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Psarakis CA, Fidelis TT, Chin KB, Journaux B, Kavner A, Sarker P, Styczinski MJ, Vance SD, Wei T. Electrical Conductivity of Subsurface Ocean Analogue Solutions from Molecular Dynamics Simulations. ACS EARTH & SPACE CHEMISTRY 2024; 8:1146-1153. [PMID: 38919853 PMCID: PMC11194852 DOI: 10.1021/acsearthspacechem.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Investigating the habitability of ocean worlds is a priority of current and future NASA missions. The Europa Clipper mission will conduct approximately 50 flybys of Jupiter's moon Europa, returning a detailed portrait of its interior from the synthesis of data from its instrument suite. The magnetometer on board has the capability of decoupling Europa's induced magnetic field to high precision, and when these data are inverted, the electrical conductivity profile from the electrically conducting subsurface salty ocean may be constrained. To optimize the interpretation of magnetic induction data near ocean worlds and constrain salinity from electrical conductivity, accurate laboratory electrical conductivity data are needed under the conditions expected in their subsurface oceans. At the high-pressure, low-temperature (HPLT) conditions of icy worlds, comprehensive conductivity data sets are sparse or absent from either laboratory data or simulations. We conducted molecular dynamics simulations of candidate ocean compositions of aqueous NaCl under HPLT conditions at multiple concentrations. Our results predict electrical conductivity as a function of temperature, pressure, and composition, showing a decrease in conductivity as the pressure increases deeper into the interior of an icy moon. These data can guide laboratory experiments at conditions relevant to icy moons and can be used in tandem to forward-model the magnetic induction signals at ocean worlds and compare with future spacecraft data. We discuss implications for the Europa Clipper mission.
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Affiliation(s)
- Catherine A. Psarakis
- University
of California, Los Angeles, Los
Angeles, California 90095, United States
- Jet
Propulsion Laboratory, California Institute
of Technology, Pasadena, California 91011, United States
| | | | - Keith B. Chin
- Jet
Propulsion Laboratory, California Institute
of Technology, Pasadena, California 91011, United States
| | - Baptiste Journaux
- University
of Washington, Seattle, Seattle, Washington 98195, United States
| | - Abby Kavner
- University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Pranab Sarker
- University
of South Carolina, Columbia, South Carolina 29208, United States
| | | | - Steven D. Vance
- Jet
Propulsion Laboratory, California Institute
of Technology, Pasadena, California 91011, United States
| | - Tao Wei
- University
of South Carolina, Columbia, South Carolina 29208, United States
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2
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Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
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Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
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3
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Jarczewska M, Sokal M, Olszewski M, Malinowska E. Studies on the Aptasensor Miniaturization for Electrochemical Detection of Lead Ions. BIOSENSORS 2024; 14:110. [PMID: 38392029 PMCID: PMC10886534 DOI: 10.3390/bios14020110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Lead poses severe effects on living organisms, and since Pb2+ ions tend to accumulate in different organs, it is crucial to monitor Pb2+ concentration in samples such as water and soil. One of the approaches is the utilization of biosensors combined with aptamer-based layers for the electrochemical detection of lead ions. Herein, we present the studies of applying miniaturized screen-printed transducers as solid surfaces to fabricate aptamer layers. As the research is the direct continuation of our previous studies regarding the use of gold disk electrodes, the working parameters of elaborated aptasensors were defined, including the range of linear response (10-100 nM), selectivity as well as stability, regeneration, and feasibility of application for the analysis of real samples. This was achieved using voltammetric techniques including cyclic and square-wave voltammetry in the presence of methylene blue redox indicator.
