1
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Das G, Harikrishna S, Gore KR. Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach. J Phys Chem B 2024. [PMID: 39172066 DOI: 10.1021/acs.jpcb.4c02557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South-type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North-type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South-type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC)2 and (GCAC*GAC)2], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.
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Affiliation(s)
- Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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2
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Fedorova L, Crossley ER, Mulyar OA, Qiu S, Freeman R, Fedorov A. Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome. BIOLOGY 2023; 12:1125. [PMID: 37627009 PMCID: PMC10452674 DOI: 10.3390/biology12081125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.
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Affiliation(s)
- Larisa Fedorova
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Emily R. Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
| | - Oleh A. Mulyar
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Shuhao Qiu
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
| | - Ryan Freeman
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA; (L.F.); (O.A.M.); (R.F.)
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA;
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA;
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3
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Nakagawa S, Kimura A, Okamoto Y. Polarizable Molecular Block Model: Toward the Development of an Induced Dipole Force Field for DNA. J Phys Chem B 2022; 126:10646-10661. [PMID: 36512703 DOI: 10.1021/acs.jpcb.2c06227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For flexible and highly ionized macromolecules such as DNA, it is important to correctly evaluate the intramolecular polarization in an induced dipole force field. In a proposed polarizable molecular block (PMB) model, a large molecule is divided into several molecular blocks. The atomic charges of the blocks are optimized by using the respective electrostatic potentials (ESPs) on the molecular surface. By using the capped hydrogen removal operation, the total charge of the blocks is controlled exactly to have an integer charge. The atomic polarizabilities of the blocks are optimized by using the respective polarized one-electron potentials that are the differences between ESPs with and without an external test charge. Induced dipole-charge interactions between the blocks are all included, but those interactions within the blocks are strictly excluded. All dipole-dipole interactions are included, but the damping functions are applied to the close dipole-dipole pairs. Several types of damping (simple scaling, exponential, linear, and Gaussian) are evaluated. The validity of the PMB model was verified by using trinucleotide duplexes which have A-, B-, and Z-DNA forms. The reference energies of trinucleotide duplexes including counterions (GGT3Na-ACC3Na, GAC3Na-GTC3Na, and GCG3Na-CGC3Na) are calculated using ωB97XD/aug-cc-pVDZ. All damping types reproduced well the reference interaction energies, dipole moments, and ESPs. Among them, the simple scaling with strong attenuation to 1-2 atomic pairs showed the highest stability against the polarization catastrophe. This study shows that it is possible to develop a high-quality polarizable force field by treating the intramolecular polarization on a block-by-block basis.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan.,Kinjo Gakuin University, Nagoya, Aichi463-8521, Japan
| | - Akihiro Kimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi464-8602, Japan.,High Performance Computing Division, Information Technology Center, Nagoya University, Nagoya, Aichi464-8601, Japan.,Global Engagement Center, International Affairs, Nagoya University, Nagoya, Aichi464-8601, Japan
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4
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Fedorova L, Mulyar OA, Lim J, Fedorov A. Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides. Genes (Basel) 2022; 13:2053. [PMID: 36360290 PMCID: PMC9690913 DOI: 10.3390/genes13112053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved.
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Affiliation(s)
| | | | - Jan Lim
- CRI Genetics LLC, Santa Monica, CA 90404, USA
| | - Alexei Fedorov
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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5
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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6
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Martin B, Dans PD, Wieczór M, Villegas N, Brun-Heath I, Battistini F, Terrazas M, Orozco M. Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. PLoS Comput Biol 2022; 18:e1009749. [PMID: 35007284 PMCID: PMC8782489 DOI: 10.1371/journal.pcbi.1009749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/21/2022] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We have used a variety of theoretical and experimental techniques to study the role of four basic amino acids-Arginine, Lysine, Ornithine and L-2,4-Diaminobutyric acid-on the structure, flexibility and sequence-dependent stability of DNA. We found that the presence of organic ions stabilizes the duplexes and significantly reduces the difference in stability between AT- and GC-rich duplexes with respect to the control conditions. This suggests that these amino acids, ingredients of the primordial soup during abiogenesis, could have helped to equalize the stability of AT- and GC-rich DNA oligomers, facilitating a general non-catalysed self-replication of DNA. Experiments and simulations demonstrate that organic ions have an effect that goes beyond the general electrostatic screening, involving specific interactions along the grooves of the double helix. We conclude that organic ions, largely ignored in the DNA world, should be reconsidered as crucial structural elements far from mimics of small inorganic cations.
