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Peng Y, Li D, Qiao B, Gao Z, Pu Q, Pang H, Lai X, Zhang R, Zhao X, Zhao G, Xu D, Han F, Wang Y, Ji Y, Pei H, Wu Q. Protonation-mediated DNA tile self-assembly with nuclease resistance characteristic for signal-amplified detection of microRNAs. Biosens Bioelectron 2024; 246:115869. [PMID: 38039736 DOI: 10.1016/j.bios.2023.115869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
DNA nanotechnology, developing rapidly in recent years, has unprecedented superiorities in biological application-oriented research including high programmability, convenient functionalization, reconfigurable structure, and intrinsic biocompatibility. However, the susceptibility to nucleases in the physiological environment has been an obstacle to applying DNA nanostructures in biological science research. In this study, a new DNA self-assembly strategy, mediated by double-protonated small molecules instead of classical metal ions, is developed to enhance the nuclease resistance of DNA nanostructures while retaining their integrality and functionality, and the relative application has been launched in the detection of microRNAs (miRNAs). Faced with low-abundance miRNAs, we integrate hybrid chain reaction (HCR) with DNA self-assembly in the presence of double-protonated small molecules to construct a chemiluminescence detection platform with nuclease resistance, which utilizes the significant difference of molecular weight between DNA arrays and false-positive products to effectively separate of reaction products and remove the detection background. This strategy attaches importance to the nucleic acid stability during the assay process via improving nuclease resistance while rendering the detection results for miRNAs more authentic and reliable, opening our eyes to more possibilities for the multiple applications of customized DNA nanostructures in biology, including bioassay, bioimaging, drug delivery, and cell modulation.
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Affiliation(s)
- Yanan Peng
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Dongxia Li
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Bin Qiao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China
| | - Zhijun Gao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Qiumei Pu
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Huajie Pang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Xiangde Lai
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Rui Zhang
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Xuan Zhao
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Guangyuan Zhao
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Dan Xu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, PR China
| | - Feng Han
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China
| | - Yuanyuan Wang
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China
| | - Yuxiang Ji
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Hua Pei
- The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China
| | - Qiang Wu
- The First Affiliated Hospital, Hainan Medical University, Haikou, 570102, PR China; The Second Affiliated Hospital, School of Tropical Medicine, Hainan Medical University, Haikou, 570311, PR China; Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, PR China.
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2
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Templeton C, Hamilton I, Russell R, Elber R. Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations. J Phys Chem B 2023; 127:8796-8808. [PMID: 37815452 PMCID: PMC11341850 DOI: 10.1021/acs.jpcb.3c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na+). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg2+) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg2+ in the ion atmosphere surrounding the DNA. Mg2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na+ ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg2+ occupancy. The entropy changes have a negligible effect at low Mg2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.
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Affiliation(s)
- Clark Templeton
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
- Department of Physics, FU Berlin, 14195 Berlin, Germany
| | - Ian Hamilton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Science, Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
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3
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Singh A, Yadav RK, Shati A, Kamboj NK, Hasssan H, Bharadwaj S, Rana R, Yadava U. Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations. PLoS One 2023; 18:e0278755. [PMID: 36753480 PMCID: PMC9907842 DOI: 10.1371/journal.pone.0278755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 02/09/2023] Open
Abstract
Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.
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Affiliation(s)
- Akanksha Singh
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | | | - Ali Shati
- Department of Biology, Faculty of Science, King Khaild University, Abha, Saudi Arabia
| | - Nitin Kumar Kamboj
- School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India
| | - Hesham Hasssan
- Department of Pathology, College of Medicine, King Khaild University, Abha, Saudi Arabia
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (SB); (RR); (UY)
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
- * E-mail: (SB); (RR); (UY)
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
- * E-mail: (SB); (RR); (UY)
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4
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The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nat Commun 2022; 13:3112. [PMID: 35662248 PMCID: PMC9166708 DOI: 10.1038/s41467-022-30779-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/04/2022] [Indexed: 12/31/2022] Open
Abstract
The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context. Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.
