1
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Sangeeta, Mishra SK, Bhattacherjee A. Role of Shape Deformation of DNA-Binding Sites in Regulating the Efficiency and Specificity in Their Recognition by DNA-Binding Proteins. JACS AU 2024; 4:2640-2655. [PMID: 39055163 PMCID: PMC11267559 DOI: 10.1021/jacsau.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]
Abstract
Accurate transcription of genetic information is crucial, involving precise recognition of the binding motifs by DNA-binding proteins. While some proteins rely on short-range hydrophobic and hydrogen bonding interactions at binding sites, others employ a DNA shape readout mechanism for specific recognition. In this mechanism, variations in DNA shape at the binding motif resulted from either inherent flexibility or binding of proteins at adjacent sites are sensed and capitalized by the searching proteins to locate them specifically. Through extensive computer simulations, we investigate both scenarios to uncover the underlying mechanism and origin of specificity in the DNA shape readout mechanism. Our findings reveal that deformation in shape at the binding motif creates an entropy funnel, allowing information about altered shapes to manifest as fluctuations in minor groove widths. This signal enhances the efficiency of nonspecific search of nearby proteins by directing their movement toward the binding site, primarily driven by a gain in entropy. We propose this as a generic mechanism for DNA shape readout, where specificity arises from the alignment between the molecular frustration of the searching protein and the ruggedness of the entropic funnel governed by molecular features of the protein and arrangement of the DNA bases at the binding site, respectively.
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Affiliation(s)
- Sangeeta
- School of Computational & Integrative
Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sujeet Kumar Mishra
- School of Computational & Integrative
Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational & Integrative
Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Farré-Gil D, Arcon JP, Laughton CA, Orozco M. CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes. Nucleic Acids Res 2024; 52:6791-6801. [PMID: 38813824 PMCID: PMC11229373 DOI: 10.1093/nar/gkae444] [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] [Received: 06/20/2023] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA. The efficiency of the method allows us to recover with a reduced computational effort high-quality atomic-resolution ensembles of segments containing many kilobases of DNA, entering into the gene range or even the entire DNA of certain cellular organelles.
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Affiliation(s)
- David Farré-Gil
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
| | - Charles A Laughton
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, E-08028 Barcelona, Spain
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3
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Segers M, Voorspoels A, Sakaue T, Carlon E. Mechanisms of DNA-Mediated Allostery. PHYSICAL REVIEW LETTERS 2023; 131:238402. [PMID: 38134780 DOI: 10.1103/physrevlett.131.238402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023]
Abstract
Proteins often regulate their activities via allostery-or action at a distance-in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins, allosteric effects have been observed in experiments with DNA as well. In these experiments two or more proteins bind at distinct DNA sites and interact indirectly with each other, via a mechanism mediated by the linker DNA molecule. We develop a mechanical model of DNA/protein interactions which predicts three distinct mechanisms of allostery. Two of these involve an enthalpy-mediated allostery, while a third mechanism is entropy driven. We analyze experiments of DNA allostery and highlight the distinctive signatures allowing one to identify which of the proposed mechanisms best fits the data.
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Affiliation(s)
- Midas Segers
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Enrico Carlon
- Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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4
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Hörberg J, Reymer A. Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape. Sci Rep 2023; 13:16125. [PMID: 37752333 PMCID: PMC10522765 DOI: 10.1038/s41598-023-43244-1] [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: 03/03/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Transcription factors (TFs) regulate eukaryotic transcription through selective DNA-binding, can also specifically interact with RNA, which may present another layer of transcriptional control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the details of TFs-RNA complexation are less understood. Here we investigate the dual recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar affinities with consensus DNA and diverse RNA hairpin motifs but discriminates against uniform dsRNA. Using atomic molecular dynamics simulations, we demonstrate that the GR binding to nucleic acids requires a wide and shallow groove pocket. The protein effectively moulds its binding site within DNA major groove, which enables base-specific interactions. Contrary, the GR binding has little effect on the grooves geometry of RNA systems, most notably in uniform dsRNA. Instead, a hairpin motif in RNA yields a wide and shallow major groove pocket, allowing the protein to anchor itself through nonspecific electrostatic contacts with RNA backbone. Addition of a bulge increases RNA hairpin flexibility, which leads to a greater number of GR-RNA contacts and, thus, higher affinity. Thus, the combination of structural motifs defines the GR-RNA selective binding: a recognition mechanism, which may be shared by other zinc finger TFs.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden
| | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30, Göteborg, Sweden.