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Affiliation(s)
- Benjamin Martin
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pablo D. Dans
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República (UdelaR), Salto, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Milosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria Villegas
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
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7
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Grupa U, Liebl K, Zacharias M. Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations. J Phys Chem B 2021; 125:13850-13857. [PMID: 34928161 DOI: 10.1021/acs.jpcb.1c07829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA blunt ends can associate mediated by stacking interactions between the terminal base pairs that form blunt ends. The blunt end association plays a role in DNA repair and recombination processes and can also be of importance for the design of DNA-based nano-materials. Its function depends on the sequence and on the geometric arrangement that leads to stable interaction. For a stacked state, the relative orientation (twisting) of the base pairs is important. Molecular dynamics and advanced sampling simulations were used to calculate free energy change associated with twist changes of the stacked blunt-end base pairs. The calculations reproduce blunt stacking arrangements found in crystal structures of DNA oligonucleotides as free energy minima. To elucidate the physical origin of the stabilization of certain angular arrangements, the interactions between backbone atoms in the blunt-end stack were switched off in additional free energy calculations. It allows us to decipher the contributions to stacking stabilization due to the nucleobases and the backbone and to analyze the sequence dependence of the angular stacking preferences. Good qualitative agreement was also found for the comparison with quantum mechanical calculations. The results may help in the design of novel DNA-based materials.
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Affiliation(s)
- Ulrich Grupa
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Korbinian Liebl
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
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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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Park G, Kang B, Park SV, Lee D, Oh SS. A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions. Nucleic Acids Res 2021; 49:4919-4933. [PMID: 33893806 PMCID: PMC8136788 DOI: 10.1093/nar/gkab285] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.
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Affiliation(s)
- Gyuri Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Donghwa Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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10
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Přerovská T, Pavlů A, Hancharyk D, Rodionova A, Vavříková A, Spiwok V. Structural Basis of the Function of Yariv Reagent-An Important Tool to Study Arabinogalactan Proteins. Front Mol Biosci 2021; 8:682858. [PMID: 34179088 PMCID: PMC8230119 DOI: 10.3389/fmolb.2021.682858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
Arabinogalactan proteins are very abundant, heavily glycosylated plant cell wall proteins. They are intensively studied because of their crucial role in plant development as well as their function in plant defence. Research of these biomacromolecules is complicated by the lack of tools for their analysis and characterisation due to their extreme heterogeneity. One of the few available tools for detection, isolation, characterisation, and functional studies of arabinogalactan proteins is Yariv reagents. Yariv reagent is a synthetic aromatic glycoconjugate originally prepared as an antigen for immunization. Later, it was found that this compound can precipitate arabinogalactan proteins, namely, their ß-D-(1→3)-galactan structures. Even though this compound has been intensively used for decades, the structural basis of arabinogalactan protein precipitation by Yariv is not known. Multiple biophysical studies have been published, but none of them attempted to elucidate the three-dimensional structure of the Yariv-galactan complex. Here we use a series of molecular dynamics simulations of systems containing one or multiple molecules of ß-D-galactosyl Yariv reagent with or without oligo ß-D-(1→3)-galactan to predict the structure of the complex. According to our model of Yariv-galactan complexes, Yariv reagent forms stacked oligomers stabilized by π-π and CH/π interactions. These oligomers may contain irregularities. Galactan structures crosslink these Yariv oligomers. The results were compared with studies in literature.