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5
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Severov V, Tsvetkov V, Barinov N, Babenko V, Klinov D, Pozmogova G. Spontaneous DNA Synapsis by Forming Noncanonical Intermolecular Structures. Polymers (Basel) 2022; 14:polym14102118. [PMID: 35632001 PMCID: PMC9144187 DOI: 10.3390/polym14102118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/14/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
We report the spontaneous formation of DNA-DNA junctions in solution in the absence of proteins visualised using atomic force microscopy. The synapsis position fits with potential G-quadruplex (G4) sites. In contrast to the Holliday structure, these conjugates have an affinity for G4 antibodies. Molecular modelling was used to elucidate the possible G4/IM-synaptic complex structures. Our results indicate a new role of the intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.
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Affiliation(s)
- Viacheslav Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Correspondence: (V.S.); (V.T.)
| | - Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, 119991 Moscow, Russia
- A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky prospect Str. 29, 119991 Moscow, Russia
- Correspondence: (V.S.); (V.T.)
| | - Nikolay Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
- Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya str.6, 117198 Moscow, Russia
| | - Galina Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119435 Moscow, Russia; (N.B.); (V.B.); (D.K.); (G.P.)
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6
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging. We conducted a comprehensive study on the formation of various complexes from a pair of oligonucleotides with two transposed complementary blocks that can be linked through a nucleotide or non-nucleotide linker. A methodology is proposed to prove the formation of a self-limited complex and to determine its molecularity. It is based on the "opening" of a self-limited complex with an oligonucleotide that effectively binds to a duplex-forming block. The complexes assembled from a pair of oligonucleotides with different block length and different linker sizes and types were investigated by theoretical analysis, several experimental methods (a gel shift assay, atomic force microscopy, and ultraviolet melting analysis), and molecular dynamics simulations. The results showed a variety of complexes formed by only a pair of oligonucleotides. Self-limited associates, concatemer complexes, or mixtures thereof can arise if we change the length of a duplex and loop-forming blocks in oligonucleotides or via introduction of overhangs and chemical modifications. We postulated basic principles of rational design of native self-limited DNA complexes of desired structure, shape, and molecularity. Our foundation makes self-limited complexes useful tools for nanotechnology, biological studies, and therapeutics.
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Affiliation(s)
- Anastasia A Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
- Moscow Institute of Physics and Technology 9 Institutskiy per., Dolgoprudny 141701 Russia
| | - Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Valeria A Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
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7
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Adendorff MR, Tang GQ, Millar D, Bathe M, Bricker W. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Res 2022; 50:717-730. [PMID: 34935970 PMCID: PMC8789063 DOI: 10.1093/nar/gkab1246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
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Affiliation(s)
- Matthew R Adendorff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guo Qing Tang
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA
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8
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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9
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Zheng Y, Lin C, Zhang JS, Tan ZJ. Ion-mediated interactions between like-charged polyelectrolytes with bending flexibility. Sci Rep 2020; 10:21586. [PMID: 33299024 PMCID: PMC7726156 DOI: 10.1038/s41598-020-78684-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
Ion-mediated interactions between polyelectrolytes (PEs) are crucial to the properties of flexible biopolymers such as nucleic acids and proteins but the effect of PE flexibility on such interactions has not been explicitly addressed until now. In this work, the potentials of mean force (PMFs) between like-charged PEs with different bending flexibility have been investigated by Monte Carlo simulations and a cylindrical confinement around each PE was involved to model two PEs in an array. We found that in the absence of trivalent salt, the PMFs between like-charged PEs in an array are apparently repulsive while the bending flexibility can visibly decrease the repulsive PMFs. With the addition of high trivalent salt, the PMFs become significantly attractive whereas the attractive PMFs can be apparently weakened by the bending flexibility. Our analyses reveal that the effect of bending flexibility is attributed to the increased PE conformational space, which allows the PEs to fluctuate away to decrease the monovalent ion-mediated repulsion or to weaken the trivalent ion-mediated attraction through disrupting trivalent ion-bridging configuration. Additionally, our further calculations show that the effect of bending flexibility on the ion-mediated interactions is less apparent for PEs without cylindrical confinement.
