1
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Gao F, Yang X, Song W. Bioinspired Supramolecular Hydrogel from Design to Applications. SMALL METHODS 2024; 8:e2300753. [PMID: 37599261 DOI: 10.1002/smtd.202300753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Indexed: 08/22/2023]
Abstract
Nature offers a wealth of opportunities to solve scientific and technological issues based on its unique structures and function. The dynamic non-covalent interaction is considered to be the main base of living functions of creatures including humans, animals, and plants. Supramolecular hydrogels formed by non-covalent bonding interactions has become a unique platform for constructing promising materials for medicine, energy, electronic, and biological substitute. In this review, the self-assemble principle of supramolecular hydrogels is summarized. Next, the stimulation of external environment that triggers the assembly or disassembly of supramolecular hydrogels are recapitulated, including temperature, mechanics, light, pH, ions, etc. The main applications of bioinspired supramolecular hydrogels in terms of bionic objects including humans, animals, and plants are also described. Although so many efforts are done for revealing the synergized mechanism of the function and non-covalent interactions on the supramolecular hydrogel, the complexity and variability between stimulus and non-covalent bonding in the supramolecular system still require impeccable theories. As an outlook, the bioinspired supramolecular hydrogel is just beginning to exhibit its great potential in human life, offering significant opportunities in drug delivery and screening, implantable devices and substitutions, tissue engineering, micro-fluidic devices, and biosensors.
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Affiliation(s)
- Feng Gao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Xuhao Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Wenlong Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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2
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Mak CH. Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair. ACS PHYSICAL CHEMISTRY AU 2024; 4:180-190. [PMID: 38560756 PMCID: PMC10979491 DOI: 10.1021/acsphyschemau.3c00058] [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: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 04/04/2024]
Abstract
Base pairing complementarity is central to DNA function. G·C and A·T pair specificity is thought to originate from the different number of hydrogen bonds the pairs make. Quantifying how many hydrogen bonds exist can be difficult because water molecules in the surrounding can make up for or disrupt direct hydrogen bonds, and the hydration structures around A·T and G·C pairs on duplex DNA are distinct. Large-scale computer simulations have been used here to create a detailed map for the hydration structure on A·T and G·C base pairs in water. The contributions of specific hydration waters to the free energy of each of the hydrogen bonds in the A·T and G·C pairs were computed. Using the equilibrium fractions of hydrated versus unhydrated states from the hydration profiles, the impact of specific bound waters on each hydrogen bond can be uniquely quantified using a thermodynamic construction. The findings suggest that hydration water in the minor groove of an A·T pair can provide up to about 2 kcal/mol of free energy advantage, effectively making up for the missing third hydrogen bond in the A·T pair compared to G·C, rendering the intrinsic thermodynamic stability of the A·T pair almost synonymous with G·C.
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Affiliation(s)
- Chi H. Mak
- Departments of Chemistry
and Quantitative and Computational Biology, and Center of Applied
Mathematical Sciences, University of Southern
California, Los Angeles, California 90089, United States
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3
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Maurer J, Albrecht CS, Herbert P, Heussman D, Chang A, von Hippel PH, Marcus AH. Studies of DNA 'Breathing' by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3) 2 Dimer-Labeled DNA Fork Constructs. J Phys Chem B 2023; 127:10730-10748. [PMID: 38060691 PMCID: PMC10754251 DOI: 10.1021/acs.jpcb.3c06463] [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: 12/22/2023]
Abstract
Local fluctuations of the sugar-phosphate backbones and bases of DNA (often called DNA 'breathing') play a variety of critical roles in controlling the functional interactions of the DNA genome with the protein complexes that regulate it. Here, we present a single-molecule fluorescence method that we have used to measure and characterize such conformational fluctuations at and near biologically important positions in model DNA replication fork constructs labeled with exciton-coupled cyanine [(iCy3)2] dimer probes. Previous work has shown that the constructs that we tested here exhibit a broad range of spectral properties at the ensemble level, and these differences can be structurally and dynamically interpreted using our present methodology at the single-molecule level. The (iCy3)2 dimer has one symmetric (+) and one antisymmetric (-) exciton, with the respective transition dipole moments oriented perpendicular to one another. We excite single-molecule samples using a continuous-wave linearly polarized laser, with the polarization direction continuously rotated at the frequency of 1 MHz. The ensuing fluorescence signal is modulated as the laser polarization alternately excites the symmetric and antisymmetric excitons of the (iCy3)2 dimer probe. Phase-sensitive detection of the modulated signal provides information about the distribution of local conformations and the conformational interconversion dynamics of the (iCy3)2 probe. We find that at most construct positions that we examined, the (iCy3)2 dimer-labeled DNA fork constructs can adopt four topologically distinct conformational macrostates. These results suggest that in addition to observing DNA breathing at and near ss-dsDNA junctions, our new methodology should be useful to determine which of these pre-existing macrostates are recognized by, bind to, and are stabilized by various genome-regulatory proteins.
