabakhsh R, Wang XA, Wang JP. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3142-3154. [PMID: 35288750 PMCID: PMC8989542 DOI: 10.1093/nar/gkac162] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.
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Affiliation(s)
- Keren Li
- Department of Statistics, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Matthew Carroll
- Weinberg College IT Solutions (WITS), Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaozhong A Wang
- Correspondence may also be addressed to Xiaozhong A. Wang. Tel: +1 847 467 4897;
| | - Ji-Ping Wang
- To whom correspondence should be addressed. Tel: +1 847 467 6896;
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8
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Li J, Sun C, Lin Y, Zhi H, Fu Y, Liu Z. The interaction of proanthocyanidins with DNA molecules studied by atomic force microscopy and spectroscopic method. Ultramicroscopy 2021; 230:113393. [PMID: 34607224 DOI: 10.1016/j.ultramic.2021.113393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 09/06/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
The interactions of the naturally available botanicals with DNA molecules have received considerable attention owing to the potential to develop for medicinal agents. In this study, the interaction of proanthocyanidins with DNA molecules was studied by atomic force microscopy (AFM) and spectroscopic method. The AFM observation indicated that proanthocyanidins induced DNA molecules from double helix chains to the thick rope and toroids. The heights of the formed DNA structures are more than eight times than that of DNA double helix. Spectroscopic measurement results revealed that proanthocyanidins intercalated between the base pairs of DNA in the intercalative binding mode, which resulted in unwinding the DNA helix, twisting the DNA strands and finally transforming into the supercoiled DNA structures. All these results implied that DNA molecule is an important interaction target of proanthocyanidins, and the formed compact DNA structures have biological significance on the gene expression and regulation.
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Affiliation(s)
- Jingchao Li
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Congcong Sun
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Yamei Lin
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Hongxin Zhi
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Yujie Fu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China
| | - Zhiguo Liu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China; College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, People's Republic of China; Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, People's Republic of China.
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9
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Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 2021; 12:5683. [PMID: 34584096 PMCID: PMC8478907 DOI: 10.1038/s41467-021-25936-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
DNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.
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Affiliation(s)
- Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Houston, TX, USA
| | - Allison K Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA
| | - Erik Stricker
- Department of Molecular Virology and Microbiology, Houston, TX, USA
| | - Hilda L Chan
- Graduate Program in Immunology and Microbiology, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Houston, TX, USA.
- Graduate Program in Immunology and Microbiology, Houston, TX, USA.
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10
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Saran R, Wang Y, Li ITS. Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7019. [PMID: 33302459 PMCID: PMC7764255 DOI: 10.3390/s20247019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
| | - Yong Wang
- Department of Physics, Materials Science and Engineering Program, Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Isaac T. S. Li
- Department of Chemistry, Biochemistry and Molecular Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Kelowna, BC V1V1V7, Canada;
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11
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Arévalo-Soliz LM, Hardee CL, Fogg JM, Corman NR, Noorbakhsh C, Zechiedrich L. Improving therapeutic potential of non-viral minimized DNA vectors. CELL & GENE THERAPY INSIGHTS 2020; 6:1489-1505. [PMID: 33953961 PMCID: PMC8095377 DOI: 10.18609/cgti.2020.163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The tragic deaths of three patients in a recent AAV-based X-linked myotubular myopathy clinical trial highlight once again the pressing need for safe and reliable gene delivery vectors. Non-viral minimized DNA vectors offer one possible way to meet this need. Recent pre-clinical results with minimized DNA vectors have yielded promising outcomes in cancer therapy, stem cell therapy, stem cell reprograming, and other uses. Broad clinical use of these vectors, however, remains to be realized. Further advances in vector design and production are ongoing. An intriguing and promising potential development results from manipulation of the specific shape of non-viral minimized DNA vectors. By improving cellular uptake and biodistribution specificity, this approach could impact gene therapy, DNA nanotechnology, and personalized medicine.