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Affiliation(s)
- Yitong Zheng
- Hongyi Honor School, Wuhan University, Wuhan, 430072, China
- Department of Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Cheng Lin
- Department of Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Jin-Si Zhang
- College of Electrical and Photoelectronic Engineering, West Anhui University, Lu'an, 237012, China
| | - Zhi-Jie Tan
- Department of 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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10
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Chen Y, Wang P, Xu Y, Li X, Zhu Y, Zhang Y, Zhu J, Huang G, He D. Different Stability of DNA Origami Nanostructure between on Interface and in Bulk Solution. ACS APPLIED BIO MATERIALS 2018; 1:1424-1429. [DOI: 10.1021/acsabm.8b00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yi Chen
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Wang
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Yan Xu
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Xiaodi Li
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Yuanjie Zhu
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Ying Zhang
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Jun Zhu
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Gang Huang
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Dannong He
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
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11
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Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States. Sci Rep 2018; 8:6163. [PMID: 29670174 PMCID: PMC5906655 DOI: 10.1038/s41598-018-24499-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 01/03/2023] Open
Abstract
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.
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12
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Zhang ZL, Wu YY, Xi K, Sang JP, Tan ZJ. Divalent Ion-Mediated DNA-DNA Interactions: A Comparative Study of Triplex and Duplex. Biophys J 2017; 113:517-528. [PMID: 28793207 DOI: 10.1016/j.bpj.2017.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg2+ can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg2+ solutions. Our calculations show that the PMF between tsDNAs is apparently attractive and becomes more strongly attractive at higher [Mg2+], although the PMF between dsDNAs cannot become apparently attractive even at high [Mg2+]. Our analyses show that Mg2+ internally binds into grooves and externally binds to phosphate groups for both tsDNA and dsDNA, whereas the external binding of Mg2+ is much stronger for tsDNA. Such stronger external binding of Mg2+ for tsDNA favors more apparent ion-bridging between helices than for dsDNA. Furthermore, our analyses illustrate that bridging ions, as a special part of external binding ions, are tightly and positively coupled to ion-mediated attraction between DNAs.
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Affiliation(s)
- Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Kun Xi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Jian-Ping Sang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- and Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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13
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Martínez-Santiago CJ, Quiñones E. Torque measurements during the spontaneous unbraiding of DNA molecules in the absence of pulling forces. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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14
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Cortini R, Cheng X, Smith JC. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:084002. [PMID: 28092632 DOI: 10.1088/1361-648x/aa4e68] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of [Formula: see text]. Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.
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Affiliation(s)
- Ruggero Cortini
- Chemistry Department, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Sorbonne Université, 4 place Jussieu, 75252 Cedex 05, Paris, France. Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain
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15
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:145-155. [PMID: 28035245 PMCID: PMC5153831 DOI: 10.1007/s12551-016-0241-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 01/09/2023] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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16
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Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
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Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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17
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:233-243. [PMID: 27738452 PMCID: PMC5039213 DOI: 10.1007/s12551-016-0208-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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18
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Mazur AK. Homologous Pairing between Long DNA Double Helices. PHYSICAL REVIEW LETTERS 2016; 116:158101. [PMID: 27127987 DOI: 10.1103/physrevlett.116.158101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments, I show here that direct recognition between homologous dsDNA is possible through the formation of short quadruplexes due to direct complementary hydrogen bonding of major-groove surfaces in parallel alignment. The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism and concomitant predictions agree with the available experimental data and shed light upon the sequence effects and the possible involvement of topoisomerase II in the recognition.
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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
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19
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Wu C, McGeehan JE, Travers A. A metastable structure for the compact 30-nm chromatin fibre. FEBS Lett 2016; 590:935-42. [PMID: 26969895 PMCID: PMC4863496 DOI: 10.1002/1873-3468.12128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/29/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022]
Abstract
The structure of compact 30‐nm chromatin fibres is still debated. We present here a novel unified model that reconciles all experimental observations into a single framework. We propose that compact fibres are formed by the interdigitation of the two nucleosome stacks in a 2‐start crossed‐linker structure to form a single stack. This process requires that the dyad orientation of successive nucleosomes relative to the helical axis alternates. The model predicts that, as observed experimentally, the fibre‐packing density should increase in a stepwise manner with increasing linker length. This model structure can also incorporate linker DNA of varying lengths.