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Affiliation(s)
- Marta Jarczewska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marta Sokal
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, 00-664 Warsaw, Poland;
| | - Elzbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Center for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, 19 Poleczki, 02-822 Warsaw, Poland
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Otovat F, Bozorgmehr MR, Mahmoudi A, Morsali A. Porphyrin-based ligand interaction with G-quadruplex: Metal cation effects. J Mol Recognit 2023; 36:e3017. [PMID: 37025015 DOI: 10.1002/jmr.3017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
The G-quadruplex planar-ligand complex is used to detect heavy metal cations such as Ag+ , Cu2+ , Pb2+ , Hg2+ , organic molecules, nucleic acids, and proteins. The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ4 -pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ4 -pyridine-4-yl) porphyrin (L3), coming from the porphyrin family, with G-quadruplex obtained from human DNA telomeres in the presence of lithium, sodium, potassium, rubidium, cesium, magnesium, and calcium ions was studied by molecular dynamics simulation. When G-quadruplex containing divalent ions of magnesium and calcium interacts with L1, L2, and L3 ligands, the hydrogen bonds of the lower G-quadruplex sheet are more affected by ligands and the distance between guanines in the lower tetrad increases. In the case of G-quadruplex interactions containing monovalent ions with ligands, the hydrogen bond between the sheets does not follow a specific trend. For example, in the presence of lithium ions, the upper and middle sheets are more affected by ligands, while they are less affected by ligands in the presence of sodium. The binding pocket and the binding energy of the three ligands to the G-quadruplex were also obtained in the various systems. The results show that ligands make the G-quadruplex more stable through the penetration between the sheets and the interaction with the loops. Among the ligands mentioned, the interaction level of the ligand L2 is greater than the others. Our calculations are consistent with the previous experimental observations so that it can help to understand the molecular mechanism of porphyrin interaction and its derivatives with the G-quadruplex.
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Affiliation(s)
- Fahimeh Otovat
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | | | - Ali Mahmoudi
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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5
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Pal S, Paul S. Theoretical investigation of conformational deviation of the human parallel telomeric G-quadruplex DNA in the presence of different salt concentrations and temperatures under confinement. Phys Chem Chem Phys 2021; 23:14372-14382. [PMID: 34179908 DOI: 10.1039/d0cp06702d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Various experimental reports address the stability of G-quadruplex DNA inside a close confinement such as α-hemolysin, nanocavity water pool and different metal-organic-frameworks (MOFs). To understand the conformational change of G-quadruplex DNA at the atomistic level, we have carried out a total of 40 μs simulation run under both non-polar and polar confinement conditions. To investigate the dynamics, we have considered two different KCl salt concentrations, i.e., 0.47 M (minimal salt concentration) and higher than 2 M (higher salt concentration), at two distinct temperatures, 300 K and 350 K. Here, we have observed that the human telomeric G-quadruplex DNA deviates more from its crystal structure at minimal salt concentration under both non-polar and polar confinement conditions. Besides, the loop regions deviate and fluctuate more compared to the other regions, i.e., sugar-phosphate backbone and tetrad regions. The presence of K+ ions is found to be primarily responsible for this phenomenon. From the spatial density function (SDF) plots, a higher density of K+ ions is observed in the backbone region. Furthermore, from the residue-wise first solvation shell estimation, we have noticed that the K+ ions mainly accumulate in the tetrad region under both non-polar and polar confinement conditions due to which the tetrad regions are more rigid than the loop regions. Higher salt concentration results in increased rigidity of the G-quadruplex DNA. Our study provides valuable insight into the conformational deviation of the G-quadruplex DNA under nanoconfinement conditions.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam-781039, India.
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam-781039, India.