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Affiliation(s)
- Lirio M Arévalo-Soliz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cinnamon L Hardee
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nathan R Corman
- Rural Medical Education Program, University of Illinois College of Medicine, Rockford, IL 61107, USA
| | - Cameron Noorbakhsh
- Weiss School of Natural Sciences, Rice University, Houston, TX 77005, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Majumdar D, Bhattacharjee SM. Softening of DNA near melting as disappearance of an emergent property. Phys Rev E 2020; 102:032407. [PMID: 33075941 DOI: 10.1103/physreve.102.032407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Near the melting transition the bending elastic constant κ, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rodlike scaling for small-length N. The reduction in κ with temperature is determined by the denatured bubbles for a continuous transition, e.g., when the two strands are Gaussian, but by the broken bonds near the open end in a Y-like configuration for a first-order transition as for strands with excluded volume interactions. In the latter case, a lever rule is operational, implying a phase coexistence although dsDNA is known to be a single phase.
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Affiliation(s)
- Debjyoti Majumdar
- Institute of Physics, Bhubaneswar, Odisha 751005, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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13
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Drozdetski AV, Mukhopadhyay A, Onufriev AV. Strongly Bent Double-Stranded DNA: Reconciling Theory and Experiment. FRONTIERS IN PHYSICS 2019; 7:195. [PMID: 32601596 PMCID: PMC7323118 DOI: 10.3389/fphy.2019.00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function. For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than ~ 2° per base-pair, equivalent to the curvature of a closed circular loop of ~ 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counter-intuitively, cyclization probability (j-factor) of very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of ≃ 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.
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Affiliation(s)
| | | | - Alexey V. Onufriev
- Department of Physics, Virginia Tech, Blacksburg, VA, United States
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, United States
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14
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Jiang W, Singh J, Allen A, Li Y, Kathiresan V, Qureshi O, Tangprasertchai N, Zhang X, Parameshwaran HP, Rajan R, Qin PZ. CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity. ACS OMEGA 2019; 4:17140-17147. [PMID: 31656887 PMCID: PMC6811856 DOI: 10.1021/acsomega.9b01469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/25/2019] [Indexed: 05/03/2023]
Abstract
Cas12a (also known as "Cpf1") is a class 2 type V-A CRISPR-associated nuclease that can cleave double-stranded DNA at specific sites. The Cas12a effector enzyme comprises a single protein and a CRISPR-encoded small RNA (crRNA) and has been used for genome editing and manipulation. Work reported here examined in vitro interactions between the Cas12a effector enzyme and DNA duplexes with varying states of base-pairing between the two strands. The data revealed that in the absence of complementarity between the crRNA guide and the DNA target-strand, Cas12a binds duplexes with unpaired segments. These off-target duplexes were bound at the Cas12a site responsible for RNA-guided double-stranded DNA binding but were not cleaved due to the lack of RNA/DNA hybrid formation. Such promiscuous binding was attributed to increased DNA flexibility induced by the unpaired segment present next to the protospacer-adjacent-motif. The results suggest that target discrimination of Cas12a can be influenced by flexibility of the DNA. As such, in addition to the linear sequence, flexibility and other physical properties of the DNA should be considered in Cas12a-based genome engineering applications.
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Affiliation(s)
- Wei Jiang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Jaideep Singh
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Aleique Allen
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Yue Li
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Venkatesan Kathiresan
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Omair Qureshi
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Narin Tangprasertchai
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Hari Priya Parameshwaran
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rakhi Rajan
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Peter Z. Qin
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
- E-mail: . Phone: (213) 821-2461. Fax: (213) 740-2701
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15
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Harrison RM, Romano F, Ouldridge TE, Louis AA, Doye JPK. Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model. J Chem Theory Comput 2019; 15:4660-4672. [PMID: 31282669 PMCID: PMC6694408 DOI: 10.1021/acs.jctc.9b00112] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
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DNA
cyclization is a powerful technique to gain insight into the nature
of DNA bending. While the wormlike chain model provides a good description
of small to moderate bending fluctuations, it is expected to break
down for large bending. Recent cyclization experiments on strongly
bent shorter molecules indeed suggest enhanced flexibility over and
above that expected from the wormlike chain. Here, we use a coarse-grained
model of DNA to investigate the subtle thermodynamics of DNA cyclization
for molecules ranging from 30 to 210 base pairs. As the molecules
get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada
and Yamakawa for a torsionally aligned looped molecule. These deviations
are due to sharp kinking, first at nicks, and only subsequently in
the body of the duplex. At the shortest lengths, substantial fraying
at the ends of duplex domains is the dominant method of relaxation.
