1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Dohnalová H, Matoušková E, Lankaš F. Temperature-dependent elasticity of DNA, RNA, and hybrid double helices. Biophys J 2024; 123:572-583. [PMID: 38340722 PMCID: PMC10938081 DOI: 10.1016/j.bpj.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.
Collapse
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic.
| |
Collapse
|
4
|
Scalvini B, Heling LWHJ, Sheikhhassani V, Sunderlikova V, Tans SJ, Mashaghi A. Cytosolic Interactome Protects Against Protein Unfolding in a Single Molecule Experiment. Adv Biol (Weinh) 2023; 7:e2300105. [PMID: 37409427 DOI: 10.1002/adbi.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/13/2023] [Indexed: 07/07/2023]
Abstract
Single molecule techniques are particularly well suited for investigating the processes of protein folding and chaperone assistance. However, current assays provide only a limited perspective on the various ways in which the cellular environment can influence the folding pathway of a protein. In this study, a single molecule mechanical interrogation assay is developed and used to monitor protein unfolding and refolding within a cytosolic solution. This allows to test the cumulative topological effect of the cytoplasmic interactome on the folding process. The results reveal a stabilization against forced unfolding for partial folds, which are attributed to the protective effect of the cytoplasmic environment against unfolding and aggregation. This research opens the possibility of conducting single molecule molecular folding experiments in quasi-biological environments.
Collapse
Affiliation(s)
- Barbara Scalvini
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | - Laurens W H J Heling
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | - Vahid Sheikhhassani
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| | | | - Sander J Tans
- AMOLF, Science Park 104, Amsterdam, 1098 XG, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333CC, The Netherlands
| |
Collapse
|
5
|
Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
Collapse
Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| |
Collapse
|
6
|
Naskar S, Bhatia D, Lin ST, Maiti PK. Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars. Phys Chem Chem Phys 2023; 25:7847-7858. [PMID: 36857659 DOI: 10.1039/d2cp04683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.
Collapse
Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Voorspoels A, Vreede J, Carlon E. Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations. J Chem Theory Comput 2023; 19:902-909. [PMID: 36695645 DOI: 10.1021/acs.jctc.2c00889] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution, however, comes at a heavy computational cost, and, within the time scales of simulations, nucleic acids weakly fluctuate around their ideal structure exploring a limited set of conformations. We introduce the RBB-NA algorithm (available as a package in the Open Source Library PLUMED), which is capable of controlling rigid base parameters in all-atom simulations of nucleic acids. With suitable biasing potentials, this algorithm can "force" a DNA or RNA molecule to assume specific values of the six rotational (tilt, roll, twist, buckle, propeller, opening) and/or the six translational parameters (shift, slide, rise, shear, stretch, stagger). The algorithm enables the use of advanced sampling techniques to probe the structure and dynamics of locally strongly deformed nucleic acids. We illustrate its performance showing some examples in which DNA is strongly twisted, bent, or locally buckled. In these examples, RBB-NA reproduces well the unconstrained simulations data and other known features of DNA mechanics, but it also allows one to explore the anharmonic behavior characterizing the mechanics of nucleic acids in the high deformation regime.
Collapse
Affiliation(s)
- Aderik Voorspoels
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3000 Leuven, Belgium
| | - Jocelyne Vreede
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3000 Leuven, Belgium
| |
Collapse
|
9
|
Gutiérrez Fosado YA, Landuzzi F, Sakaue T. Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length. PHYSICAL REVIEW LETTERS 2023; 130:058402. [PMID: 36800451 DOI: 10.1103/physrevlett.130.058402] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
While the behavior of double-stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base-pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off-site couplings between deformations with different parity.
Collapse
Affiliation(s)
- Yair Augusto Gutiérrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Fabio Landuzzi
- Centro CMP3VdA, Istituto Italiano di Tecnologia, via Lavoratori Vittime del Col du Mont 28, 11100, Aosta, Italy
| | - Takahiro Sakaue
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan
| |
Collapse
|
10
|
Aggarwal A, Naskar S, Maiti PK. Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA. J Phys Chem B 2022; 126:4636-4646. [PMID: 35729785 DOI: 10.1021/acs.jpcb.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.
Collapse
Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
11
|
Segers M, Voorspoels A, Sakaue T, Carlon E. Mechanical properties of nucleic acids and the non-local twistable wormlike chain model. J Chem Phys 2022; 156:234105. [PMID: 35732531 DOI: 10.1063/5.0089166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mechanical properties of nucleic acids play an important role in many biological processes that often involve physical deformations of these molecules. At sufficiently long length scales (say, above ∼20-30 base pairs), the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales, this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites get coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model that clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables that describe the twist and bending of the molecule. Different from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior that matches experimental data.