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Affiliation(s)
- Tereza Přerovská
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Anna Pavlů
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czechia
| | - Dzianis Hancharyk
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czechia
| | - Anna Rodionova
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czechia
| | - Anna Vavříková
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czechia
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
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11
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Krepl M, Dendooven T, Luisi BF, Sponer J. MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes. J Biol Chem 2021; 296:100656. [PMID: 33857481 PMCID: PMC8121710 DOI: 10.1016/j.jbc.2021.100656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023] Open
Abstract
The conserved protein Hfq is a key factor in the RNA-mediated control of gene expression in most known bacteria. The transient intermediates Hfq forms with RNA support intricate and robust regulatory networks. In Pseudomonas, Hfq recognizes repeats of adenine–purine–any nucleotide (ARN) in target mRNAs via its distal binding side, and together with the catabolite repression control (Crc) protein, assembles into a translation–repression complex. Earlier experiments yielded static, ensemble-averaged structures of the complex, but details of its interface dynamics and assembly pathway remained elusive. Using explicit solvent atomistic molecular dynamics simulations, we modeled the extensive dynamics of the Hfq–RNA interface and found implications for the assembly of the complex. We predict that syn/anti flips of the adenine nucleotides in each ARN repeat contribute to a dynamic recognition mechanism between the Hfq distal side and mRNA targets. We identify a previously unknown binding pocket that can accept any nucleotide and propose that it may serve as a ‘status quo’ staging point, providing nonspecific binding affinity, until Crc engages the Hfq–RNA binary complex. The dynamical components of the Hfq–RNA recognition can speed up screening of the pool of the surrounding RNAs, participate in rapid accommodation of the RNA on the protein surface, and facilitate competition among different RNAs. The register of Crc in the ternary assembly could be defined by the recognition of a guanine-specific base–phosphate interaction between the first and last ARN repeats of the bound RNA. This dynamic substrate recognition provides structural rationale for the stepwise assembly of multicomponent ribonucleoprotein complexes nucleated by Hfq–RNA binding.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; MRC-LMB, Cambridge, United Kingdom
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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12
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Harris PD, Hamdan SM, Habuchi S. Relative Contributions of Base Stacking and Electrostatic Repulsion on DNA Nicks and Gaps. J Phys Chem B 2020; 124:10663-10672. [PMID: 33179916 DOI: 10.1021/acs.jpcb.0c06941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In duplex DNA, the continuous sugar phosphate backbones prevent the double helix from significant bending, but breaks in the duplex such as nicks, gaps, and flaps present points at which significant bending is possible. The conformational dynamics of these aberrant structures remains poorly understood. Two factors can maintain the duplexlike conformation of these aberrant structures, these being the hydrophobic and aromatic stacking interactions of the nucleobases, and the electrostatic repulsion of the negatively charged backbones. Using confocal single-molecule Förster resonance energy transfer on nicked and gapped DNA structures, we compare the relative contributions of these two factors by modulating the electrostatic repulsion through mono- and divalent cation concentrations. Base stacking interactions dominate the dynamics of nicked DNA, making it behave essentially like duplex DNA. Gapped structures have weaker base stacking and thus backbone electrostatic repulsion becomes important, and shielding from cations results in an average increase in bending around the gap. This bending of gapped structures could be interpreted by increased flexibility of unstacked structures, transient unstacking events, or a combination of the two. Burst variance analysis (BVA) and analysis by photon-by-photon hidden Markov modeling (H2MM), methods capable of detecting submillisecond dynamics of single molecules in solution, only revealed a single state, indicating that dynamics are occurring at time scales shorter than microseconds.
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Affiliation(s)
- Paul D Harris
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
| | - Samir M Hamdan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia
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13
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Wang Y, Zhang C, Zhao YL, Zhao R, Houk KN. Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis. Biomolecules 2020; 10:E815. [PMID: 32466453 PMCID: PMC7355926 DOI: 10.3390/biom10060815] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/22/2022] Open
Abstract
Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.
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Affiliation(s)
- Yuanqi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resource and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China;
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Rosalinda Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
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14
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Shepherd JW, Greenall RJ, Probert M, Noy A, Leake M. The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA. Nucleic Acids Res 2020; 48:1748-1763. [PMID: 31930331 PMCID: PMC7038985 DOI: 10.1093/nar/gkz1227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/26/2022] Open
Abstract
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.
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Affiliation(s)
- Jack W Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
| | | | | | - Agnes Noy
- Department of Physics, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York,YO10 5NG, UK
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15
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Qin KS, Ichibha T, Hongo K, Maezono R. Inconsistencies in ab initio evaluations of non-additive contributions of DNA stacking energies. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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17
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Kruse H, Šponer J. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. J Phys Chem A 2019; 123:9209-9222. [PMID: 31560201 DOI: 10.1021/acs.jpca.9b05940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic.,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , 62500 Brno , Czech Republic
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18
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Wenholz DS, Bhadbhade M, Kandemir H, Ho J, Kumar N, Black DS. Substituent effects in solid-state assembly of activated benzotriazoles. CrystEngComm 2019. [DOI: 10.1039/c8ce01757c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Aromatic donor–acceptor stacking involving electron-rich π-donors and electron-deficient π-acceptors has been utilized in a broad spectrum of diverse applications to great effect.