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Affiliation(s)
- Chenyi Wu
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, UK
| | - John E McGeehan
- Molecular Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, UK
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Biochemistry, University of Cambridge, UK
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20
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Estácio SG, Martiniano HFMC, Faísca PFN. Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR. MOLECULAR BIOSYSTEMS 2016; 12:2834-48. [DOI: 10.1039/c6mb00193a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The deletion of phenylalanine 508 reshapes the conformational space of the NBD1 domain that populates unique intermediate states that provide insights into the molecular events that underlie the impaired folding of F508del-NBD1.
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Affiliation(s)
- Sílvia G. Estácio
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Hugo F. M. C. Martiniano
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Patrícia F. N. Faísca
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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21
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Wu YY, Zhang ZL, Zhang JS, Zhu XL, Tan ZJ. Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA. Nucleic Acids Res 2015; 43:6156-65. [PMID: 26019178 PMCID: PMC4499160 DOI: 10.1093/nar/gkv570] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/20/2015] [Indexed: 01/30/2023] Open
Abstract
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.
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Affiliation(s)
- Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhong-Liang Zhang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Jin-Si Zhang
- Department of Physics and Key Laboratory of Artificial Micro & 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 & Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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22
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Lee DJO. Collapse and coexistence for a molecular braid with an attractive interaction component subject to mechanical forces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:145101. [PMID: 25788398 DOI: 10.1088/0953-8984/27/14/145101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Dual mechanical braiding experiments provide a useful tool with which to investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an appearance of a local minimum in the interaction potential between the two molecules. We investigate this situation, introducing an attractive component into the interaction potential, using a model developed for describing such experiments. We consider both attractive interactions that do not depend on molecular structure and those which depend on a DNA-like helix structure. In braiding experiments, an attractive term may lead to certain effects. A local minimum may cause molecules to collapse from a loosely braided configuration into a tight one, occurring at a critical value of the moment applied about the axis of the braid. For a fixed number of braid pitches, this may lead to coexistence between the two braiding states, tight and loose. Coexistence implies certain proportions of the braid are in each state, their relative size depending on the number of braid pitches. This manifests itself as a linear dependence in numerically calculated quantities as functions of the number of braid pitches. Also, in the collapsed state, the braid radius stays roughly constant. Furthermore, if the attractive interaction is helix dependent, the left-right handed braid symmetry is broken. For a DNA like charge distribution, using the Kornyshev-Leikin interaction model, our results suggest that significant braid collapse and coexistence only occurs for left handed braids. Regardless of the interaction model, the study highlights the possible qualitative physics of braid collapse and coexistence; and the role helix specific forces might play, if important. The model could be used to connect other microscopic theories of interaction with braiding experiments.
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Affiliation(s)
- Dominic J O' Lee
- Department of Chemistry, Imperial College London, SW7 2AZ, London, UK
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23
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Zhang TB, Zhang CL, Dong ZL, Guan YF. Determination of base binding strength and base stacking interaction of DNA duplex using atomic force microscope. Sci Rep 2015; 5:9143. [PMID: 25772017 PMCID: PMC4360479 DOI: 10.1038/srep09143] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/19/2015] [Indexed: 01/23/2023] Open
Abstract
As one of the most crucial properties of DNA, the structural stability and the mechanical strength are attracting a great attention. Here, we take advantage of high force resolution and high special resolution of Atom Force Microscope and investigate the mechanical force of DNA duplexes. To evaluate the base pair hydrogen bond strength and base stacking force in DNA strands, we designed two modes (unzipping and stretching) for the measurement rupture forces. Employing k-means clustering algorithm, the ruptured force are clustered and the mean values are estimated. We assessed the influence of experimental parameters and performed the force evaluation for DNA duplexes of pure dG/dC and dA/dT base pairs. The base binding strength of single dG/dC and single dA/dT were estimated to be 20.0 ± 0.2 pN and 14.0 ± 0.3 pN, respectively, and the base stacking interaction was estimated to be 2.0 ± 0.1 pN. Our results provide valuable information about the quantitative evaluation of the mechanical properties of the DNA duplexes.