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Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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8
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Pal S, Paul S. Understanding The Role of Reline, a Natural DES, on Temperature-Induced Conformational Changes of C-Kit G-Quadruplex DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:3123-3136. [PMID: 32207949 DOI: 10.1021/acs.jpcb.0c00644] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The noncanonical guanine-rich DNAs have drawn particular attention to the scientific world due to their controllable diverse and polymorphic structures. Apart from biological and medical significance, G-quadruplex DNAs are widely used in various fields such as nanotechnology, nanomachine, biosensors, and biocatalyst. So far, the applications of the G-quadruplex DNA are mainly limited in the water medium. Recently, a new generation of solvent named deep eutectic solvent (DES) has become very popular and has been widely used as a reaction medium of biocatalytic reactions and long-term storage medium for nucleic acids, even at high temperature. Hence, it is essential to understand the role of DES on temperature-induced conformational changes of a G-quadruplex DNA. In this research work, we have explored the temperature-mediated conformational dynamics of c-kit oncogene promoter G-quadruplex DNA in reline medium in the temperature range of 300-500 K, using a total of 10 μs unbiased all-atom molecular dynamics simulation. Here, from RMSD, RMSF, Rg and principal component analyses, we notice that the c-kit G-quadruplex DNA is stable up to 450 K in reline medium. However, it unfolds in water medium at 450 K. It is found that the hydrogen bonding interactions between c-kit G-quadruplex DNA and reline play a key role in the stabilization of the G-quadruplex DNA even at high temperature. Furthermore, in this work we have observed a very interesting and distinctive phenomenon of the central cation of the G-quadruplex DNA. Its position was seen to fluctuate between the two tetrad cores, that is, the region between tetrad-1 and tetrad-2 and that between tetrad-2 and tetrad-3 and vice versa at 450 and 500 K in reline medium which is absent in water medium at 450 K. Moreover, the rate of its oscillation is increased when temperature is increased.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India, 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, India, 781039
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9
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Milovanović B, Stanojević A, Etinski M, Petković M. Intriguing Intermolecular Interplay in Guanine Quartet Complexes with Alkali and Alkaline Earth Cations. J Phys Chem B 2020; 124:3002-3014. [DOI: 10.1021/acs.jpcb.0c01165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Ana Stanojević
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
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10
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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11
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García-Arriaga M, Acosta-Santiago M, Cruz A, Rivera-Rivera JM, López GE, Rivera JM. Probing the Limits of Supramolecular G-Quadruplexes Using Atomistic Molecular Dynamics Simulations. Inorganica Chim Acta 2017; 468:209-222. [PMID: 29062143 PMCID: PMC5649357 DOI: 10.1016/j.ica.2017.08.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Guanosine and related derivatives self-assemble in the presence of cations like potassium into supramolecular G-quadruplexes (SGQs), where four guanine moieties form planar tetrads (T) that coaxially stack into columnar aggregates with broad size distributions. However, SGQs made from 8-aryl-2'-deoxyguanosine derivatives (8ArGs), form mostly octamers, or two-tetrad (2T)-SGQs, while some form dodecamers (3T-SGQs), or hexadecamers (4T-SGQs), and none reported to date form higher assemblies. A theoretical model that addresses the configurational space available for the multiple pathways available for 8ArGs to self-assemble into SGQs is used to frame a series of molecular dynamics simulations (MDS) with selected SGQs. Some key insights from this work include: (a) The predicted entropic costs are not significantly higher for SGQs with more subunits due to their hierarchical assembly pathways; (b) The multiple isomeric SGQs vary in the interfacial contacts between consecutive tetrads, due to their two distinct sides (head, h; tail, t), with the MDS supporting the predicted order of stability of hh > ht > tt for octamers. (c) Such order also applies to dodecamers and hexadecamers, but with context-dependent exceptions due to strong allosteric effects. (d) The main factor disfavoring the tt interface is the repulsive dipolar interactions between the O4' from ribose moieties on adjacent tetrads. (e) SGQs with 5 or more tetrads are disfavored because the attractive interactions are not large or strong enough to overcome the many repulsive forces resulting from the addition of further tetrads. We expect these findings provide some guidelines to enable the further development of SGQs into functional materials.