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Affiliation(s)
- Jack Maurer
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Claire S. Albrecht
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Physics, University of Oregon, Eugene, Oregon 97403
| | - Patrick Herbert
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Dylan Heussman
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Anabel Chang
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Peter H. von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
| | - Andrew H. Marcus
- Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403
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4
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Drobotenko MI, Svidlov AA, Dorohova АA, Baryshev MG, Dzhimak SS. Medium viscosity influence on the open states genesis in a DNA molecule. J Biomol Struct Dyn 2023:1-9. [PMID: 38102872 DOI: 10.1080/07391102.2023.2294178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
The studies were carried out by the mathematical modeling of DNA mechanical deformations. Numerical calculations done for the interferon alpha 17 gene, which consists of 980 base pairs. It has been established that the genesis and dynamics of open states in the DNA molecule depends on the magnitude of the external influence (torque) and on the viscosity of the environment. In addition, it is shown that the dynamics of open states zones can have a jump-like character with a small change in the magnitude of the torque. When torque is applied to all 980 base pairs of the gene, the following effect is observed: an increase in the viscosity of the medium leads to an increase in the value of the torque necessary for the occurrence of OS and DNA unwinding, i.e. viscosity plays an important stabilizing role in DNA dynamics. Under the influence of a localized torque on different (by the content of A-T and G-C pairs and location) regions of the interferon alpha 17 gene, it was found that the magnitude of the external torque necessary for the occurrence of open states at all calculated values of viscosity depends on the nucleotide composition. The dependence of the torque magnitude required for the open states occurrence on viscosity is observed when the torque is applied to areas close to the gene boundaries. At the same time, the significance of the end effect, which weakens DNA, decreased with increasing viscosity of the medium.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mikhail I Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
| | - Alexandr A Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Аnna A Dorohova
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Mikhail G Baryshev
- Department of Safety and Productivity of agroecosystems, All-Russian Research Institute of Phytopathology, Russia
| | - Stepan S Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
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5
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Liebl K, Zacharias M. Toward Force Fields with Improved Base Stacking Descriptions. J Chem Theory Comput 2023; 19:1529-1536. [PMID: 36795949 DOI: 10.1021/acs.jctc.2c01121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Recent DNA force fields indicate good performance in describing flexibility and structural stability of double-stranded B-DNA. However, it is not clear how accurately base stacking interactions are represented that are critical for simulating structure formation processes and conformational changes. Based on the equilibrium nucleoside association and base pair nicking, we find that the recent Tumuc1 force field improves the description of base stacking compared to previous state-of-the-art force fields. Nevertheless, base pair stacking is still overstabilized compared to experiment. We propose a rapid method to reweight calculated free energies of stacking upon force field modifications in order to generate improved parameters. A decrease of the Lennard-Jones attraction between nucleo-bases alone appears insufficient; however, adjustments in the partial charge distribution on base atoms could help to further improve the force field description of base stacking.
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Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Garching 85748, Germany
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6
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Gao A, Remsing RC, Weeks JD. Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions. J Phys Chem B 2023; 127:809-821. [PMID: 36669139 DOI: 10.1021/acs.jpcb.2c06988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions but present conceptual and computational challenges to both theory and simulations. We review recent developments in an approach addressing these challenges─local molecular field (LMF) theory. LMF theory exploits an exact and physically suggestive separation of intermolecular Coulomb interactions into strong short-range and uniformly slowly varying long-range components. This allows us to accurately determine the averaged effects of the long-range components on the short-range structure using effective single particle fields and analytical corrections, greatly reducing the need for complex lattice summation techniques used in most standard approaches. The simplest use of these ideas in aqueous solutions leads to the short solvent (SS) model, where both solvent-solvent and solute-solvent Coulomb interactions have only short-range components. Here we use the SS model to give a simple description of pairing of nucleobases and biologically relevant ions in water.