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Affiliation(s)
- Tian-biao Zhang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China. 110001
| | - Chang-lin Zhang
- State Key Laboratory of Robotics, Shenyang Institute of Automatics, Chinese Academy of Sciences, Shenyang, China. 110016
| | - Zai-li Dong
- State Key Laboratory of Robotics, Shenyang Institute of Automatics, Chinese Academy of Sciences, Shenyang, China. 110016
| | - Yi-fu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China. 110001
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24
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Yanao T, Sano S, Yoshikawa K. Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Abstract
Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg(2+) ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg(2+) or Na(+), benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg(2+) bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.
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Affiliation(s)
- Weifeng Li
- Institute of Quantitative Biology and Medicine, School for Radiological & Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China 215123
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26
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Wang K, Hamill JM, Wang B, Guo C, Jiang S, Huang Z, Xu B. Structure determined charge transport in single DNA molecule break junctions. Chem Sci 2014. [DOI: 10.1039/c4sc00888j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single DNA conductance measurements with increasing MgCl2concentrations unambiguously revealed two DNA (B and Z) conformations and the B–Z transition process.
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Affiliation(s)
- Kun Wang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Joseph M. Hamill
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Bin Wang
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Cunlan Guo
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
| | - Sibo Jiang
- Department of Chemistry
- Georgia State University
- Atlanta, USA
| | - Zhen Huang
- Department of Chemistry
- Georgia State University
- Atlanta, USA
| | - Bingqian Xu
- Single Molecule Study Laboratory
- College of Engineering and Nanoscale Science and Engineering Center
- University of Georgia
- Athens, USA
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27
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Lee D. Effect of undulations on spontaneous braid formation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:022719. [PMID: 24032876 DOI: 10.1103/physreve.88.022719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 06/02/2023]
Abstract
This paper is an extension of a recent study where it was shown that forces dependent on molecular helical structure may cause two DNA molecules to spontaneously braid [R. Cortini et al., Biophys. J. 101, 875 (2011)]. Here, bending fluctuations of molecular center lines about the braid axis are incorporated into the braiding theory, which may be generalized to other helix-dependent interactions and other helical molecules. The free energy of the pair of molecules is recalculated and compared to its value without incorporating undulations. We find that the loss of configurational entropy due to confinement of the molecules in the braid is quite high. This contribution to the free energy increases the amount of attraction needed for spontaneous braiding due to helix-dependent forces. The theory will be further developed for plectonemes and braids under mechanical forces in later work.
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Affiliation(s)
- Dominic Lee
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
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28
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Chatake T, Sunami T. Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2. J Inorg Biochem 2013; 124:15-25. [DOI: 10.1016/j.jinorgbio.2013.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/25/2022]
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29
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DNA self-assembly: from chirality to evolution. Int J Mol Sci 2013; 14:8252-70. [PMID: 23591841 PMCID: PMC3645741 DOI: 10.3390/ijms14048252] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/03/2013] [Accepted: 03/21/2013] [Indexed: 01/12/2023] Open
Abstract
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are tightly packed into stable right-handed crossovers. Simple packing rules that are imposed by DNA geometry and sequence dictate the overall architecture of higher order DNA structures. Close DNA-DNA interactions also provide the missing link between local interactions and DNA topology, thus explaining how type II DNA topoisomerases may sense locally the global topology. Finally this paper proposes that through its influence on DNA self-assembled structures, DNA chirality played a critical role during the early steps of evolution.