We also estimate the dynamic j-factor measured in
recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart—with
the deviation larger for shorter molecules—because not all
the stress present in the fully cyclized state is present in the transition
state. These observations are important for the interpretation of
recent cyclization experiments, suggesting that measured anomalously
high j-factors may not necessarily indicate non-WLC
behavior in the body of duplexes.
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Affiliation(s)
- Ryan M Harrison
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Universitá Ca' Foscari Venezia , I-30123 Venezia , Italy
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology and Department of Bioengineering , Imperial College London , 180 Queen's Road , London SW7 2AZ , United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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16
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Brunet A, Salomé L, Rousseau P, Destainville N, Manghi M, Tardin C. How does temperature impact the conformation of single DNA molecules below melting temperature? Nucleic Acids Res 2019; 46:2074-2081. [PMID: 29294104 PMCID: PMC5829751 DOI: 10.1093/nar/gkx1285] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/19/2017] [Indexed: 01/26/2023] Open
Abstract
The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.
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Affiliation(s)
- Annaël Brunet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.,Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Laurence Salomé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique (IRSAMC), Université de Toulouse, CNRS, Toulouse, France
| | - Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
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17
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Tran T, Cannon B. Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops. Biochemistry 2017; 56:6448-6459. [PMID: 29141138 DOI: 10.1021/acs.biochem.7b00930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Internal loops within structured nucleic acids disrupt local base stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities of structured nucleic acids. Variations in the size, distribution of loop nucleotides on opposing strands (strand asymmetry), and sequence alter their biophysical properties. Here, the thermodynamics and structural flexibility of oligo-T-rich DNA internal loops were systematically investigated in terms of loop size and strand asymmetry. From optical melting experiments, a thermodynamic prediction model is proposed for the energetic penalty of internal loops that accounts for diminishing enthalpic and increasing entropic contributions due to loop size and strand asymmetry for bulges, asymmetric loops, and symmetric loops. These single-stranded domains become less sequence-dependent and more polymeric as the loop size increases. Single-molecule fluorescence resonance energy transfer studies reveal a gradual transition in conformation and structural flexibility from an elongated domain to an increasingly flexible bend that results from increasing strand asymmetry. The findings provide a framework for understanding the thermodynamic and conformational effects of internal loops for the rational design of functional DNA nanostructures.
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Affiliation(s)
- Thao Tran
- Department of Physics, Loyola University Chicago , Chicago, Illinois 60660, United States
| | - Brian Cannon
- Department of Physics, Loyola University Chicago , Chicago, Illinois 60660, United States
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18
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Cong P, Dai L, Chen H, van der Maarel JRC, Doyle PS, Yan J. Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA. Biophys J 2016; 109:2338-51. [PMID: 26636945 PMCID: PMC4675846 DOI: 10.1016/j.bpj.2015.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 11/25/2022] Open
Abstract
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.
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Affiliation(s)
- Peiwen Cong
- Mechanobiology Institute, National University of Singapore, Singapore; Singapore-MIT Alliance, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore
| | - Liang Dai
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore
| | - Hu Chen
- Department of Physics, Xiamen University, Xiamen, Fujian, China
| | | | - Patrick S Doyle
- BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore; BioSystems and Micromechanics IRG, Singapore-MIT Alliance for Research and Technology Centre, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore.
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19
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20
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Abstract
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.