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Affiliation(s)
- Ang Gao
- Department of Physics, Beijing University of Posts and Telecommunications, Beijing, China 100876
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - John D Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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7
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Dutta D, Baishya T, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Bhattacharyya MK. Supramolecular Assemblies involving Energetically Significant Unconventional π(CN)-π and Anion-π(nitrile) Contacts in Zn(II) Coordination Compounds: Antiproliferative Evaluation and Theoretical Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Vener MV, Makhrov DE, Voronin AP, Shalafan DR. Molecular Dynamics Simulation of Association Processes in Aqueous Solutions of Maleate Salts of Drug-like Compounds: The Role of Counterion. Int J Mol Sci 2022; 23:ijms23116302. [PMID: 35682979 PMCID: PMC9181654 DOI: 10.3390/ijms23116302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
The study of the formation of microstructures during the interaction of a protonated drug-like compound (API) with a maleic acid monoanion sheds light on the assembly processes in an aqueous solution at the molecular level. Molecular dynamics (MD) simulations coupled with density functional theory (DFT) calculations made it possible to find initial hydrogen bonding motifs during the assembly process, leading to the formation of heterodimers and trimers. The process of trimer formation [protonated API—maleic acid monoanion—protonated API] proceeds through the formation of three intermolecular H-bonds by the CO2− group of the maleic acid monoanion in both systems. The total enthalpy/energy of these H-bonds is more than 70 kJ/mol. Thus, the maleic acid monoanion plays a key role in the processes of association in aqueous solution, and the interaction of the maleic acid monoanion with API is more preferable than the interaction of API molecules with each other. DFT computations in the discrete continuum approximation reveal the spectral features of heterodimers and trimers, and the ATR-IR spectra confirmed these findings. MD simulations followed by DFT calculations made it possible to describe the initial stages of the formation of pharmaceutical cocrystals in an aqueous solution.
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Affiliation(s)
- Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, 119991 Moscow, Russia
- Correspondence:
| | - Denis E. Makhrov
- Faculty of Natural Science, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia;
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia; (A.P.V.); (D.R.S.)
| | - Daria R. Shalafan
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia; (A.P.V.); (D.R.S.)
- Ivanovo State University for Chemistry and Technology, 153000 Ivanovo, Russia
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9
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Diclofenac Ion Hydration: Experimental and Theoretical Search for Anion Pairs. Molecules 2022; 27:molecules27103350. [PMID: 35630826 PMCID: PMC9146526 DOI: 10.3390/molecules27103350] [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: 04/07/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Self-assembly of organic ions in aqueous solutions is a hot topic at the present time, and substances that are well-soluble in water are usually studied. In this work, aqueous solutions of sodium diclofenac are investigated, which, like most medicinal compounds, is poorly soluble in water. Classical MD modeling of an aqueous solution of diclofenac sodium showed equilibrium between the hydrated anion and the hydrated dimer of the diclofenac anion. The assignment and interpretation of the bands in the UV, NIR, and IR spectra are based on DFT calculations in the discrete-continuum approximation. It has been shown that the combined use of spectroscopic methods in various frequency ranges with classical MD simulations and DFT calculations provides valuable information on the association processes of medical compounds in aqueous solutions. Additionally, such a combined application of experimental and calculation methods allowed us to put forward a hypothesis about the mechanism of the effect of diclofenac sodium in high dilutions on a solution of diclofenac sodium.
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10
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Mak CH. Nucleic acid folding simulations using a physics-based atomistic free energy model. J Chem Phys 2022; 156:174114. [PMID: 35525642 DOI: 10.1063/5.0086304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces-base stacking, counterion-induced backbone self-interactions, and base pairing-via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach.
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Affiliation(s)
- Chi H Mak
- Departments of Chemistry and Quantitative and Computational Biology, and Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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11
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Sarma P, Sharma P, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Baruwa B, Bhattacharyya MK. Charge assisted hydrogen bonded assemblies and unconventional O···O dichalcogen bonding interactions in pyrazole-based isostructural Ni(II) and Mn(II) compounds involving anthraquinone disulfonate: Antiproliferative evaluation and theoretical studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Heussman D, Kittell J, von Hippel PH, Marcus AH. Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy. J Chem Phys 2022; 156:045101. [PMID: 35105081 PMCID: PMC9448411 DOI: 10.1063/5.0076261] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.
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Affiliation(s)
| | - Justin Kittell
- Center for Optical, Molecular and Quantum Science, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, USA
| | - Peter H. von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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13
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Sharma P, Baishya T, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Das J, Bhattacharyya MK. Structural topologies involving energetically significant antiparallel π-stacking and unconventional N(nitrile)⋯π(fumarate) contacts in dinuclear Zn( ii) and polymeric Mn( ii) compounds: antiproliferative evaluation and theoretical studies. NEW J CHEM 2022. [DOI: 10.1039/d1nj04786h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Anticancer activities considering cell viability, apoptosis and molecular docking have been explored in dinuclear Zn(ii) and polymeric Mn(ii) compounds involving energetically significant unconventional N(nitrile)⋯π(fum) contacts.