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Affiliation(s)
- Marilyn García-Arriaga
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Maxier Acosta-Santiago
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Antony Cruz
- School of Natural and Social Sciences, Department of Chemistry, Lehman College-CUNY, Bronx, NY 10468
| | - José M Rivera-Rivera
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
| | - Gustavo E López
- School of Natural and Social Sciences, Department of Chemistry, Lehman College-CUNY, Bronx, NY 10468
| | - José M Rivera
- Department of Chemistry and Molecular Sciences Research Center, University of Puerto Rico at Río Piedras, San Juan, PR, 00926
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12
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Distinct differences in metal ion specificity of RNA and DNA G-quadruplexes. J Biol Inorg Chem 2016; 21:975-986. [PMID: 27704222 DOI: 10.1007/s00775-016-1393-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023]
Abstract
RNA G-quadruplexes, as their well-studied DNA analogs, require the presence of cations to fold and remain stable. This is the first comprehensive study on the interaction of RNA quadruplexes with metal ions. We investigated the formation and stability of two highly conserved and biologically relevant RNA quadruplex-forming sequences (24nt-TERRA and 18nt-NRAS) in the presence of several monovalent and divalent metal ions, namely Li+, Na+, K+, Rb+, Cs+, NH4+, Mg2+, Ca2+, Sr2+, and Ba2+. Circular dichroism was used to probe the influence of these metal ions on the folded fraction of the parallel G-quadruplexes, and UV thermal melting experiments allowed to assess the relative stability of the structures in each cationic condition. Our results show that the RNA quadruplexes are more stable than their DNA counterparts under the same buffer conditions. We have observed that the addition of mainly Na+, K+, Rb+, NH4+, as well as Sr2+ and Ba2+ in water, shifts the equilibrium to the folded quadruplex form, whereby the NRAS sequence responds stronger than TERRA. However, only K+ and Sr2+ lead to a significant increase in the stability of the folded structures, which is consistent with their coordination to the O6 atoms from the G-quartet guanosines. Compared to the respective DNA motives, dNRAS and htelo, the RNA sequences are not stabilized by Na+ ions. Finally, the difference in response between NRAS and TERRA, as well as to the corresponding DNA sequences with respect to different metal ions, could potentially be exploited for selective targeting purposes.
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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14
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Zaccaria F, Paragi G, Fonseca Guerra C. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K+ is the best. Phys Chem Chem Phys 2016; 18:20895-904. [DOI: 10.1039/c6cp01030j] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The desolvation and size of monovalent alkali metal ions are of equal importance for the cation affinity of guanine quadruplexes.
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Affiliation(s)
- F. Zaccaria
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
| | - G. Paragi
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
- MTA-SZTE Supramolecular and Nanostructured Materials Research Group
| | - C. Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling
- Vrije Universiteit Amsterdam
- 1081 HV Amsterdam
- The Netherlands
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15
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Bergues-Pupo AE, Arias-Gonzalez JR, Morón MC, Fiasconaro A, Falo F. Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes. Nucleic Acids Res 2015; 43:7638-47. [PMID: 26170233 PMCID: PMC4551928 DOI: 10.1093/nar/gkv690] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022] Open
Abstract
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of \documentclass[12pt]{minimal}
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}{}$\rm {K}^+$\end{document} central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery.
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Affiliation(s)
- Ana Elisa Bergues-Pupo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain Departamento de Física, Universidad de Oriente, 90500 Santiago de Cuba, Cuba
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Cantoblanco, 28049 Madrid, Spain CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología, Madrid, Spain'
| | - María Carmen Morón
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alessandro Fiasconaro
- School of Mathematical Sciences, Queen Mary University of London - Mile End Road, London E1 4NS, UK
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain
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16
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Chaubey AK, Dubey KD, Ojha RP. MD simulation of LNA-modified human telomeric G-quadruplexes: a free energy calculation. Med Chem Res 2015. [DOI: 10.1007/s00044-014-1182-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Ali A, Bansal M, Bhattacharya S. Ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) prefers the parallel propeller-type human telomeric G-quadruplex DNA over its other polymorphs. J Phys Chem B 2014; 119:5-14. [PMID: 25526532 DOI: 10.1021/jp505792z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.