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Affiliation(s)
- Tanmoy Pal
- Institute of Physics, Bhubaneswar 751005, India
| | - Somendra M Bhattacharjee
- Institute of Physics, Bhubaneswar 751005, India.,Department of Physics, Ramakrishna Mission Vivekananda University, P.O. Belur Math, Dist. Howrah, West Bengal 711202, India
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21
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Zrimec J, Lapanje A. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1137-1145. [PMID: 26451825 DOI: 10.1109/tcbb.2015.2396057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA melting bubbles are the basis of many DNA-protein interactions, such as those in regulatory DNA regions driving gene expression, DNA replication and bacterial horizontal gene transfer. Bubble formation is affected by DNA duplex stability and thermally induced duplex destabilization (TIDD). Although prediction of duplex stability with the nearest neighbor (NN) method is much faster than prediction of TIDD with the Peyrard-Bishop-Dauxois (PBD) model, PBD predicted TIDD defines regulatory DNA regions with higher accuracy and detail. Here, we considered that PBD predicted TIDD is inherently related to the intrinsic duplex stabilities of destabilization regions. We show by regression modeling that NN duplex stabilities can be used to predict TIDD almost as accurately as is predicted with PBD. Predicted TIDD is in fact ascribed to non-linear transformation of NN duplex stabilities in destabilization regions as well as effects of neighboring regions relative to destabilization size. Since the prediction time of our models is over six orders of magnitude shorter than that of PBD, the models present an accessible tool for researchers. TIDD can be predicted on our webserver at http://tidd.immt.eu.
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22
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Traverso JJ, Manoranjan VS, Bishop AR, Rasmussen KØ, Voulgarakis NK. Allostery through protein-induced DNA bubbles. Sci Rep 2015; 5:9037. [PMID: 25762409 PMCID: PMC4356955 DOI: 10.1038/srep09037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.
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Affiliation(s)
- Joseph J Traverso
- 1] Department of Mathematics, Washington State University, Richland, WA 99354, USA [2] Department of Mechanical Engineering, Washington State University, Richland, WA 99354, USA
| | | | - A R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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23
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Mazur AK, Maaloum M. Atomic force microscopy study of DNA flexibility on short length scales: smooth bending versus kinking. Nucleic Acids Res 2014; 42:14006-12. [PMID: 25414337 PMCID: PMC4267637 DOI: 10.1093/nar/gku1192] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The apparently anomalous flexibility of DNA on short length scales has attracted a lot of attention in recent years. We use atomic force microscopy (AFM) in solution to directly study the DNA bending statistics for small lengths down to one helical turn. The accuracy of experimental estimates could be improved due to a large data volume and a refined algorithm for image processing and measuring bend angles. It is found that, at length scales beyond two helical turns (7 nm), DNA is well described by the harmonic worm-like chain (WLC) model with the bending persistence length of 56 nm. Below this threshold, the AFM data are also described by the WLC model assuming that the accuracy of measured bend angles is limited by the physical width of the double helix. We conclude that the double helical DNA behaves as a uniform elastic rod even at very short length scales. Strong bends due to kinks, melting bubbles and other deviations from the WLC model are statistically negligible.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
| | - Mounir Maaloum
- Institut Charles Sadron, CNRS-University of Strasbourg, 23 rue du Loess, BP 84087, 67034 Strasbourg Cedex 2, France
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24
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Driessen RPC, Sitters G, Laurens N, Moolenaar GF, Wuite GJL, Goosen N, Dame RT. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry 2014; 53:6430-8. [PMID: 25291500 PMCID: PMC5451147 DOI: 10.1021/bi500344j] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
helical structure of double-stranded DNA is destabilized by
increasing temperature. Above a critical temperature (the melting
temperature), the two strands in duplex DNA become fully separated.