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Affiliation(s)
- Pranay Sharma
- Department of Chemistry, Cotton University, Guwahati-781001, Assam, India
| | | | - Rosa M. Gomila
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Miquel Barcelo-Oliver
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Akalesh K. Verma
- Department of Zoology, Cell & Biochemical Technology Laboratory, Cotton University, Guwahati-781001, India
| | - Jumi Das
- Department of Zoology, Cell & Biochemical Technology Laboratory, Cotton University, Guwahati-781001, India
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14
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Substituent effects on the regium-π stacking interactions between Au 6 cluster and substituted benzene. J Mol Model 2021; 27:328. [PMID: 34687368 DOI: 10.1007/s00894-021-04944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/07/2021] [Indexed: 11/27/2022]
Abstract
The regium-π stacking interactions in the Au6···PhX (X = H, CH3, OH, OCH3, NH2, F, Cl, Br, CN, NO2) complexes are studied using quantum chemical methods. The present study focuses on the different effects of electron-donating and electron-withdrawing substituent. The structure and binding strength of the complexes are examined. The interactions between Au6 cluster and various substituted benzene become strengthened relative to the Au6···benzene complex. The interaction region indicator analysis was performed, and the interaction region and interaction between the substituent and Au6 cluster are discussed. It is found that the substituent effects on the regium-π stacking interactions between Au6 cluster and substituted benzene are different from π···π interactions of benzene dimer. Energy decomposition analysis was carried out to study the nature of regium-π stacking interactions, and the substituent effects are mainly reflected on the electrostatic interaction and dispersion.
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15
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Stellwagen NC. Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations. Electrophoresis 2021; 43:309-326. [PMID: 34510492 DOI: 10.1002/elps.202100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/08/2022]
Abstract
This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.
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16
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Nosov VG, Podryadrova KA, Vasilyeva MS, Bogachev NA, Skripkin MY, Mereshchenko AS. Dimerization of Phthalate Ion in Non-Aqueous
Solvents. RUSS J GEN CHEM+ 2021. [DOI: 10.1134/s1070363221050017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Lu T, Nakashima KK, Spruijt E. Temperature-Responsive Peptide-Nucleotide Coacervates. J Phys Chem B 2021; 125:3080-3091. [PMID: 33757284 PMCID: PMC8020381 DOI: 10.1021/acs.jpcb.0c10839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Coacervates are a
type of liquid–liquid phase separated
(LLPS) droplets that can serve as models of membraneless organelles
(MLOs) in living cells. Peptide–nucleotide coacervates have
been widely used to mimic properties of ribonucleoprotein (RNP) granules,
but the thermal stability and the role of base stacking is still poorly
understood. Here, we report a systematic investigation of coacervates
formed by five different nucleoside triphosphates (NTPs) with poly-l-lysine and poly-l-arginine as a function of temperature.
All studied combinations exhibit an upper critical solution temperature
(UCST), and a temperature-dependent critical salt concentration, originating
from a significant nonelectrostatic contribution to the mixing free
energy. Both the enthalpic and entropic parts of this nonelectrostatic
interaction decrease in the order G/A/U/C/T, in accordance with nucleobase
stacking free energies. Partitioning of two dyes proves that the local
hydrophobicity inside the peptide–nucleotide coacervates is
different for every nucleoside triphosphate. We derive a simple relation
between the temperature and salt concentration at the critical point
based on a mean-field model of phase separation. Finally, when different
NTPs are mixed with one common oppositely charged peptide, hybrid
coacervates were formed, characterized by a single intermediate UCST
and critical salt concentration. NTPs with lower critical salt concentrations
can remain condensed in mixed coacervates far beyond their original
critical salt concentration. Our results show that NTP-based coacervates
have a strong temperature sensitivity due to base stacking interactions
and that mixing NTPs can significantly influence the stability of
condensates and, by extension, their bioavailability.
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Affiliation(s)
- Tiemei Lu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Karina K Nakashima
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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18
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Zhang Z, Yu S, Zuo H. DNA Ring-Opening Polymerization Driven by Base Stacking. Chembiochem 2021; 22:1621-1626. [PMID: 33404185 DOI: 10.1002/cbic.202000776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/01/2021] [Indexed: 11/06/2022]
Abstract
Supramolecular polymers, relying on reversible intermolecular interactions, promise a wide range of applications, including optoelectronic materials, self-healing materials, and biomedical delivery materials. Among potential molecular candidates, DNA strands act as an excellent platform. DNA has a well-established secondary structure (double helix), and its intermolecular interactions can be readily thermodynamically engineered and kinetically controlled. Extensive studies have demonstrated that various DNA motifs can polymerize/assemble into large polymers with different topology, geometry, and dimensionalities. Most of the reported polymerization is driven by hybridization of DNA strands. Herein, we report a novel system of DNA supramolecular polymerization that is driven by DNA base stacking. The polymerization has been confirmed by native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM). We believe that this work will expand the toolbox for DNA supramolecular polymerization and would, with further development, increase further control of DNA supramolecular polymerization.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Shuang Yu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715, P. R. China
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19
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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20
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Abstract
Base pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent's contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ∼1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a "freezing" behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of the solvent's thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.