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Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science , Bangalore 560 012, India
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18
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Gkionis K, Kruse H, Platts JA, Mládek A, Koča J, Šponer J. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations. J Chem Theory Comput 2014; 10:1326-40. [DOI: 10.1021/ct4009969] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Konstantinos Gkionis
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Holger Kruse
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - James A. Platts
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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19
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Koirala D, Ghimire C, Bohrer C, Sannohe Y, Sugiyama H, Mao H. Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences. J Am Chem Soc 2013; 135:2235-41. [PMID: 23327686 DOI: 10.1021/ja309668t] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Single-stranded guanine (G)-rich sequences at the 3' end of human telomeres provide ample opportunities for physiologically relevant structures, such as G-quadruplexes, to form and interconvert. Population equilibrium in this long sequence is expected to be intricate and beyond the resolution of ensemble-average techniques, such as circular dichroism, NMR, or X-ray crystallography. By combining a force-jump method at the single-molecular level and a statistical population deconvolution at the sub-nanometer resolution, we reveal a complex population network with unprecedented transition dynamics in human telomeric sequences that contain four to eight TTAGGG repeats. Our kinetic data firmly establish that G-triplexes are intermediates to G-quadruplexes while long-loop G-quadruplexes are misfolded population minorities whose formation and disassembly are faster than G-triplexes or regular G-quadruplexes. The existence of misfolded DNA supports the emerging view that structural and kinetic complexities of DNA can rival those of RNA or proteins. While G-quadruplexes are the most prevalent species in all the sequences studied, the abundance of a misfolded G-quadruplex in a particular telomeric sequence decreases with an increase in the loop length or the number of long-loops in the structure. These population patterns support the prediction that in the full-length 3' overhang of human telomeres, G-quadruplexes with shortest TTA loops would be the most dominant species, which justifies the modeling role of regular G-quadruplexes in the investigation of telomeric structures.
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Affiliation(s)
- Deepak Koirala
- Department of Chemistry & Biochemistry, Kent State University, Kent, Ohio 44242, USA
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20
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New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA. J Comput Aided Mol Des 2012; 26:1355-68. [PMID: 23239169 DOI: 10.1007/s10822-012-9619-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/27/2012] [Indexed: 01/06/2023]
Abstract
G-quadruplexes are higher-order DNA and RNA structures formed from guanine-rich sequences. These structures have recently emerged as a new class of potential molecular targets for anticancer drugs. An understanding of the three-dimensional interactions between small molecular ligands and their G-quadruplex targets in solution is crucial for rational drug design and the effective optimization of G-quadruplex ligands. Thus far, rational ligand design has been focused mainly on the G-quartet platform. It should be noted that small molecules can also bind to loop nucleotides, as observed in crystallography studies. Hence, it would be interesting to elucidate the mechanism underlying how ligands in distinct binding modes influence the flexibility of G-quadruplex. In the present study, based on a crystal structure analysis, the models of a tetra-substituted naphthalene diimide ligand bound to a telomeric G-quadruplex with different modes were built and simulated with a molecular dynamics simulation method. Based on a series of computational analyses, the structures, dynamics, and interactions of ligand-quadruplex complexes were studied. Our results suggest that the binding of the ligand to the loop is viable in aqueous solutions but dependent on the particular arrangement of the loop. The binding of the ligand to the loop enhances the flexibility of the G-quadruplex, while the binding of the ligand simultaneously to both the quartet and the loop diminishes its flexibility. These results add to our understanding of the effect of a ligand with different binding modes on G-quadruplex flexibility. Such an understanding will aid in the rational design of more selective and effective G-quadruplex binding ligands.
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21
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Benda L, Straka M, Sychrovský V, Bouř P, Tanaka Y. Detection of mercury-TpT dinucleotide binding by Raman spectra: a computational study. J Phys Chem A 2012; 116:8313-20. [PMID: 22803635 DOI: 10.1021/jp3045077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.