Below this temperature, the structural effects are localized. Using
tethered particle motion in a temperature-controlled sample chamber,
we systematically investigated the effect of increasing temperature
on DNA structure and the interplay between this effect and protein
binding. Our measurements revealed that (1) increasing temperature
enhances DNA flexibility, effectively leading to more compact folding
of the double-stranded DNA chain, and (2) temperature differentially
affects different types of DNA-bending chromatin proteins from mesophilic
and thermophilic organisms. Thus, our findings aid in understanding
genome organization in organisms thriving at moderate as well as extreme
temperatures. Moreover, our results underscore the importance of carefully
controlling and measuring temperature in single-molecule DNA (micromanipulation)
experiments.
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Affiliation(s)
- Rosalie P C Driessen
- Molecular Genetics, Leiden Institute of Chemistry and Cell Observatory, Leiden University , 2333 CC Leiden, The Netherlands
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25
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Taranova M, Hirsh AD, Perkins NC, Andricioaei I. Role of microscopic flexibility in tightly curved DNA. J Phys Chem B 2014; 118:11028-36. [PMID: 25155114 PMCID: PMC4174995 DOI: 10.1021/jp502233u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
genetic material in living cells is organized into complex
structures in which DNA is subjected to substantial contortions. Here
we investigate the difference in structure, dynamics, and flexibility
between two topological states of a short (107 base pair) DNA sequence
in a linear form and a covalently closed, tightly curved circular
DNA form. By employing a combination of all-atom molecular dynamics
(MD) simulations and elastic rod modeling of DNA, which allows capturing
microscopic details while monitoring the global dynamics, we demonstrate
that in the highly curved regime the microscopic flexibility of the
DNA drastically increases due to the local mobility of the duplex.
By analyzing vibrational entropy and Lipari–Szabo NMR order
parameters from the simulation data, we propose a novel model for
the thermodynamic stability of high-curvature DNA states based on
vibrational untightening of the duplex. This novel view of DNA bending
provides a fundamental explanation that bridges the gap between classical
models of DNA and experimental studies on DNA cyclization, which so
far have been in substantial disagreement.
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Affiliation(s)
- Maryna Taranova
- Department of Chemistry, University of California , 1102 Natural Sciences 2, Irvine, California 92697, United States
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26
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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27
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Mazur AK, Maaloum M. DNA flexibility on short length scales probed by atomic force microscopy. PHYSICAL REVIEW LETTERS 2014; 112:068104. [PMID: 24580711 DOI: 10.1103/physrevlett.112.068104] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Indexed: 06/03/2023]
Abstract
Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It appears that DNA behaves as a Gaussian chain and is well described by the wormlike chain model at length scales beyond 3 helical turns (10.5 nm). Below this threshold, the AFM data exhibit growing noise because of experimental limitations. This noise may hide small deviations from the Gaussian behavior, but they can hardly be significant.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, 75005, France
| | - Mounir Maaloum
- Institut Charles Sadron, CNRS-University of Strasbourg, 23 rue du Loess, BP 84087, 67034 Strasbourg cedex 2, France
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28
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Johnson S, Chen YJ, Phillips R. Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. PLoS One 2013; 8:e75799. [PMID: 24146776 PMCID: PMC3795714 DOI: 10.1371/journal.pone.0075799] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/19/2013] [Indexed: 01/31/2023] Open
Abstract
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will occur, less is known about the role played by the intervening DNA. In this work we explore the effect of sequence flexibility on transcription factor-mediated DNA looping, by drawing on sequences identified in nucleosome formation and ligase-mediated cyclization assays as being especially favorable for or resistant to large deformations. We examine a poly(dA:dT)-rich, nucleosome-repelling sequence that is often thought to belong to a class of highly inflexible DNAs; two strong nucleosome positioning sequences that share a set of particular sequence features common to nucleosome-preferring DNAs; and a CG-rich sequence representative of high G+C-content genomic regions that correlate with high nucleosome occupancy in vivo. To measure the flexibility of these sequences in the context of DNA looping, we combine the in vitro single-molecule tethered particle motion assay, a canonical looping protein, and a statistical mechanical model that allows us to quantitatively relate the looping probability to the looping free energy. We show that, in contrast to the case of nucleosome occupancy, G+C content does not positively correlate with looping probability, and that despite sharing sequence features that are thought to determine nucleosome affinity, the two strong nucleosome positioning sequences behave markedly dissimilarly in the context of looping. Most surprisingly, the poly(dA:dT)-rich DNA that is often characterized as highly inflexible in fact exhibits one of the highest propensities for looping that we have measured. These results argue for a need to revisit our understanding of the mechanical properties of DNA in a way that will provide a basis for understanding DNA deformation over the entire range of biologically relevant scenarios that are impacted by DNA deformability.