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21
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Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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22
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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. Proc Natl Acad Sci U S A 2019; 116:17169-17174. [PMID: 31413203 PMCID: PMC6717297 DOI: 10.1073/pnas.1909122116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. We report that certain semihydrophobic agents depress the stacking energy (measurable in single-molecule experiments), leading to transiently occurring holes in the base-pair stack (monitorable via binding of threading intercalators). Similar structures observed in DNA complexes with RecA and Rad51, and previous observations of spontaneous strand exchange catalyzed in semihydrophobic model systems, make us propose that some hydrophobic protein residues may have roles in catalyzing homologous recombination. We speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes. Hydrophobic base stacking is a major contributor to DNA double-helix stability. We report the discovery of specific unstacking effects in certain semihydrophobic environments. Water-miscible ethylene glycol ethers are found to modify structure, dynamics, and reactivity of DNA by mechanisms possibly related to a biologically relevant hydrophobic catalysis. Spectroscopic data and optical tweezers experiments show that base-stacking energies are reduced while base-pair hydrogen bonds are strengthened. We propose that a modulated chemical potential of water can promote “longitudinal breathing” and the formation of unstacked holes while base unpairing is suppressed. Flow linear dichroism in 20% diglyme indicates a 20 to 30% decrease in persistence length of DNA, supported by an increased flexibility in single-molecule nanochannel experiments in poly(ethylene glycol). A limited (3 to 6%) hyperchromicity but unaffected circular dichroism is consistent with transient unstacking events while maintaining an overall average B-DNA conformation. Further information about unstacking dynamics is obtained from the binding kinetics of large thread-intercalating ruthenium complexes, indicating that the hydrophobic effect provides a 10 to 100 times increased DNA unstacking frequency and an “open hole” population on the order of 10−2 compared to 10−4 in normal aqueous solution. Spontaneous DNA strand exchange catalyzed by poly(ethylene glycol) makes us propose that hydrophobic residues in the L2 loop of recombination enzymes RecA and Rad51 may assist gene recombination via modulation of water activity near the DNA helix by hydrophobic interactions, in the manner described here. We speculate that such hydrophobic interactions may have catalytic roles also in other biological contexts, such as in polymerases.
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23
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Mak CH, Phan ENH. Topological Constraints and Their Conformational Entropic Penalties on RNA Folds. Biophys J 2019; 114:2059-2071. [PMID: 29742400 PMCID: PMC5961522 DOI: 10.1016/j.bpj.2018.03.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/08/2018] [Accepted: 03/22/2018] [Indexed: 02/01/2023] Open
Abstract
Functional RNAs can fold into intricate structures using a number of different secondary and tertiary structural motifs. Many factors contribute to the overall free energy of the target fold. This study aims at quantifying the entropic costs coming from the loss of conformational freedom when the sugar-phosphate backbone is subjected to constraints imposed by secondary and tertiary contacts. Motivated by insights from topology theory, we design a diagrammatic scheme to represent different types of RNA structures so that constraints associated with a folded structure may be segregated into mutually independent subsets, enabling the total conformational entropy loss to be easily calculated as a sum of independent terms. We used high-throughput Monte Carlo simulations to simulate large ensembles of single-stranded RNA sequences in solution to validate the assumptions behind our diagrammatic scheme, examining the entropic costs for hairpin initiation and formation of many multiway junctions. Our diagrammatic scheme aids in the factorization of secondary/tertiary constraints into distinct topological classes and facilitates the discovery of interrelationships among multiple constraints on RNA folds. This perspective, which to our knowledge is novel, leads to useful insights into the inner workings of some functional RNA sequences, demonstrating how they might operate by transforming their structures among different topological classes.
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Affiliation(s)
- Chi H Mak
- Department of Chemistry, University of Southern California, Los Angeles, California; Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California.
| | - Ethan N H Phan
- Department of Chemistry, University of Southern California, Los Angeles, California
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24
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Kim HW, Rhee YM, Shin SK. Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Phys Chem Chem Phys 2019; 20:21068-21074. [PMID: 30074033 DOI: 10.1039/c8cp03050b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.