Collapse
Affiliation(s)
- Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| |
Collapse
|
12
|
Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
Collapse
Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
13
|
Chhetri KB, Dasgupta C, Maiti PK. Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement. Front Chem 2022; 10:879746. [PMID: 35586267 PMCID: PMC9108266 DOI: 10.3389/fchem.2022.879746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Carbon nanotubes (CNTs) are considered promising candidates for biomolecular confinement, including DNA encapsulation for gene delivery. Threshold values of diameters have been reported for double-stranded DNA (dsDNA) encapsulation inside CNTs. We have performed all-atom molecular dynamics (MD) simulations of dsDNAs confined inside single-walled CNTs (SWCNTs) at the physiologically relevant temperature of 300 K. We found that the dsDNA can be confined without being denatured only when the diameter of the SWCNT exceeds a threshold value. Below this threshold diameter, the dsDNA gets denatured and melts even at the temperature of 300 K. Our simulations using SWCNTs with chirality indices (20,20) to (30,30) at 300 K found the critical diameter to be 3.25 nm (corresponding to (24,24) chirality). Analyses of the hydrogen bonds (H-bonds), Van der Walls (VdW) energy, and other inter-base interactions show drastic reduction in the number of H-bonds, VdW energy, and electrostatic energies between the bases of dsDNA when it is confined in narrower SWCNTs (up to diameter of 3.12 nm). On the other hand, the higher interaction energy between the dsDNA and the SWCNT surface in narrower SWCNTs assists in the melting of the dsDNA. Electrostatic mapping and hydration status analyses show that the dsDNA is not adequately hydrated and the counter ion distribution is not uniform below the critical diameter of the SWCNT. As properly hydrated counter ions provide stability to the dsDNA, we infer that the inappropriate hydration of counter ions and their non-uniform distribution around the dsDNA cause the melting of the dsDNA inside SWCNTs of diameter below the critical value of 3.25 nm. For confined dsDNAs that do not get denatured, we computed their elastic properties. The persistence length of dsDNA was found to increase by a factor of about two and the torsional stiffness by a factor of 1.5 for confinement inside SWCNTs of diameters up to 3.79 nm, the stretch modulus also following nearly the same trend. Interestingly, for higher diameters of SWCNT, 3.79 nm and above, the dsDNA becomes more flexible, demonstrating that the mechanical properties of the dsDNA under cylindrical confinement depend non-monotonically on the confinement diameter.
Collapse
Affiliation(s)
- Khadka B. Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Chandan Dasgupta
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- *Correspondence: Prabal K. Maiti,
| |
Collapse
|
14
|
Feric M, Misteli T. Function moves biomolecular condensates in phase space. Bioessays 2022; 44:e2200001. [PMID: 35243657 PMCID: PMC9277701 DOI: 10.1002/bies.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure-function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mitochondrial and bacterial nucleoids. In vitro and in vivo observations suggest that transcriptional activity of condensates influences their supramolecular structure, which in turn affects their function. Condensate organization thus becomes driven by differences in miscibility among the DNA and proteins of the transcription machinery and the RNA transcripts they generate. These considerations are in line with the notion that cellular processes shape the structural properties of condensates, leading to a dynamic, mutual interplay between structure and function in the cell.
Collapse
Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
15
|
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.
Collapse
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;
| |
Collapse
|
16
|
Lee K, Kim JY, Kim K, Jeon J, Kang H, Sohn BH. Porous self-supporting film of semi-flexible supracolloidal chains of diblock copolymer micelles. J Colloid Interface Sci 2021; 600:804-810. [PMID: 34052531 DOI: 10.1016/j.jcis.2021.05.077] [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: 02/08/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/25/2022]
Abstract
Patchy micelles of diblock copolymers can be polymerized into a linear supracolloidal chain. We measure the persistence and contour lengths of supracolloidal chains coated on a solid substrate to evaluate their flexibility. Based on the analysis, the chain is semi-flexible, and the conformation is suitably explained by the worm-like chain model. In addition, utilizing a spin-coating technique with the semi-flexible nature of the chains, we produce a self-supporting film of supracolloidal chains having nanoscale pores essentially from colloidal constituents that tend to form dense packing if there is no prior organization of them into a semi-flexible chain.