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Affiliation(s)
| | | | - Hakan Kandemir
- School of Chemistry
- UNSW Sydney
- Australia
- Department of Chemistry
- Faculty of Art and Science
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19
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Kruse H, Banáš P, Šponer J. Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects. J Chem Theory Comput 2018; 15:95-115. [DOI: 10.1021/acs.jctc.8b00643] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 Listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiřı́ Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 Listopadu 12, 77146 Olomouc, Czech Republic
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20
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Villani G. Quantum Mechanical Investigation of the G-Quadruplex Systems of Human Telomere. ACS OMEGA 2018; 3:9934-9944. [PMID: 31459122 PMCID: PMC6644616 DOI: 10.1021/acsomega.8b01678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/09/2018] [Indexed: 05/17/2023]
Abstract
The three G-quadruplexes involved in the human telomere have been studied with an accurate quantum mechanical approach, and the possibility of reducing them to a simpler model has been tested. The similarities and the differences of these three systems are shown and discussed. Each system has been analyzed through different properties and compared to the others. In particular, we have considered: (1) the shape of the cavity and the atomic charges around it; (2) the electric field in and out of the cavity; (3) the stabilization energy due to the stacking of G-tetrads, to the H-bonds and to the ion interactions; and, finally, (4) to study the mechanism of the process of the ion inclusion in the cavity, the curves of potential energy due to the movement of the Na+ and K+ ions toward the cavity. The results suggest that a detailed study is essential in order to obtain the quantitative properties of these complex systems, but also that some qualitative behaviors can be schematized. Our study makes it clear that the entry of an ion in the cavity of these systems is a complex process, where it is possible to find stable structures with the ion out and in the cavity. Moreover, it is possible that more than one diabatic state is involved in this process.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM—CNR
(UOS Pisa), Area della Ricerca di Pisa, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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21
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Jena NR, Das P, Behera B, Mishra PC. Analogues of P and Z as Efficient Artificially Expanded Genetic Information System. J Phys Chem B 2018; 122:8134-8145. [PMID: 30063353 DOI: 10.1021/acs.jpcb.8b04207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
To artificially expand the genetic information system and to realize artificial life, it is necessary to discover new functional DNA bases that can form stable duplex DNA and participate in error-free replication. It is recently proposed that the 2-amino-imidazo[1,2- a]-1,3,5-triazin-4(8 H)one (P) and 6-amino-5-nitro-2(1 H)-pyridone (Z) would form a base pair complex, which is more stable than that of the normal G-C base pair and would produce an unperturbed duplex DNA. Here, by using quantum chemical calculations in aqueous medium, it is shown that the P and Z molecules can be modified with the help of electron-withdrawing and -donating substituents mainly found in B-DNA to generate new bases that can produce even more stable base pairs. Among the various bases studied, P3, P4, Z3, and Z5 are found to produce base pairs, which are about 2-15 kcal/mol more stable than the P-Z base pair. It is further shown that these base pairs can be stacked onto the G-C and A-T base pairs to produce stable dimers. The consecutive stacking of these base pairs is found to yield even more stable dimers. The influence of charge penetration effects and backbone atoms in stabilizing these dimers are also discussed. It is thus proposed that the P3, P4, Z3, and Z5 would form promiscuous artificial genetic information system and can be used for different biological applications. However, the evaluations of the dynamical effects of these bases in DNA-containing several nucleotides and the efficacy of DNA polymerases to replicate these bases would provide more insights.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Khamaria, Jabalpur 482005 , India
| | - P Das
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Khamaria, Jabalpur 482005 , India
| | - B Behera
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Khamaria, Jabalpur 482005 , India
| | - P C Mishra
- Department of Physics , Banaras Hindu University , Varanasi 221005 , India
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22
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Zhang Y, Petit E, Barboiu M. Multivalent Dendrimers and their Differential Recognition of Short Single-Stranded DNAs of Various Length and Sequence. Chempluschem 2018; 83:354-360. [PMID: 31957369 DOI: 10.1002/cplu.201800081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/22/2018] [Indexed: 12/18/2022]
Abstract
Polycationic dendrimers were generated through simple and versatile reversible amine/aldehyde-imine chemistry. The inherent CD spectroscopic signal arising from the helical structures of single-stranded DNA (ssDNA) undergoes a dramatic amplification in the presence of the synthesised polycationic dendrimers. Compared to the first-generation core molecule, the second-generation dendrimer shows high spectroscopic responses upon chiral recognition of short ssDNA, owing to the combination of self-assembly and multivalency effects. The maximum signal variation is reached at the molar ratio at which the ratio between the negative charges in ssDNA balance the positive charges of the dendrimers, thus the approach enables differential recognition of ssDNAs of different lengths. Altogether, these results accelerate the simple and systematic discovery of efficient adaptive molecules for biomimetic recognition of ssDNA with high accuracy.