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Affiliation(s)
- Hyun Woo Kim
- Center for Molecular Modeling and Simulation, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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25
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Molčanov K, Kojić-Prodić B. Towards understanding π-stacking interactions between non-aromatic rings. IUCRJ 2019; 6:156-166. [PMID: 30867913 PMCID: PMC6400184 DOI: 10.1107/s2052252519000186] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/04/2019] [Indexed: 05/16/2023]
Abstract
The first systematic study of π interactions between non-aromatic rings, based on the authors' own results from an experimental X-ray charge-density analysis assisted by quantum chemical calculations, is presented. The landmark (non-aromatic) examples include quinoid rings, planar radicals and metal-chelate rings. The results can be summarized as: (i) non-aromatic planar polyenic rings can be stacked, (ii) interactions are more pronounced between systems or rings with little or no π-electron delocalization (e.g. quinones) than those involving delocalized systems (e.g. aromatics), and (iii) the main component of the interaction is electrostatic/multipolar between closed-shell rings, whereas (iv) interactions between radicals involve a significant covalent contribution (multicentric bonding). Thus, stacking covers a wide range of interactions and energies, ranging from weak dispersion to unlocalized two-electron multicentric covalent bonding ('pancake bonding'), allowing a face-to-face stacking arrangement in some chemical species (quinone anions). The predominant interaction in a particular stacked system modulates the physical properties and defines a strategy for crystal engineering of functional materials.
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Affiliation(s)
- Krešimir Molčanov
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Biserka Kojić-Prodić
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
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26
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Remington JM, McCullagh M, Kohler B. Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics. J Phys Chem B 2019; 123:2291-2304. [PMID: 30767498 DOI: 10.1021/acs.jpcb.8b12172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments. Analysis of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments. Combining MD simulations with HMSM analysis is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
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27
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Mak CH. Theoretical Model for Solvent-Induced Base Stacking Interactions in Solvent-Free DNA Simulations. J Phys Chem B 2019; 123:1939-1949. [PMID: 30727734 DOI: 10.1021/acs.jpcb.8b10848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrahigh-throughput conformational sampling of biopolymers like nucleic acids are most effectively carried out without explicit solvents, but the physical origins of almost all inter- and intramolecular interactions controlling nucleic acid structures are rooted in water. Single-stranded (ss) DNAs or RNAs in water are characterized by ensembles of diverse conformations. To properly capture solvent-induced nucleobase stacking interactions in an otherwise solvent-free Monte Carlo algorithm, theoretical models are developed here to describe the solvent entropy and dispersion terms in base stacking free energies. To validate these models, equilibrium ensembles of ss (dA) n and (dT) n sequences ( n = 30, 40, and 50) were simulated, and they quantitatively reproduced experimental small-angle X-ray scattering (SAXS) data. Simulated dA ensembles show substantial stacking. While less prevalent, stacking in dT chains is not negligible. Analysis of SAXS profiles suggests that excess features between wavevector 0.03 and 0.18 Å-1 correlate with stacking, and stacking in dA versus dT chains is chain length-dependent, where (dT)30 and (dA)30 chains have more similar structures, but longer dA chains show more stacking over dT. The average stack length in ss-dA chains is 5-10 nucleotides, yielding an estimate for the overall A|A stacking free energy at ∼1 kcal/mol.
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Affiliation(s)
- Chi H Mak
- Departments of Chemistry and Biological Sciences, and Center of Applied Mathematical Sciences , University of Southern California , Los Angeles , California 90089 , United States
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28
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McCormack K. The cardioprotective effect of dexrazoxane (Cardioxane) is consistent with sequestration of poly(ADP-ribose) by self-assembly and not depletion of topoisomerase 2B. Ecancermedicalscience 2018; 12:889. [PMID: 30792806 PMCID: PMC6351063 DOI: 10.3332/ecancer.2018.889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Indexed: 01/12/2023] Open
Abstract
Following systematic scrutiny of the evidence in support of the hypothesis that the cardioprotective mechanism of action of dexrazoxane is mediated by a ‘depletion’ or ‘downregulation’ of Top2β protein levels in heart tissue, the author concludes that this hypothesis is untenable. In seeking to understand how dexrazoxane protects the heart, the outcomes of a customised association rule learning algorithm incorporating the use of antecedent surrogate variables (CEME, 2017 McCormack Pharma) reveal a previously unknown relationship between dexrazoxane and poly(ADP-ribose) (PAR) polymer. The author shows how this previously unknown relationship explains both acute and long-term cardioprotection in patients receiving anthracyclines. In addition, as a direct inhibitor of PAR dexrazoxane has access to the epigenome and this offers a new insight into protection by dexrazoxane against doxorubicin-induced late-onset damage [McCormack K, manuscript in preparation]. Notably, through this review article, the author illustrates the practical application of probing natural language text using an association rule learning algorithm for the discovery of new and interesting associations that, otherwise, would remain lost. Historically, the use of CEME enabled the first report of the capacity of a small molecule to catalyse the hybrid self-assembly of a nucleic acid biopolymer via canonical and non-canonical, non-covalent interactions analogous to Watson Crick and Hoogsteen base pairing, respectively.