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5
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Leben K, Strmšek Ž, Lebar T, Verbič A, Dragovan M, Omersa N, Anderluh G, Jerala R. Binding of the transcription activator-like effector augments transcriptional regulation by another transcription factor. Nucleic Acids Res 2022; 50:6562-6574. [PMID: 35670660 PMCID: PMC9226504 DOI: 10.1093/nar/gkac454] [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: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
DNA transcription is regulated by a range of diverse mechanisms and primarily by transcription factors that recruit the RNA polymerase complex to the promoter region on the DNA. Protein binding to DNA at nearby or distant sites can synergistically affect this process in a variety of ways, but mainly through direct interactions between DNA-binding proteins. Here we show that a Transcription Activator-Like Effector (TALE), which lacks an activation domain, can enhance transcription in mammalian cells when it binds in the vicinity of and without direct interaction with several different dimeric or monomeric transcription factors. This effect was observed for several TALEs regardless of the recognition sequences and their DNA-bound orientation. TALEs can exert an effect over the distance of tens of nucleotides and it also potentiated KRAB-mediated repression. The augmentation of transcriptional regulation of another transcription factor is characteristic of TALEs, as it was not observed for dCas9/gRNA, zinc finger, or Gal4 DNA-binding domains. We propose that this mechanism involves an allosteric effect exerted on DNA structure or dynamics. This mechanism could be used to modulate transcription but may also play a role in the natural context of TALEs.
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Affiliation(s)
- Katja Leben
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tina Lebar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Matej Dragovan
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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6
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Nechipurenko YD, Buchelnikov AS. Ligand Binding to Nucleic Acids in Solution and on Microchips. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922030162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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7
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Hacisuleyman A, Erman B. Information Flow and Allosteric Communication in Proteins. J Chem Phys 2022; 156:185101. [DOI: 10.1063/5.0088522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Based on Schreiber's work on transfer entropy, a molecular theory of nonlinear information transfer in proteins is developed. The joint distribution function for residue fluctuations is expressed in terms of tensor Hermite polynomials which conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. Amount and speed of information transfer between residues, important for understanding allosteric activity in proteins, are discussed. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in Human NAD-dependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Estimated transfer rates are in the order of 1-20 megabits per second. Information transfer from third order contributions are one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer.
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Affiliation(s)
- Aysima Hacisuleyman
- Chemical and Biological Engineering, Koc University College of Engineering, Turkey
| | - Burak Erman
- College of Engineering, Koc University, Turkey
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8
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- 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
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9
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Dale J, Howe CP, Toncrova H, Fritzsch R, Greetham GM, Clark IP, Towrie M, Parker AW, McLeish TC, Hunt NT. Combining steady state and temperature jump IR spectroscopy to investigate the allosteric effects of ligand binding to dsDNA. Phys Chem Chem Phys 2021; 23:15352-15363. [PMID: 34254612 DOI: 10.1039/d1cp02233d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.
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Affiliation(s)
- Jessica Dale
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
| | - C Peter Howe
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
| | - Hedvika Toncrova
- Department of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Robby Fritzsch
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK
| | - Thomas C McLeish
- Department of Physics, University of York, Heslington, York YO10 5DD, UK.
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK.
