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Jiang C, Liu Y, Wang L, Lu F. Interaction between Heavy Water and Single-Strand DNA: A SERS Study. Molecules 2022; 27:molecules27186023. [PMID: 36144761 PMCID: PMC9505314 DOI: 10.3390/molecules27186023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/03/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental D2O. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between D2O and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing D2O proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and D2O and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and D2O. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules.
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Affiliation(s)
- Chengshun Jiang
- College of Pharmacy, Naval Medical University, Shanghai 200433, China
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Yan Liu
- College of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Lianghua Wang
- College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Feng Lu
- College of Pharmacy, Naval Medical University, Shanghai 200433, China
- College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Naval Medical University, Shanghai 200433, China
- Correspondence:
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2
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Wang Y, Li G, Meng T, Qi L, Yan H, Wang Z. Molecular insights into the selective binding mechanism targeting parallel human telomeric G-quadruplex. J Mol Graph Model 2021; 110:108058. [PMID: 34736054 DOI: 10.1016/j.jmgm.2021.108058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022]
Abstract
Stabilizing human telomere DNA G-quadruplex (G4) proves a promising anti-cancer strategy. Though plenty of G4 stabilizing molecules have been reported, little is known about their selective binding mechanism among various G4s. Recently, a designed monohydrazone derivative (compound 15) was reported to display specific preference in binding and stabilizing parallel human telomeric G4. To reveal the selective binding mechanism, a comparative theoretical investigation was performed on two monohydrazone derivatives (compounds 1 and 15) and three telomeric G4s showing parallel, hybrid-I, and hybrid-II conformations. Two probable binding modes, i.e. the end-stacking binding and the groove binding, were predicted by molecular dockings for each monohydrazone in its binding with the telomeric G4s. Further long-timescale molecular dynamics simulations reveal the conversion from the groove binding to the end-stacking binding for both compounds, indicating the preference of the end-stacking binding mode. Structural analysis together with binding free energy calculations show that the van der Waals interaction plays a leading role in ranking the binding affinity. By forming extensive van der Waals interactions, the parallel G4-15 binding complex shows the highest binding affinity, and the corresponding compound 15 exhibits the strongest stabilizing effect to the telomeric G4. These findings agree well with the experimental observations. Through characterizing the selective binding between monohydrazones and telomeric G4s at the atomic level, the current study provides support to the design of novel selective stabilizers targeting telomeric G4s.
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Affiliation(s)
- Yue Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Guo Li
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan Province, 571199, China
| | - Tong Meng
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China
| | - Lin Qi
- Railway Police College, Zhengzhou, Henan Province, 450053, China
| | - Hui Yan
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong Province, 252059, China.
| | - Zhiguo Wang
- Institute of Ageing Research, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, China.
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3
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Zhang Y, El Omari K, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 2020; 48:9886-9898. [PMID: 32453431 PMCID: PMC7515729 DOI: 10.1093/nar/gkaa439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.
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Affiliation(s)
- Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, UK
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Science, Huazhong Agricultural University, Wuhan 430070, China
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4
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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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5
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Islam B, Stadlbauer P, Krepl M, Havrila M, Haider S, Sponer J. Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations. J Chem Theory Comput 2018; 14:5011-5026. [DOI: 10.1021/acs.jctc.8b00543] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Barira Islam
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marek Havrila
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of
Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Jiri Sponer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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Ghoshdastidar D, Bansal M. Dynamics of physiologically relevant noncanonical DNA structures: an overview from experimental and theoretical studies. Brief Funct Genomics 2018; 18:192-204. [DOI: 10.1093/bfgp/ely026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 12/23/2022] Open
Abstract
Abstract
DNA is a complex molecule with phenomenal inherent plasticity and the ability to form different hydrogen bonding patterns of varying stabilities. These properties enable DNA to attain a variety of structural and conformational polymorphic forms. Structurally, DNA can exist in single-stranded form or as higher-order structures, which include the canonical double helix as well as the noncanonical duplex, triplex and quadruplex species. Each of these structural forms in turn encompasses an ensemble of dynamically heterogeneous conformers depending on the sequence composition and environmental context. In vivo, the widely populated canonical B-DNA attains these noncanonical polymorphs during important cellular processes. While several investigations have focused on the structure of these noncanonical DNA, studying their dynamics has remained nontrivial. Here, we outline findings from some recent advanced experimental and molecular simulation techniques that have significantly contributed toward understanding the complex dynamics of physiologically relevant noncanonical forms of DNA.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Mukherjee D, Bhattacharyya D. Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. J Mol Model 2017; 23:300. [DOI: 10.1007/s00894-017-3470-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/10/2017] [Indexed: 10/18/2022]
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8
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Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J. Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J Chem Theory Comput 2017; 13:3911-3926. [PMID: 28657760 DOI: 10.1021/acs.jctc.7b00257] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG]4 GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]4 simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na+ ions move inside the GQs in a concerted manner, while larger relocations of the K+ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K+ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.
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Affiliation(s)
- Marek Havrila
- 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
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , 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, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 771 46 Olomouc, 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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Rebič M, Laaksonen A, Šponer J, Uličný J, Mocci F. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models. J Phys Chem B 2016; 120:7380-91. [PMID: 27379924 DOI: 10.1021/acs.jpcb.6b06485] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew model are found to be closest to the experimental data at all of the studied ion concentrations.
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Affiliation(s)
- Matúš Rebič
- Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.,Science for Life Laboratory (SciLifelab) , 17121 Solna, Sweden
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.,Science for Life Laboratory (SciLifelab) , 17121 Solna, Sweden.,Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University , 7600 Stellenbosch, South Africa.,Department of Chemical and Geological Sciences, University of Cagliari , I-09042 Monserrato, Italy
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic (AVČR) , Kralovopolska 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology (CEITEC) , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Francesca Mocci
- Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University , 10691 Stockholm, Sweden.,Science for Life Laboratory (SciLifelab) , 17121 Solna, Sweden.,Department of Chemical and Geological Sciences, University of Cagliari , I-09042 Monserrato, Italy
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