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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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Zoli M. Non-linear Hamiltonian models for DNA. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:431-447. [PMID: 35976412 DOI: 10.1007/s00249-022-01614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Nucleic acids' physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse-grained models, e.g., the worm-like-chain, taken from polymer physics. In this review article, I discuss an intermediate (mesoscopic) approach and show how to build a three-dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical and structural properties of molecules in solution. Relying on the idea that the base pair fluctuations can be conceived as trajectories, I have built over the past years a computational method based on the time-dependent path integral formalism to derive the partition function. While the main features of the method are presented, I focus here in particular on a newly developed statistical method to set the maximum amplitude of the base pair fluctuations, a key parameter of the theory. Some applications to the calculation of DNA flexibility properties are discussed together with the available experimental data.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
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Sefidkar N, Fathizadeh S, Nemati F, Simserides C. Energy Transport along α-Helix Protein Chains: External Drives and Multifractal Analysis. MATERIALS 2022; 15:ma15082779. [PMID: 35454472 PMCID: PMC9029186 DOI: 10.3390/ma15082779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains. We examine the influence of different factors such as temperature, salt concentration, and external mechanical drive on the energy flux through protein chains. We obtain that energy fluctuations around the average value for short chains are greater than for longer chains. In addition, the external mechanical load is the most effective agent on bioenergy transport along the studied protein systems. Our results can help design a functional nano-scaled molecular motor based on energy transport along protein chains.
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Affiliation(s)
- Narmin Sefidkar
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran; (N.S.); (F.N.)
| | - Samira Fathizadeh
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran; (N.S.); (F.N.)
- Correspondence:
| | - Fatemeh Nemati
- Department of Physics, Urmia University of Technology, Urmia 5716693187, Iran; (N.S.); (F.N.)
| | - Constantinos Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos, GR-15784 Athens, Greece;
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Abstract
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, bending, and slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with ∼10.5 base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff increases. The cutoff is found to increase also in the presence of a sliding motion, which shortens the helix contour length, a situation peculiar of dsRNA molecules.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, I-62032 Camerino, Italy
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Zoli M. First-passage probability: a test for DNA Hamiltonian parameters. Phys Chem Chem Phys 2020; 22:26901-26909. [DOI: 10.1039/d0cp04046k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A method is developed to chose the set of input parameters for DNA mesoscopic Hamiltonian models.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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Abstract
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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Zhang X, Bao L, Wu YY, Zhu XL, Tan ZJ. Radial distribution function of semiflexible oligomers with stretching flexibility. J Chem Phys 2018; 147:054901. [PMID: 28789545 DOI: 10.1063/1.4991689] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The radial distribution of the end-to-end distance Ree is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of Ree ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of Ree. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of Ree for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of Ree becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.
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Affiliation(s)
- Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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Zoli M. End-to-end distance and contour length distribution functions of DNA helices. J Chem Phys 2018; 148:214902. [DOI: 10.1063/1.5021639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, I-62032 Camerino, Italy
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Abstract
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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Piantanida L, Naumenko D, Torelli E, Marini M, Bauer DM, Fruk L, Firrao G, Lazzarino M. Plasmon resonance tuning using DNA origami actuation. Chem Commun (Camb) 2015; 51:4789-92. [PMID: 25692733 DOI: 10.1039/c5cc00778j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A strategy for an innovative, continuous and reversible LSPR tuning using DNA origami actuation to modulate the nanometric separation of two gold nanoparticles has been developed. The actuation mechanism is based on DNA hybridization, in particular three different DNA sequences were shown to induce resonance shift of up to 6 nm.
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Affiliation(s)
- Luca Piantanida
- CNR-IOM Laboratorio TASC, Area Science Park, Basovizza, 34149, Trieste, Italy.
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