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Affiliation(s)
- Stephanie Johnson
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Yi-Ju Chen
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Rob Phillips
- Departments of Applied Physics and Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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29
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Wang J, Qu H, Zocchi G. Critical bending torque of DNA is a materials parameter independent of local base sequence. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:032712. [PMID: 24125299 DOI: 10.1103/physreve.88.032712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Indexed: 06/02/2023]
Abstract
Short double-stranded DNA molecules exhibit a softening transition under large bending which is quantitatively described by a critical bending torque τ_{c} at which the molecule develops a kink. Through equilibrium measurements of the elastic energy of short (∼10 nm), highly stressed DNA molecules with a nick at the center we determine τ_{c} for different sequences around the nick. We find that τ_{c} is a robust materials parameter essentially independent of sequence. The measurements also show that, at least for nicked DNA, the local structure at the origin of the softening transition is not a single-stranded "bubble."
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Affiliation(s)
- Juan Wang
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, CA 90095-1547, USA
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30
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Fields AP, Meyer EA, Cohen AE. Euler buckling and nonlinear kinking of double-stranded DNA. Nucleic Acids Res 2013; 41:9881-90. [PMID: 23956222 PMCID: PMC3834817 DOI: 10.1093/nar/gkt739] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe experimentally, and literature results have not been consistent. We created a 'molecular vise' in which base-pairing interactions generated a compressive force on sub-persistence length segments of dsDNA. Short dsDNA strands (<41 base pairs) resisted this force and remained straight; longer strands became bent, a phenomenon called 'Euler buckling'. We monitored the buckling transition via Förster Resonance Energy Transfer (FRET) between appended fluorophores. For low-to-moderate concentrations of monovalent salt (up to ∼150 mM), our results are in quantitative agreement with the worm-like chain (WLC) model of DNA elasticity, without the need to invoke any 'kinked' states. Greater concentrations of monovalent salts or 1 mM Mg(2+) induced an apparent softening of the dsDNA, which was best accounted for by a kink in the region of highest curvature. We tested the effects of all single-nucleotide mismatches on the DNA bending. Remarkably, the propensity to kink correlated with the thermodynamic destabilization of the mismatched DNA relative the perfectly complementary strand, suggesting that the kinked state is locally melted. The molecular vise is exquisitely sensitive to the sequence-dependent linear and nonlinear elastic properties of dsDNA.
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Affiliation(s)
- Alexander P Fields
- Biophysics Program, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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31
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Padinhateeri R, Menon GI. Stretching and bending fluctuations of short DNA molecules. Biophys J 2013; 104:463-71. [PMID: 23442868 DOI: 10.1016/j.bpj.2012.11.3820] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/01/2012] [Accepted: 11/27/2012] [Indexed: 11/28/2022] Open
Abstract
Recent measurements of the distribution of end-to-end distance in short DNA molecules infer cooperative stretching fluctuations. The assumptions underlying the analysis can be questioned if transient, thermally induced defects producing a localized decrease in bending stiffness are present in thermal equilibrium, such as regions in which DNA melts locally (bubbles), sustains large-angle bends (kinks), or can locally transform into an alternative (S-DNA) state. We study a generalized discrete worm-like chain model for DNA, capable of describing these experiments, showing that the model yields accurate fits to available experimental data. Our results indicate that DNA bending arising from such localized defects, rather than solely stretching, can be an equal contributor to end-to-end distance fluctuations for 35-bp DNA and contributes nontrivially to such fluctuations at all scales below the persistence length. The analysis suggests that such fluctuations should exhibit a scale-dependent cooperativity, specifically relevant in determining the behavior of short chains, but which saturates rapidly to a length-independent value for longer DNA, to ensure a consistent physical description of DNA across multiple scales. Our approach provides a minimal, yet accurate, coarse-grained description of DNA at the subpersistence length scales of current experimental interest.