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Affiliation(s)
- Keith McCormack
- McCormack Pharma, a division of McCormack Ltd, Stirling House, 9 Burroughs Gardens, London NW4 4AU, UK
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29
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Raman spectra of aqueous uracil stacked dimer: First principle molecular dynamics simulation. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. J Chem Theory Comput 2018; 14:6598-6612. [PMID: 30375860 DOI: 10.1021/acs.jctc.8b00633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
To benchmark RNA force fields, we compared the folding stabilities of three 12-nucleotide hairpin stem loops estimated by simulation to stabilities determined by experiment. We used umbrella sampling and a reaction coordinate of end-to-end (5' to 3' hydroxyl oxygen) distance to estimate the free energy change of the transition from the native conformation to a fully extended conformation with no hydrogen bonds between non-neighboring bases. Each simulation was performed four times using the AMBER FF99+bsc0+χOL3 force field, and each window, spaced at 1 Å intervals, was sampled for 1 μs, for a total of 552 μs of simulation. We compared differences in the simulated free energy changes to analogous differences in free energies from optical melting experiments using thermodynamic cycles where the free energy change between stretched and random coil sequences is assumed to be sequence-independent. The differences between experimental and simulated ΔΔ G° are, on average, 0.98 ± 0.66 kcal/mol, which is chemically accurate and suggests that analogous simulations could be used predictively. We also report a novel method to identify where replica free energies diverge along a reaction coordinate, thus indicating where additional sampling would most improve convergence. We conclude by discussing methods to more economically perform these simulations.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Zhen Tan
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Aleksandar Spasic
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Debapratim Dutta
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
| | - Leslie A Salas-Estrada
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - Alan Grossfield
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States
| | - David H Mathews
- Department of Biochemistry & Biophysics , University of Rochester , Rochester , New York 14642 , United States.,Department of Biostatistics and Computational Biology , University of Rochester , Rochester , New York 14642 , United States.,Center for RNA Biology , University of Rochester , Rochester , New York 14642 , United States
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31
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Milovanović B, Kojić M, Petković M, Etinski M. New Insight into Uracil Stacking in Water from ab Initio Molecular Dynamics. J Chem Theory Comput 2018; 14:2621-2632. [DOI: 10.1021/acs.jctc.8b00139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marko Kojić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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32
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Chakraborty D, Chattaraj PK. Host-guest interactions between octa acid and cations/nucleobases. J Comput Chem 2018; 39:161-175. [PMID: 29105789 DOI: 10.1002/jcc.25097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022]
Abstract
The nature of host-guest interaction in between octa acid cavitand (OA) and some representative cationic guests (Li+ , Na+ , K+ , Be+2 , Mg+2 , Ca+2 , Li3 O+ , Na3 O+ , K3 O+ ) as well as heterocyclic moieties like [adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U), and tetrathiafulvalene (TTF)] has been examined with the aid of density functional theory (DFT)-based computations. Thermochemical results indicate that all the guests bind with OA in a thermodynamically favorable fashion at 298.15 K temperature and one atmospheric pressure. OA exhibits high selectivity in binding the lighter cations/metal cluster cations as compared to the heavier congeners along each given series. Moreover, OA exhibits enhanced affinity as well as selectivity in binding A/G/TTF molecules as compared to C/T/U. Noncovalent interaction and energy decomposition analyses reveal that in addition to the van der Waals interaction, significant contribution from electrostatic as well as orbital interactions dictate the outcome in all the host-guest complexes. Time dependent DFT calculations have been carried out to assess the role of the guests in tuning the electronic properties as well as absorption spectrum of OA. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry and Centre for Theoretical Studies, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India
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Jacobs M, Greff Da Silveira L, Prampolini G, Livotto PR, Cacelli I. Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach. J Chem Theory Comput 2018; 14:543-556. [DOI: 10.1021/acs.jctc.7b00602] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Matheus Jacobs
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Leandro Greff Da Silveira
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
- Departamento
de Ciências Exatas e da Terra, Universidade Regional Integrada do Alto Uruguay e da Missões (URI), Avenida Assis Brasil 709, CEP 98400-00 Frederico Westphalen, Brazil
| | - Giacomo Prampolini
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Paolo Roberto Livotto
- Instituto
de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP 91501-970 Porto Alegre, Brazil
| | - Ivo Cacelli
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi
3, I-56124 Pisa, Italy
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Plumridge A, Meisburger SP, Andresen K, Pollack L. The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res 2017; 45:3932-3943. [PMID: 28334825 PMCID: PMC5397193 DOI: 10.1093/nar/gkx140] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/17/2017] [Indexed: 12/17/2022] Open
Abstract
Single-stranded DNA (ssDNA) is notable for its interactions with ssDNA binding proteins (SSBs) during fundamentally important biological processes including DNA repair and replication. Previous work has begun to characterize the conformational and electrostatic properties of ssDNA in association with SSBs. However, the conformational distributions of free ssDNA have been difficult to determine. To capture the vast array of ssDNA conformations in solution, we pair small angle X-ray scattering with novel ensemble fitting methods, obtaining key parameters such as the size, shape and stacking character of strands with different sequences. Complementary ion counting measurements using inductively coupled plasma atomic emission spectroscopy are employed to determine the composition of the ion atmosphere at physiological ionic strength. Applying this combined approach to poly dA and poly dT, we find that the global properties of these sequences are very similar, despite having vastly different propensities for single-stranded helical stacking. These results suggest that a relatively simple mechanism for the binding of ssDNA to non-specific SSBs may be at play, which explains the disparity in binding affinities observed for these systems.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | | | - Kurt Andresen
- Department of Physics, Gettysburg College, Gettysburg, PA 17325, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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35
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Barone V, Cacelli I, Ferretti A, Prampolini G. Noncovalent Interactions in the Catechol Dimer. Biomimetics (Basel) 2017; 2:E18. [PMID: 31105180 PMCID: PMC6352673 DOI: 10.3390/biomimetics2030018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/02/2022] Open
Abstract
Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller⁻Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri, I-56126 Pisa, Italy.