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Affiliation(s)
- Yan Zhang
- Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France.,School of Pharmaceutical Sciences, Jiangnan University, Lihu Road 1800, 214122, Wuxi, P. R. China
| | - Eddy Petit
- Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
| | - Mihail Barboiu
- Institut Européen des Membranes, Adaptive Supramolecular Nanosystems Group, University of Montpellier, ENSCM, CNRS, Place Eugène Bataillon, CC 047, 34095, Montpellier, France
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23
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SAMANTA SUDIPTA, RAGHUNATHAN DEVANATHAN, MUKHERJEE SANCHITA, SANYAL BIPLAB. DEPENDENCE OF HOMO–LUMO GAP OF DNA BASE PAIR STEPS ON TWIST ANGLE: A DENSITY FUNCTIONAL APPROACH. J BIOL SYST 2018. [DOI: 10.1142/s021833901850002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electronic structure calculations of all 10 unique base pair (bp) steps have been calculated to study the interaction energies of the bp steps, density of states (DOS), projected density of states (pDOS) using the density functional theory (DFT). Plane wave basis with ultrasoft pseudo-potential method has been used within the local density approximation (LDA) for the exchange correlation functional. Electron densities of the bp steps corresponding to HOMO and LUMO level have been calculated to understand the difference in stacking energies of the bp steps. The variation of HOMO–LUMO gap (g) of all possible bp steps on twist angle has been studied. We have observed that out of the 10 bp steps, 4 purine–purine bp steps (d(AA), d(GG), d(AG) and d(GA)), show significant variation of [Formula: see text] on twist angle. The observed variation on twist angle of d(AA) bp step has been explained by the calculated DOS and electron densities.
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Affiliation(s)
- SUDIPTA SAMANTA
- BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, Republic of Singapore 138602, Singapore
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - DEVANATHAN RAGHUNATHAN
- Prochem Solutions Pte. Ltd., 89C Science Park Drive, The Rutherford, # 04-13, Singapore Science Park 1, Singapore 118261, Singapore
| | - SANCHITA MUKHERJEE
- Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal 741246, India
| | - BIPLAB SANYAL
- Department of Physics and Astronomy, Uppsala University, Box-516, 75120 Uppsala, Sweden
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24
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Smith LG, Zhao J, Mathews DH, Turner DH. Physics-based all-atom modeling of RNA energetics and structure. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 8. [PMID: 28815951 DOI: 10.1002/wrna.1422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/03/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422.
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Affiliation(s)
- Louis G Smith
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Jianbo Zhao
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY, USA
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25
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines. Biophys Chem 2018; 234:24-33. [PMID: 29407768 DOI: 10.1016/j.bpc.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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26
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Jahiruddin S, Mandal N, Datta A. Structure and Electronic Properties of Unnatural Base Pairs: The Role of Dispersion Interactions. Chemphyschem 2017; 19:67-74. [PMID: 29139595 DOI: 10.1002/cphc.201700997] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Indexed: 12/18/2022]
Abstract
Recent reports of the successful incorporation of unnatural base pairs (UBPs), such as d5SICS-dNaM, in the gene sequence and replication with DNA is an important milestone in synthetic biology. Followed by this, several other UBPs, such as dTPT3-dNaM, dTPT3-dFIMO, dTPT3-IMO, dTPT3-FEMO, FTPT3-NaM, FTPT3-FIMO, FTPT3-IMO, and FTPT3-FEMO, have demonstrated similar or better retention and fidelity inside cells. Of these base pairs, dNaM-dTPT3 has been optimized to be a better fit inside a pAIO plasmid. Based on both implicit and explicit dispersion-corrected density functional theory (DFT) calculations, we show that although this set of UBPs is significantly diverse in elemental and structural configuration, the members do share a common trait of favoring a slipped parallel stacked dimer arrangement. Unlike the natural bases (A, T, G, C, and U), this set of UBPs has a negligible affinity for a Watson-Crick (WC)-type planar structure because they are invariably more stable within slipped parallel stacked orientations. We also observed that all the UBPs have either similar or higher binding energies with the natural bases in similar stacked orientations. When arranged between two natural base pairs, the UBPs exhibited a binding energy similar to that of three-base sequences of natural bases. Our computational data show that the most promising base pairs are 5SICS-NaM, TPT3-NaM, and TPT3-FEMO. These results are consistent with recent progress on experimental research into UBPs along with our previous calculations on the d5SICS-dNaM pair and, therefore, strengthen the hypothesis that hydrogen bonding might not be absolutely essential and that interbase stacking dispersion interactions play a key role in the stabilization of genetic materials.