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Affiliation(s)
- Ranjith Padinhateeri
- Department of Biosciences and Bioengineering and Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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32
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Abstract
During the past decade, the issue of strong bending of the double helix has attracted a lot of attention. Here, we overview the major experimental and theoretical developments in the field sorting out reliably established facts from speculations and unsubstantiated claims. Theoretical analysis shows that sharp bends or kinks have to facilitate strong bending of the double helix. It remains to be determined what is the critical curvature of DNA that prompts the appearance of the kinks. Different experimental and computational approaches to the problem are analyzed. We conclude that there is no reliable evidence that any anomalous behavior of the double helix happens when DNA fragments in the range of 100 bp are circularized without torsional stress. The anomaly starts at the fragment length of about 70 bp when sharp bends or kinks emerge in essentially every molecule. Experimental data and theoretical analysis suggest that kinks may represent openings of isolated base pairs, which had been experimentally detected in linear DNA molecules. The calculation suggests that although the probability of these openings in unstressed DNA is close to 10−5, it increases sharply in small DNA circles reaching 1 open bp per circle of 70 bp.
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33
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Leforestier A. Polymorphism of DNA conformation inside the bacteriophage capsid. J Biol Phys 2013; 39:201-13. [PMID: 23860869 PMCID: PMC3662419 DOI: 10.1007/s10867-013-9315-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/20/2013] [Indexed: 10/27/2022] Open
Abstract
Double-stranded DNA bacteriophage genomes are packaged into their icosahedral capsids at the highest densities known so far (about 50 % w:v). How the molecule is folded at such density and how its conformation changes upon ejection or packaging are fascinating questions still largely open. We review cryo-TEM analyses of DNA conformation inside partially filled capsids as a function of the physico-chemical environment (ions, osmotic pressure, temperature). We show that there exists a wide variety of DNA conformations. Strikingly, the different observed structures can be described by some of the different models proposed over the years for DNA organisation inside bacteriophage capsids: either spool-like structures with axial or concentric symmetries, or liquid crystalline structures characterised by a DNA homogeneous density. The relevance of these conformations for the understanding of DNA folding and unfolding upon ejection and packaging in vivo is discussed.
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Affiliation(s)
- Amélie Leforestier
- Laboratoire de Physqiue des Solides, CNRS, UMR 8502, Université Paris Sud, Orsay, France.
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34
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Sanchez DS, Qu H, Bulla D, Zocchi G. DNA kinks and bubbles: temperature dependence of the elastic energy of sharply bent 10-nm-size DNA molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022710. [PMID: 23496551 DOI: 10.1103/physreve.87.022710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 06/01/2023]
Abstract
A 10-nm-long DNA molecule can bend through large angles reversibly. Past the linear regime, its equilibrium nonlinear bending elasticity is governed by a critical bending torque τ(c)≈30pN×nm at which the molecule develops a kink. This nonlinearity has long been attributed to the nucleation of a bubble or melted region in the molecule. Here we measure the temperature dependence of the critical bending torque for nicked DNA, and determine that the entropy associated with the kink in the nonlinear regime is negligible. Thus in the case of nicked DNA the kink is not a bubble, but a compact region deformed beyond a yield strain. We further argue that, with our boundary conditions, the same is likely true for intact DNA. The present measurements confirm that the critical bending torque τ(c) is a materials parameter of DNA mechanics analogous to the bending modulus B≈200pN×nm.