| | - Ivo Cacelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy.
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy.
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36
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37
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Venkataramanan NS, Suvitha A. Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches. J Phys Chem B 2017; 121:4733-4744. [DOI: 10.1021/acs.jpcb.7b01808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Natarajan Sathiyamoorthy Venkataramanan
- Centre
for Computational Chemistry and Materials Science, SASTRA University, Thanjavur 614 001, India
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
| | - Ambigapathy Suvitha
- Department
of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA University, Thanjavur 614 001, India
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38
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Sedova A, Banavali NK. Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands. Biochemistry 2017; 56:1426-1443. [PMID: 28187685 DOI: 10.1021/acs.biochem.6b01101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.
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Affiliation(s)
- Ada Sedova
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, Wadsworth Center, New York State Department of Health, CMS 2008, Biggs Laboratory, Empire State Plaza, P.O. Box 509, Albany, New York 12201-0509, United States.,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
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39
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Vangaveti S, Ranganathan SV, Chen AA. Advances in RNA molecular dynamics: a simulator's guide to RNA force fields. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1396] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/17/2016] [Accepted: 08/25/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Sweta Vangaveti
- The RNA Institute; University at Albany State University of New York; Albany NY USA
| | | | - Alan A. Chen
- The RNA Institute; University at Albany State University of New York; Albany NY USA
- Department of Chemistry; University at Albany State University of New York; Albany NY USA
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40
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Serec K, Babić SD, Podgornik R, Tomić S. Effect of magnesium ions on the structure of DNA thin films: an infrared spectroscopy study. Nucleic Acids Res 2016; 44:8456-64. [PMID: 27484473 PMCID: PMC5041487 DOI: 10.1093/nar/gkw696] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/27/2016] [Indexed: 11/14/2022] Open
Abstract
Utilizing Fourier transform infrared spectroscopy we have investigated the vibrational spectrum of thin dsDNA films in order to track the structural changes upon addition of magnesium ions. In the range of low magnesium concentration ([magnesium]/[phosphate] = [Mg]/[P] < 0.5), both the red shift and the intensity of asymmetric PO2 stretching band decrease, indicating an increase of magnesium-phosphate binding in the backbone region. Vibration characteristics of the A conformation of the dsDNA vanish, whereas those characterizing the B conformation become fully stabilized. In the crossover range with comparable Mg and intrinsic Na DNA ions ([Mg]/[P] ≈ 1) B conformation remains stable; vibrational spectra show moderate intensity changes and a prominent blue shift, indicating a reinforcement of the bonds and binding in both the phosphate and the base regions. The obtained results reflect the modified screening and local charge neutralization of the dsDNA backbone charge, thus consistently demonstrating that the added Mg ions interact with DNA via long-range electrostatic forces. At high Mg contents ([Mg]/[P] > 10), the vibrational spectra broaden and show a striking intensity rise, while the base stacking remains unaffected. We argue that at these extreme conditions, where a charge compensation by vicinal counterions reaches 92-94%, DNA may undergo a structural transition into a more compact form.
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Affiliation(s)
- Kristina Serec
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - Sanja Dolanski Babić
- Department of Physics and Biophysics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute, Ljubljana, 1000, Slovenia Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, 1000, Slovenia
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41
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Häse F, Zacharias M. Free energy analysis and mechanism of base pair stacking in nicked DNA. Nucleic Acids Res 2016; 44:7100-8. [PMID: 27407106 PMCID: PMC5009751 DOI: 10.1093/nar/gkw607] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/23/2016] [Indexed: 11/14/2022] Open
Abstract
The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner.
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Affiliation(s)
- Florian Häse
- Physik-Department T38, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, James-Franck-Strasse 1, D-85748 Garching, Germany
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