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Affiliation(s)
- Ladislav Benda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Praha 6, Czech Republic
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22
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Akhshi P, Acton G, Wu G. Molecular dynamics simulations to provide new insights into the asymmetrical ammonium ion movement inside of the [d(G3T4G4)]2 G-quadruplex DNA structure. J Phys Chem B 2012; 116:9363-70. [PMID: 22780684 DOI: 10.1021/jp304760k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH(4)(+) ion movement inside of a bimolecular G-quadruplex DNA structure [d(G(3)T(4)G(4))](2). The free-energy landscapes obtained from ABF MD simulations suggest that the NH(4)(+) ion exiting the [d(G(3)T(4)G(4))](2) G-quadruplex stem in the direction toward the edge-type loop (denoted as the upper direction) experiences a lower free-energy barrier than that toward the diagonal loop (denoted as the lower direction) by approximately 3-4 kcal mol(-1). This result is in qualitative agreement with the previous discovery made by Šket and Plavec on the same G-quadruplex structure from (15)N NMR experiments (J. Am. Chem. Soc. 2007, 129, 8794). In the Na(+) form of the same G-quadruplex, Na(+) ion movement was found to be symmetrical, with a free-energy barrier of only 5-7 kcal mol(-1) to cross all three G-quartets, that is, [d(G(3)T(4)G(4))](2) still exhibits ion-channel-like behaviors for Na(+) ions. On the basis of the new computational results, we hypothesize that the stiffness of a G-quartet is primarily determined by the base stacking interactions within the G-quadruplex stem. Therefore, the structural origin for the asymmetrical NH(4)(+) ion movement in [d(G(3)T(4)G(4))](2) is the presence of two different modes of base stacking around the NH(4)(+) binding sites, a more stable 5'-syn-anti mode between lower and central G-quartets and a less stable 5'-anti-anti mode between upper and central G-quartets. Simulations also suggest that loop topology at the end of a G-quadruplex stem only controls the direction at which an exiting NH(4)(+) ion reaches bulk solution but does not impose significant free-energy barriers.
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Affiliation(s)
- Parisa Akhshi
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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23
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- 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
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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24
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Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study. J Comput Aided Mol Des 2012; 26:289-99. [PMID: 22456858 DOI: 10.1007/s10822-012-9548-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 01/23/2012] [Indexed: 10/28/2022]
Abstract
Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)₄. Here we report the relative stabilities of these structures under K⁺ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.
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25
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Akhshi P, Mosey NJ, Wu G. Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Akhshi P, Mosey NJ, Wu G. Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel. Angew Chem Int Ed Engl 2012; 51:2850-4. [DOI: 10.1002/anie.201107700] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Indexed: 11/09/2022]
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27
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Liu W, Fu Y, Zheng B, Cheng S, Li W, Lau TC, Liang H. Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+. J Phys Chem B 2011; 115:13051-6. [PMID: 21950308 DOI: 10.1021/jp2074489] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been shown that guanine-rich DNA can fold into a G-quadruplex with certain metal cations. The spectral characteristics, thermostability, and kinetics for the formation of a Pb(2+)-driven G-quadruplex of thrombin-binding aptamer (TBA) were measured in the current work using a combination of ultraviolet (UV) and circular dichroism (CD) spectroscopy along with stopped-flow technique. CD spectra demonstrated that TBA could fold into a unique G-quadruplex with a strong positive peak at 312 nm. Analysis of the titration data reveals that the binding stoichiometry is 1:1 for the titration of TBA with Pb(NO(3))(2), which is in accordance with the localization of the Pb(2+) ion between the adjacent G-quartets. Thermal denaturation profiles indicate that the Pb(2+)-induced intramolecular G-quadruplex is more stable than those driven by Na(+) or K(+) ions. Kinetic studies suggest that the Pb(2+)-induced folding G-quadruplex of TBA probably proceeds through the rapid formation of an intermediate Pb(2+)-TBA complex, which then isomerizes to the fully folded structure. Conformational changes transpire after the addition of Pb(NO(3))(2) to the Na(+)- or K(+)-induced G-quadruplexes, which may be attributed to the replacement of Na(+) or K(+) ions by Pb(2+) ions and the generation of a more compact structure of the Pb(2+)-TBA structure. The relaxation time, τ, of folding the G-quadruplex is reduced from 1.05 s in the presence of Pb(2+) ions alone to 0.34 s under the cooperation of initially added Na(+) ions, while τ is increased to 8.33 s under the competition of initially added K(+) ions.