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Affiliation(s)
- Daniel S Sanchez
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095-1547, USA
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35
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Sivak DA, Geissler PL. Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA. J Chem Phys 2012; 136:045102. [PMID: 22299918 DOI: 10.1063/1.3679654] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1-10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of microscopic models which allow for disruption of base pairing (i.e., a "melt" or "kink", generically an "excitation") and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.
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Affiliation(s)
- David A Sivak
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
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36
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Spiriti J, Kamberaj H, de Graff AMR, Thorpe MF, van der Vaart A. DNA Bending through Large Angles Is Aided by Ionic Screening. J Chem Theory Comput 2012; 8:2145-56. [PMID: 26593845 DOI: 10.1021/ct300177r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model. Persistence lengths calculated directly from the simulated structures and indirectly through the use of sequence-independent coarse-grained models based on simulation data were similar to literature values. On short length scales, the free energy cost of bending DNA was found to be consistent with the worm-like chain model for small and intermediate bending angles. At large angles, the bending free energy as a function of the roll angle became linear, suggesting a relative increase in flexibility at larger roll angles. Counterions congregated on the concave side of the highly bent DNA and screened the repulsion of the phosphate groups, facilitating the bending.
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Affiliation(s)
- Justin Spiriti
- Department of Chemistry, University of South Florida, 4202 E Fowler Ave. CHE 205, Tampa, Florida 33620, United States
| | - Hiqmet Kamberaj
- Faculty of Technical Sciences, International Balkan University, Skopje, Republic of Macedonia
| | - Adam M R de Graff
- Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States.,Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - M F Thorpe
- Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, United States.,Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 E Fowler Ave. CHE 205, Tampa, Florida 33620, United States
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37
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Kabakçıoğlu A, Bar A, Mukamel D. Macroscopic loop formation in circular DNA denaturation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051919. [PMID: 23004799 DOI: 10.1103/physreve.85.051919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Indexed: 06/01/2023]
Abstract
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.
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Affiliation(s)
- Alkan Kabakçıoğlu
- Department of Physics, Koç University, Sarıyer 34450 İstanbul, Turkey
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38
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Lee OC, Sung W. Enhanced bubble formation in looped short double-stranded DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021902. [PMID: 22463239 DOI: 10.1103/physreve.85.021902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 12/13/2011] [Indexed: 05/31/2023]
Abstract
Recent experiments have shown the double-stranded (ds) DNAs readily bend and loop over the scale much shorter than their persistence length (50 nm). In an effort to unveil this seemingly surprising phenomenon, we study the emergence of bubbles in short ds DNA loops by simulating the breathing DNA model. We analyze the bubble size distributions and the melting curves for varying contour lengths, which are critically compared with those of linear DNA of the same lengths. We analytically evaluate the free energies associated with double-strand bending and single-strand bubble formation to explain the simulation data. It is found that in shorter looped DNA the bubbles are more easily initiated and formed to release the large bending energy, giving rise to melting at a lower temperature and a lower contour length.
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Affiliation(s)
- O-chul Lee
- Department of Physics and PCTP, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea. ochul
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39
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Geggier S, Kotlyar A, Vologodskii A. Temperature dependence of DNA persistence length. Nucleic Acids Res 2010; 39:1419-26. [PMID: 20952402 PMCID: PMC3045604 DOI: 10.1093/nar/gkq932] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We have determined the temperature dependence of DNA persistence length, a, using two different methods. The first approach was based on measuring the j-factors of short DNA fragments at various temperatures. Fitting the measured j-factors by the theoretical equation allowed us to obtain the values of a for temperatures between 5°C and 42°C. The second approach was based on measuring the equilibrium distribution of the linking number between the strands of circular DNA at different temperatures. The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a. The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C. We found a good agreement between the results obtained by these two methods. Our data show that DNA persistence length strongly depends on temperature and accounting for this dependence is important in quantitative comparison between experimental results obtained at different temperatures.
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Affiliation(s)
- Stephanie Geggier
- Department of Chemistry, New York University, New York, NY 10003, USA
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