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10
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González-Jiménez M, Ramakrishnan G, Tukachev NV, Senn HM, Wynne K. Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids. Phys Chem Chem Phys 2021; 23:13250-13260. [PMID: 34095914 PMCID: PMC8207511 DOI: 10.1039/d0cp05404f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile. Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition.![]()
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11
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Mondal M, Yang L, Cai Z, Patra P, Gao YQ. A perspective on the molecular simulation of DNA from structural and functional aspects. Chem Sci 2021; 12:5390-5409. [PMID: 34168783 PMCID: PMC8179617 DOI: 10.1039/d0sc05329e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Accordingly, molecular simulations can provide atomistic details of interactions and conformational dynamics involved in different biological processes of DNA, including those inaccessible by current experimental methods. In this perspective, which is mainly based on our recent studies, we provide a brief overview of the atomistic simulations on how the hierarchical structure and dynamics of DNA can be influenced by its sequences, base modifications, environmental factors and protein binding in the context of the protein-DNA interactions, gene regulation and structural organization of chromatin. We try to connect the DNA sequence, the hierarchical structures of DNA and gene regulation.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China
| | - Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China .,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University 100871 Beijing China.,Biomedical Pioneering Innovation Center, Peking University 100871 Beijing China.,Beijing Advanced Innovation Center for Genomics, Peking University 100871 Beijing China
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12
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Clauvelin N, Olson WK. Synergy between Protein Positioning and DNA Elasticity: Energy Minimization of Protein-Decorated DNA Minicircles. J Phys Chem B 2021; 125:2277-2287. [DOI: 10.1021/acs.jpcb.0c11612] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolas Clauvelin
- Center for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Wilma K. Olson
- Center for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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13
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020; 11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals. The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.![]()
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China +886 3 5712121 ext. 56996
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15
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Walther J, Dans PD, Balaceanu A, Hospital A, Bayarri G, Orozco M. A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level. Nucleic Acids Res 2020; 48:e29. [PMID: 31956910 PMCID: PMC7049737 DOI: 10.1093/nar/gkaa015] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/10/2019] [Accepted: 01/04/2020] [Indexed: 12/13/2022] Open
Abstract
We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbsc1 atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.
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Affiliation(s)
- Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Biological Sciences, CENUR North Coast, University of the Republic, 50000 Salto, Uruguay
| | - Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, The University of Barcelona, 08028 Barcelona, Spain
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16
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Velasco-Berrelleza V, Burman M, Shepherd JW, Leake MC, Golestanian R, Noy A. SerraNA: a program to determine nucleic acids elasticity from simulation data. Phys Chem Chem Phys 2020; 22:19254-19266. [DOI: 10.1039/d0cp02713h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly.
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Affiliation(s)
| | | | | | - Mark C. Leake
- Department of Physics
- University of York
- York
- UK
- Department of Biology
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS)
- Göttingen
- Germany
- Rudolf Peierls Center for Theoretical Physics
- University of Oxford
| | - Agnes Noy
- Department of Physics
- University of York
- York
- UK
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17
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Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M. Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond. Nucleic Acids Res 2019; 47:4418-4430. [PMID: 30957854 PMCID: PMC6511876 DOI: 10.1093/nar/gkz255] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022] Open
Abstract
We used extensive molecular dynamics simulations to study the structural and dynamic properties of the central d(TpA) step in the highly polymorphic d(CpTpApG) tetranucleotide. Contrary to the assumption of the dinucleotide-model and its nearest neighbours (tetranucleotide-model), the properties of the central d(TpA) step change quite significantly dependent on the next-to-nearest (hexanucleotide) sequence context and in a few cases are modulated by even remote neighbours (beyond next-to-nearest from the central TpA). Our results highlight the existence of previously undescribed dynamical mechanisms for the transmission of structural information into the DNA and demonstrate the existence of certain sequences with special physical properties that can impact on the global DNA structure and dynamics.
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Affiliation(s)
- Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Diana Buitrago
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
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Constructing Controllable Logic Circuits Based on DNAzyme Activity. Molecules 2019; 24:molecules24224134. [PMID: 31731630 PMCID: PMC6891523 DOI: 10.3390/molecules24224134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022] Open
Abstract
Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.
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Zheng X, Yang J, Zhou C, Zhang C, Zhang Q, Wei X. Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis. Nucleic Acids Res 2019; 47:1097-1109. [PMID: 30541100 PMCID: PMC6379719 DOI: 10.1093/nar/gky1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/29/2022] Open
Abstract
Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers. However, those regulations required to change the sequences of whole DNAzyme, as separating parts and inserting extra DNA sequence. Inspired by the allosteric regulation of proteins in nature, a new allosteric strategy is proposed to regulate the activity of DNAzyme without DNA sequences changes. In this strategy, DNA strand displacement was used to regulate the DNAzyme structure, through which the activity of DNAzyme was well controlled. The strategy was applied to E6-type DNAzymes, and the operations of DNA logic circuit (YES, OR, AND, cascading and feedback) were established and simulated with the dynamic analyses. The allosteric regulation has potential to construct more complicated molecular systems, which can be applied to bio-sensing and detection.
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Affiliation(s)
- Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Changjun Zhou
- College of Mathematics and Computer sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing 100871, China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
- School of Computer Scicence and Technology, Dalian University of Technology, Dalian 116024, China
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