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Affiliation(s)
- Sk Jahiruddin
- Department of Physics, Sister Nibedita Government General Degree College for Girls, 20B Judges Court Road, Hastings House, Kolkata, 700027, West Bengal, India
| | - Nilangshu Mandal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
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27
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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28
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Nazarychev VM, Larin SV, Lyulin AV, Dingemans T, Kenny JM, Lyulin SV. Atomistic Molecular Dynamics Simulations of the Initial Crystallization Stage in an SWCNT-Polyetherimide Nanocomposite. Polymers (Basel) 2017; 9:polym9100548. [PMID: 30965851 PMCID: PMC6418835 DOI: 10.3390/polym9100548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/13/2017] [Accepted: 10/19/2017] [Indexed: 01/23/2023] Open
Abstract
Crystallization of all-aromatic heterocyclic polymers typically results in an improvement of their thermo-mechanical properties. Nucleation agents may be used to promote crystallization, and it is well known that the incorporation of nanoparticles, and in particular carbon-based nanofillers, may induce or accelerate crystallization through nucleation. The present study addresses the structural properties of polyetherimide-based nanocomposites and the initial stages of polyetherimide crystallization as a result of single-walled carbon nanotube (SWCNT) incorporation. We selected two amorphous thermoplastic polyetherimides ODPA-P3 and aBPDA-P3 based on 3,3′,4,4′-oxydiphthalic dianhydride (ODPA), 2,3′,3,4′-biphenyltetracarboxylic dianhydride (aBPDA) and diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (P3) and simulated the onset of crystallization in the presence of SWCNTs using atomistic molecular dynamics. For ODPA-P3, we found that the planar phthalimide and phenylene moieties show pronounced ordering near the CNT (carbon nanotube) surface, which can be regarded as the initial stage of crystallization. We will discuss two possible mechanisms for ODPA-P3 crystallization in the presence of SWCNTs: the spatial confinement caused by the CNTs and π–π interactions at the CNT-polymer matrix interface. Based on our simulation results, we propose that ODPA-P3 crystallization is most likely initiated by favorable π–π interactions between the carbon nanofiller surface and the planar ODPA-P3 phthalimide and phenylene moieties.
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Affiliation(s)
- Victor M Nazarychev
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31 (V.O.), St. Petersburg 199004, Russia.
| | - Sergey V Larin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31 (V.O.), St. Petersburg 199004, Russia.
| | - Alexey V Lyulin
- Theory of Polymers and Soft Matter Group, Technische Universiteit Eindhoven, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Theo Dingemans
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Murray Hall 1113, 121 South Road, Chapel Hill, NC 27599-3050, USA.
| | - Jose M Kenny
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31 (V.O.), St. Petersburg 199004, Russia.
- Materials Science and Technology Centre, University of Perugia, Loc. Pentima, 4, 05100 Terni, Italy.
| | - Sergey V Lyulin
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bol'shoi pr. 31 (V.O.), St. Petersburg 199004, Russia.
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29
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Molt RW, Georgiadis MM, Richards NG. Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations. Nucleic Acids Res 2017; 45:3643-3653. [PMID: 28334863 PMCID: PMC5397145 DOI: 10.1093/nar/gkx144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/12/2017] [Accepted: 02/24/2017] [Indexed: 12/25/2022] Open
Abstract
Z Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure. In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a 'control' oligonucleotide in which nucleobase pairs are replaced by . The molecular origins of these structural changes are likely associated with at least two differences between and . First, the electrostatic properties of differ from in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with π-electrons of the adjacent base.