Collapse
Affiliation(s)
- Kyunghyeon Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Joon Young Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyungtae Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonghyuk Jeon
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Heejung Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Byeong-Hyeok Sohn
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
17
|
Naskar S, Maiti PK. Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, Martini and oxDNA models. J Mater Chem B 2021; 9:5102-5113. [PMID: 34127998 DOI: 10.1039/d0tb02970j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The flexibility and stiffness of small DNA molecules play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) with lengths ranging from 12 base-pairs (bp) to 56 bp, paranemic crossover (PX) DNA and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grained models - Martini and oxDNA. To calculate the persistence length (Lp) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for the DNTs, we implement our previously developed theoretical framework. We compare and contrast all of the results with previously reported all-atom molecular dynamics (MD) simulations and experimental results. The mechanical properties of dsDNA (Lp ∼ 50 nm, γ ∼ 800-1500 pN), PX DNA (γ ∼ 1600-2000 pN) and DNTs (Lp ∼ 1-10 μm, γ ∼ 6000-8000 pN) estimated using the Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces values of Lp and γ which are an order of magnitude higher. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on the small dsDNA mechanics. But it is found to be ineffective for reproducing the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.
Collapse
Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| |
Collapse
|
18
|
Skoruppa E, Voorspoels A, Vreede J, Carlon E. Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models. Phys Rev E 2021; 103:042408. [PMID: 34005944 DOI: 10.1103/physreve.103.042408] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
We investigate the influence of nonlocal couplings on the torsional and bending elasticities of DNA. Such couplings have been observed in the past by several simulation studies. Here, we use a description of DNA conformations based on the variables tilt, roll, and twist. Our analysis of both coarse-grained (oxDNA) and all-atom models indicates that these share strikingly similar features: there are strong off-site couplings for tilt-tilt and twist-twist, while they are much weaker in the roll-roll case. By developing an analytical framework to estimate bending and torsional persistence lengths in nonlocal DNA models, we show how off-site interactions generate a length-scale-dependent elasticity. Based on the simulation-generated elasticity data, the theory predicts a significant length-scale-dependent effect on torsional fluctuations but only a modest effect on bending fluctuations. These results are in agreement with experiments probing DNA mechanics from single base pair to kilobase pair scales.
Collapse
Affiliation(s)
- Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jocelyne Vreede
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| |
Collapse
|
19
|
Aggarwal A, Sahoo AK, Bag S, Kaliginedi V, Jain M, Maiti PK. Fine-tuning the DNA conductance by intercalation of drug molecules. Phys Rev E 2021; 103:032411. [PMID: 33862831 DOI: 10.1103/physreve.103.032411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
In this work we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modeling approach where extensive ab initio calculations are performed on numerous MD-simulated configurations of dsDNA and dsDNA intercalated with two different intercalators, ethidium and daunomycin. DNA conductance is found to increase by one order of magnitude upon drug intercalation due to the local unwinding of the DNA base pairs adjacent to the intercalated sites, which leads to modifications of the density of states in the near-Fermi-energy region of the ligand-DNA complex. Our study suggests that the intercalators can be used to enhance or tune the DNA conductance, which opens new possibilities for their potential applications in nanoelectronics.
Collapse
Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Veerabhadrarao Kaliginedi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manish Jain
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
20
|
Marzec M. Uncovering the Mechanical Code of DNA Using 'Loop-seq'. Trends Genet 2021; 37:494-495. [PMID: 33622494 DOI: 10.1016/j.tig.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/18/2022]
Abstract
DNA mechanical properties play a critical role in different biological processes. Basu and coworkers described a method that measures DNA mechanics on the genome scale. Access to a high-throughput tool for measuring DNA mechanics opens up new possibilities to investigate this phenomenon with respect to establishing the chromatin regulatory landscape.
Collapse
Affiliation(s)
- Marek Marzec
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
| |
Collapse
|
21
|
Aggarwal A, Vinayak V, Bag S, Bhattacharyya C, Waghmare UV, Maiti PK. Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model. J Chem Inf Model 2020; 61:106-114. [PMID: 33320660 DOI: 10.1021/acs.jcim.0c01072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.
Collapse
Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Vinayak Vinayak
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chiranjib Bhattacharyya
- Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560064, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
22
|
Aggarwal A, Bag S, Venkatramani R, Jain M, Maiti PK. Multiscale modelling reveals higher charge transport efficiencies of DNA relative to RNA independent of mechanism. NANOSCALE 2020; 12:18750-18760. [PMID: 32970051 DOI: 10.1039/d0nr02382e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we compare the charge transport properties of multiple double-stranded (ds)RNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA : RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in the coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has a smaller end-to-end length relative to that of dsDNA.
Collapse
Affiliation(s)
- Abhishek Aggarwal
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | | | | | | | | |
Collapse
|
23
|
Bag S, Aggarwal A, Maiti PK. Machine Learning Prediction of Electronic Coupling between the Guanine Bases of DNA. J Phys Chem A 2020; 124:7658-7664. [DOI: 10.1021/acs.jpca.0c04368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saientan Bag
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|