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Affiliation(s)
- Wei Liu
- Hefei National Laboratory for Physics Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, P R China
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28
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Andrushchenko V, Tsankov D, Krasteva M, Wieser H, Bour P. Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism. J Am Chem Soc 2011; 133:15055-64. [PMID: 21823674 DOI: 10.1021/ja204630k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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29
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Maruyama Y, Matsushita T, Ueoka R, Hirata F. Solvent and Salt Effects on Structural Stability of Human Telomere. J Phys Chem B 2011; 115:2408-16. [DOI: 10.1021/jp1096019] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yutaka Maruyama
- Department of Theoretical Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
| | - Taku Matsushita
- Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Ryuichi Ueoka
- Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Fumio Hirata
- Department of Theoretical Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
- Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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30
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Hou JQ, Tan JH, Wang XX, Chen SB, Huang SY, Yan JW, Chen SH, Ou TM, Luo HB, Li D, Gu LQ, Huang ZS. Impact of planarity of unfused aromatic molecules on G-quadruplex binding: Learning from isaindigotone derivatives. Org Biomol Chem 2011; 9:6422-36. [DOI: 10.1039/c1ob05884c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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31
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Hou JQ, Chen SB, Tan JH, Ou TM, Luo HB, Li D, Xu J, Gu LQ, Huang ZS. New Insights into the Structures of Ligand−Quadruplex Complexes from Molecular Dynamics Simulations. J Phys Chem B 2010; 114:15301-10. [DOI: 10.1021/jp106683n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jin-Qiang Hou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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32
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Taylor A, Taylor J, Watson GW, Boyd RJ. Electronic Energy Changes Associated with Guanine Quadruplex Formation: An Investigation at the Atomic Level. J Phys Chem B 2010; 114:9833-9. [DOI: 10.1021/jp912013k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexis Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Justine Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Graeme W. Watson
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
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33
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Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J Chem Theory Comput 2009; 5:2514-30. [DOI: 10.1021/ct900200k] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Nad’a Špačková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Joanna Sarzyñska
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Modesto Orozco
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Thomas E. Cheatham
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Tadeusz Kulinski
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jiří Šponer
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
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Targeting DNA quadruplexes with distamycin A and its derivatives: An ITC and NMR study. Biochimie 2008; 90:1224-32. [DOI: 10.1016/j.biochi.2008.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 03/14/2008] [Indexed: 11/15/2022]
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Petrovic AG, Polavarapu PL. The quadruplex-duplex structural transition of polyriboguanylic acid. J Phys Chem B 2008; 112:2245-54. [PMID: 18225881 DOI: 10.1021/jp0758723] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyriboguanylic acid (polyG) as a function of time, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyG. From the progression of IR and VCD spectral features with respect to time, it is observed that stabilization of the quadruplex structure at pH 6.4 (near-neutral environment) takes place within 5 days. This stabilization process is most clearly evidenced by a downshift of the carbonyl absorption band and the corresponding positive VCD couplet, from 1689 to approximately 1682 cm(-1) in time. Time-induced spectral modifications also indicated that, in an acidic environment (pH 3.1) and within a 5 day waiting period, polyG develops a duplex structure. An additional positive VCD couplet associated with an absorption band at 1589 cm(-1) is identified as a marker of the polyG duplex structure. From the progression of spectral features with respect to temperature at pH 6.4, it is found that heating induces structural changes that favor the formation of a duplex structure. This duplex structure, at pH 6.4, would not form at room temperature simply by the passage of time. When polyG is in an acidic environment (pH 3.1), heating accelerates the conversion to the duplex structure that could also be obtained with passage of time at that pH. On the basis of the comparison of experimental and quantum theoretical VCD spectra for polyG, the key spectral signature for the quadruplex form is considered to be a single positive VCD couplet, while the spectral signature for a duplex form is considered to contain an additional positive VCD couplet at a lower frequency.