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Affiliation(s)
- Robert W. Molt
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, FL 32940, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
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30
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Lemkul JA, MacKerell AD. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics. J Chem Theory Comput 2017; 13:2053-2071. [PMID: 28399366 DOI: 10.1021/acs.jctc.7b00067] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.
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Affiliation(s)
- Justin A Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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31
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Yurenko YP, Novotný J, Marek R. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry 2017; 23:5573-5584. [PMID: 28225208 DOI: 10.1002/chem.201700236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/30/2022]
Abstract
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.
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Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
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32
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Abstract
More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the "sugar" GC DNA model, and obtain the potentials of the CG interactions between the sites by the "bottom-up" approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions. Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.
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33
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Zhang C, Bell D, Harger M, Ren P. Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases. J Chem Theory Comput 2017; 13:666-678. [PMID: 28030769 PMCID: PMC5312700 DOI: 10.1021/acs.jctc.6b00918] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - David Bell
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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34
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Albrecht L, Wilson KA, Wetmore SD. Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4. Molecules 2016; 21:molecules21070822. [PMID: 27347908 PMCID: PMC6273265 DOI: 10.3390/molecules21070822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 11/25/2022] Open
Abstract
Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1’–C1’ base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases.
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Affiliation(s)
- Laura Albrecht
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
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35
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Jambrec D, Haddad R, Lauks A, Gebala M, Schuhmann W, Kokoschka M. DNA Intercalators for Detection of DNA Hybridisation: SCS(MI)-MP2 Calculations and Electrochemical Impedance Spectroscopy. Chempluschem 2016; 81:604-612. [DOI: 10.1002/cplu.201600173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Raoudha Haddad
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Anna Lauks
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Magdalena Gebala
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
- Department of Biochemistry; Stanford University; Stanford CA 94305 USA
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
| | - Malte Kokoschka
- Analytical Chemistry-Center for Electrochemical Sciences (CES); Ruhr-Universität Bochum; Universitätstrasse 150 44780 Bochum Germany
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36
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Gkionis K, Kruse H, Šponer J. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. J Chem Theory Comput 2016; 12:2000-16. [DOI: 10.1021/acs.jctc.5b01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Konstantinos Gkionis
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
- CEITEC
− Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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37
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Nguyen K, Whitford PC. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nat Commun 2016; 7:10586. [PMID: 26838673 PMCID: PMC4742886 DOI: 10.1038/ncomms10586] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/31/2015] [Indexed: 12/01/2022] Open
Abstract
Translocation of mRNA and tRNA through the ribosome is associated with large-scale rearrangements of the head domain in the 30S ribosomal subunit. To elucidate the relationship between 30S head dynamics and mRNA–tRNA displacement, we apply molecular dynamics simulations using an all-atom structure-based model. Here we provide a statistical analysis of 250 spontaneous transitions between the A/P–P/E and P/P–E/E ensembles. Consistent with structural studies, the ribosome samples a chimeric ap/P–pe/E intermediate, where the 30S head is rotated ∼18°. It then transiently populates a previously unreported intermediate ensemble, which is characterized by a ∼10° tilt of the head. To identify the origins of head tilting, we analyse 781 additional simulations in which specific steric features are perturbed. These calculations show that head tilting may be attributed to specific steric interactions between tRNA and the 30S subunit (PE loop and protein S13). Taken together, this study demonstrates how molecular structure can give rise to large-scale collective rearrangements. During protein elongation, the translocation of mRNA and tRNA molecules across the 30S ribosomal subunit is associated with large-scale motions of the 30S head domain. Here the authors carry out MD simulations to probe the associated steric interactions and identify novel tilting motions during the late stages of translocation.
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Affiliation(s)
- Kien Nguyen
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
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38
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Kulkarni M, Mukherjee A. Computational Approach to Explore the B/A Junction Free Energy in DNA. Chemphyschem 2016; 17:147-54. [PMID: 26538133 DOI: 10.1002/cphc.201500690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/07/2022]
Abstract
Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.
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Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune-, 411008, India.
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39
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Kocsis I, Rotaru A, Legrand YM, Grosu I, Barboiu M. Supramolecular rulers enabling selective detection of pure short ssDNA via chiral self-assembly. Chem Commun (Camb) 2016; 52:386-9. [DOI: 10.1039/c5cc08283h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
TPA propellers appear to be compatible with the general requirements for amplified chiral supramolecular rulers used to determine the number of base pairs of short ssDNAs.