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30
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Tan ZJ, Chen SJ. Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J 2013; 103:827-36. [PMID: 22947944 DOI: 10.1016/j.bpj.2012.06.048] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 06/25/2012] [Accepted: 06/27/2012] [Indexed: 12/28/2022] Open
Abstract
RNAs are negatively charged molecules that reside in cellular environments with macromolecular crowding. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for ion fluctuation and correlation, we investigate the effect of confinement on ion-mediated RNA structural collapse for a simple model system. We find that for both Na(+) and Mg(2+), the ion efficiencies in mediating structural collapse/folding are significantly enhanced by the structural confinement. This enhancement of ion efficiency is attributed to the decreased electrostatic free-energy difference between the compact conformation ensemble and the (restricted) extended conformation ensemble due to the spatial restriction.
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Affiliation(s)
- Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, People's Republic of China.
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Timsit Y. DNA-directed base pair opening. Molecules 2012; 17:11947-64. [PMID: 23060287 PMCID: PMC6268293 DOI: 10.3390/molecules171011947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/28/2012] [Accepted: 10/09/2012] [Indexed: 11/16/2022] Open
Abstract
Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination. However, DNA melting in physiological conditions in which the double helix is expected to be stable represents a challenging problem. Current models propose that negative supercoiling destabilizes the double helix and promotes the spontaneous, sequence-dependent DNA melting. The present review examines an alternative view and reveals how DNA compaction may trigger the sequence dependent opening of the base pairs. This analysis shows that in DNA crystals, tight DNA-DNA interactions destabilize the double helices at various degrees, from the alteration of the base-stacking to the opening of the base-pairs. The electrostatic repulsion generated by the DNA close approach of the negatively charged sugar phosphate backbones may therefore provide a potential source of the energy required for DNA melting. These observations suggest a new molecular mechanism for the initial steps of strand separation in which the coupling of the DNA tertiary and secondary interactions both actively triggers the base pair opening and stabilizes the intermediate states during the melting pathway.
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Affiliation(s)
- Youri Timsit
- CNRS, Aix-Marseille Université, IGS UMR7256, FR-13288 Marseille, France.
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Guéroult M, Boittin O, Mauffret O, Etchebest C, Hartmann B. Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One 2012; 7:e41704. [PMID: 22844516 PMCID: PMC3402463 DOI: 10.1371/journal.pone.0041704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022] Open
Abstract
This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.
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Affiliation(s)
- Marc Guéroult
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | - Olivier Boittin
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Oliver Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
| | - Catherine Etchebest
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Brigitte Hartmann
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
- * E-mail:
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Cortini R, Kornyshev AA, Lee DJ, Leikin S. Electrostatic braiding and homologous pairing of DNA double helices. Biophys J 2011; 101:875-84. [PMID: 21843478 DOI: 10.1016/j.bpj.2011.06.058] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 06/16/2011] [Accepted: 06/30/2011] [Indexed: 10/17/2022] Open
Abstract
Homologous pairing and braiding (supercoiling) have crucial effects on genome organization, maintenance, and evolution. Generally, the pairing and braiding processes are discussed in different contexts, independently of each other. However, analysis of electrostatic interactions between DNA double helices suggests that in some situations these processes may be related. Here we present a theory of DNA braiding that accounts for the elastic energy of DNA double helices as well as for the chiral nature of the discrete helical patterns of DNA charges. This theory shows that DNA braiding may be affected, stabilized, or even driven by chiral electrostatic interactions. For example, electrostatically driven braiding may explain the surprising recent observation of stable pairing of homologous double-stranded DNA in solutions containing only monovalent salt. Electrostatic stabilization of left-handed braids may stand behind the chiral selectivity of type II topoisomerases and positive plasmid supercoiling in hyperthermophilic bacteria and archea.
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Affiliation(s)
- Ruggero Cortini
- Department of Chemistry, Imperial College London, London, UK.
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Li W, Nordenskiöld L, Mu Y. Sequence-Specific Mg2+–DNA Interactions: A Molecular Dynamics Simulation Study. J Phys Chem B 2011; 115:14713-20. [DOI: 10.1021/jp2052568] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weifeng Li
- School of Physical and Mathematical Sciences, 21 Nanyang Link, and ‡School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore
| | - Lars Nordenskiöld
- School of Physical and Mathematical Sciences, 21 Nanyang Link, and ‡School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore
| | - Yuguang Mu
- School of Physical and Mathematical Sciences, 21 Nanyang Link, and ‡School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore
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35
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Timsit Y. Local sensing of global DNA topology: from crossover geometry to type II topoisomerase processivity. Nucleic Acids Res 2011; 39:8665-76. [PMID: 21764774 PMCID: PMC3203592 DOI: 10.1093/nar/gkr556] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes that control the topology and higher order structures of DNA. Type IIA enzymes have the remarkable property to sense locally the global DNA topology. Although many theoretical models have been proposed, the molecular mechanism of chiral discrimination is still unclear. While experimental studies have established that topoisomerases IIA discriminate topology on the basis of crossover geometry, a recent single-molecule experiment has shown that the enzyme has a different processivity on supercoiled DNA of opposite sign. Understanding how cross-over geometry influences enzyme processivity is, therefore, the key to elucidate the mechanism of chiral discrimination. Analysing this question from the DNA side reveals first, that the different stability of chiral DNA cross-overs provides a way to locally sense the global DNA topology. Second, it shows that these enzymes have evolved to recognize the G- and T-segments stably assembled into a right-handed cross-over. Third, it demonstrates how binding right-handed cross-overs across their large angle imposes a different topological link between the topoIIA rings and the plectonemes of opposite sign thus directly affecting the enzyme freedom of motion and processivity. In bridging geometry and kinetic data, this study brings a simple solution for type IIA topoisomerase chiral discrimination.
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Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS - UPR2589, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, Parc Scientifique de Luminy, Marseille, France
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Abstract
DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.
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Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS-UPR2589, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Marseille, 13288, France.
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Mitchell JS, Laughton CA, Harris SA. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 2011; 39:3928-38. [PMID: 21247872 PMCID: PMC3089460 DOI: 10.1093/nar/gkq1312] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA.
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Affiliation(s)
- J S Mitchell
- Polymer IRC, School of Physics and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds, LS2 9JT, UK
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38
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Timsit Y, Várnai P. Helical chirality: a link between local interactions and global topology in DNA. PLoS One 2010; 5:e9326. [PMID: 20174470 PMCID: PMC2824830 DOI: 10.1371/journal.pone.0009326] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 01/29/2010] [Indexed: 01/03/2023] Open
Abstract
DNA supercoiling plays a major role in many cellular functions. The global DNA conformation is however intimately linked to local DNA-DNA interactions influencing both the physical properties and the biological functions of the supercoiled molecule. Juxtaposition of DNA double helices in ubiquitous crossover arrangements participates in multiple functions such as recombination, gene regulation and DNA packaging. However, little is currently known about how the structure and stability of direct DNA-DNA interactions influence the topological state of DNA. Here, a crystallographic analysis shows that due to the intrinsic helical chirality of DNA, crossovers of opposite handedness exhibit markedly different geometries. While right-handed crossovers are self-fitted by sequence-specific groove-backbone interaction and bridging Mg(2+) sites, left-handed crossovers are juxtaposed by groove-groove interaction. Our previous calculations have shown that the different geometries result in differential stabilisation in solution, in the presence of divalent cations. The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions. While the unstable left-handed crossovers are exclusively formed in negatively supercoiled DNA, stable right-handed crossovers constitute the local signature of an unusual topological state in the cell, such as the positively supercoiled or relaxed DNA. These findings not only provide a simple mechanism for locally sensing the DNA topology but also lead to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Sticky inter-segmental interactions in positively supercoiled or relaxed DNA are expected to greatly slow down the slithering dynamics of DNA. We therefore suggest that the intrinsic helical chirality of DNA may have oriented the early evolutionary choices for DNA topology.
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Affiliation(s)
- Youri Timsit
- Information Génomique et Structurale, CNRS-UPR2589, Institut de Microbiologie de la Méditerranée, Parc Scientifique de Luminy, Marseille, France.
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