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Affiliation(s)
- Istvan Kocsis
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
| | - Alexandru Rotaru
- “Petru Poni” Institute of Macromolecular Chemistry of Romanian Academy – 41A
- Iasi
- Romania
| | - Yves-Marie Legrand
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
| | - Ion Grosu
- Chemistry Department
- Babeş-Bolyai University
- 400028 Cluj -Napoca
- Romania
| | - Mihail Barboiu
- Adaptive Supramolecular Nanosystems Group
- Institut Européen des Membranes
- University of Montpellier/ENSCM/CNRS 5635
- Pl. Eugène Bataillon
- 34095 Montpellier, Cedex 5
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40
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41
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Abstract
We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
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42
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Bartocci A, Frati F, Roncaratti LF, Cappelletti D, Tarantelli F, Belpassi L, Pirani F. Anab initioelectronic density study of the CH4–Ar, CH4–Xe, CH4–H2O and CH4–H2S complexes: insights into the nature of the intermolecular interaction. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1100344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Karabıyık H, Sevinçek R, Karabıyık H. π-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds? Phys Chem Chem Phys 2015; 16:15527-38. [PMID: 24953339 DOI: 10.1039/c4cp00997e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The results from absolutely localized molecular orbital (ALMO)-energy decomposition analysis (EDA) and ALMO-charge transfer analysis (CTA) at M06-2X/cc-pVTZ level reveal that double-proton transfer (DPT) reactions through base pairing H-bonds have nonignorable effects on the stacking energies of dinucleotide steps, which introduces us to a novel stabilization (or destabilization) factor in the DNA duplex. Thus, intra- and inter-strand base stacking interactions are coalesced with each other mediated by H-bridged quasirings between base pairs. Changes in stacking energies of dinucleotide steps depending on the positions of H atoms are due to variations in local aromaticities of individual nucleobases, manifesting π-cooperativity effects. CT analyses show that dispersion forces in dinucleotide steps can lead to radical changes in the redox properties of nucleobases, in particular those of adenine and guanine stacked dimers in a strand. Besides Watson-Crick rules, novel base pairing rules were propounded by considering CT results. According to these, additional base pairing through π-stacks of nucleobases in dinucleotide steps does not cause any intrinsic oxidative damage to the associated nucleobases throughout DPT.
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Affiliation(s)
- Hande Karabıyık
- Department of Physics, Dokuz Eylül University, 35160-Tınaztepe, İzmir, Turkey.
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44
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Parker TM, Sherrill CD. Assessment of Empirical Models versus High-Accuracy Ab Initio Methods for Nucleobase Stacking: Evaluating the Importance of Charge Penetration. J Chem Theory Comput 2015; 11:4197-204. [DOI: 10.1021/acs.jctc.5b00588] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Trent M. Parker
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- Center for Computational
Molecular Science and Technology, School of Chemistry and Biochemistry,
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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45
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Gresh N, Sponer JE, Devereux M, Gkionis K, de Courcy B, Piquemal JP, Sponer J. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. J Phys Chem B 2015; 119:9477-95. [DOI: 10.1021/acs.jpcb.5b01695] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Judit E. Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mike Devereux
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH 4056, Switzerland
| | - Konstantinos Gkionis
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
| | - Benoit de Courcy
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jiri Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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46
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Parrish RM, Sherrill CD. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition. J Chem Phys 2015; 141:044115. [PMID: 25084889 DOI: 10.1063/1.4889855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Jahiruddin S, Datta A. What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds. J Phys Chem B 2015; 119:5839-45. [DOI: 10.1021/acs.jpcb.5b03293] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sk Jahiruddin
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur, 700032 Kolkata, West Bengal, India
| | - Ayan Datta
- Department
of Spectroscopy, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road,
Jadavpur, 700032 Kolkata, West Bengal, India
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays. Sci Rep 2014; 4:7391. [PMID: 25487346 PMCID: PMC4260214 DOI: 10.1038/srep07391] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/20/2014] [Indexed: 01/18/2023] Open
Abstract
The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10−14 cm2 and 7.06 · 10−14 cm2. The highest cross section was found for 5′-TT(ATA)3TT and 5′-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.
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