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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Sponer J, Spacková N. Molecular dynamics simulations and their application to four-stranded DNA. Methods 2007; 43:278-90. [PMID: 17967698 PMCID: PMC2431124 DOI: 10.1016/j.ymeth.2007.02.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 02/14/2007] [Indexed: 11/30/2022] Open
Abstract
This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules. We characterize the relations of simulations to the experimental techniques and explain the actual meaning and significance of the results. The following aspects are discussed: pair-additive approximation of the empirical force fields, sampling limitations stemming from the simulation time and accuracy of description of base stacking, H-bonding, sugar-phosphate backbone and ions by force fields. Several methodological approaches complementing the classical explicit solvent molecular dynamics simulations are commented on, including enhanced sampling methods, continuum solvent methods, free energy calculations and gas phase simulations. The successes and pitfalls of recent simulation studies of G-DNA are demonstrated on selected results, including studies of cation interactions and dynamics of G-DNA stems, studies of base substitutions (inosine, thioguanine and mixed tetrads), analysis of possible kinetic intermediates in folding pathway of a G-DNA stem and analysis of loop regions of G-DNA molecules.
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Affiliation(s)
- Jirí Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
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Cavallari M, Calzolari A, Garbesi A, Di Felice R. Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J Phys Chem B 2007; 110:26337-48. [PMID: 17181293 DOI: 10.1021/jp064522y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations.
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Affiliation(s)
- Manuela Cavallari
- National Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A, 41100 Modena, Italy. cavallari.
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Fadrná E, Spacková N, Stefl R, Koca J, Cheatham TE, Sponer J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J 2005; 87:227-42. [PMID: 15240460 PMCID: PMC1304345 DOI: 10.1529/biophysj.103.034751] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.
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Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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Sket P, Crnugelj M, Kozminski W, Plavec J. 15NH4+ ion movement inside d(G4T4G4)2 G-quadruplex is accelerated in the presence of smaller Na+ ions. Org Biomol Chem 2004; 2:1970-3. [PMID: 15254621 DOI: 10.1039/b406815g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2D NMR studies demonstrate that the residence lifetime of 15NH4+ ions within the bimolecular G-quadruplex adopted by d(G4T4G4) is reduced from 270 ms in the presence of ammonium ions alone to 36 ms in the presence of Na+ ions.
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Affiliation(s)
- Primoz Sket
- NMR center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Stefl R, Cheatham TE, Spacková N, Fadrná E, Berger I, Koca J, Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys J 2003; 85:1787-804. [PMID: 12944293 PMCID: PMC1303352 DOI: 10.1016/s0006-3495(03)74608-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The formation of a cation-stabilized guanine quadruplex (G-DNA) stem is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. Here, we investigate the formation of a parallel stranded G-DNA stem consisting of four strands of d(GGGG) using molecular dynamics simulations with explicit inclusion of counterions and solvent. Due to the limitations imposed by the nanosecond timescale of the simulations, rather than watching for the spontaneous formation of G-DNA, our approach probes the stability of possible supramolecular intermediates (including two-, three-, and four-stranded assemblies with out-of-register base pairing between guanines) on the formation pathway. The simulations suggest that "cross-like" two-stranded assemblies may serve as nucleation centers in the initial formation of parallel stranded G-DNA quadruplexes, proceeding through a series of rearrangements involving trapping of cations, association of additional strands, and progressive slippage of strands toward the full stem. To supplement the analysis, approximate free energies of the models are obtained with explicit consideration of the integral cations. The approach applied here serves as a prototype for qualitatively investigating other G-DNA molecules using molecular dynamics simulation and free-energy analysis.
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Affiliation(s)
- Richard Stefl
- National Center for Biomolecular Research, Masaryk University, 612 37 Brno, Czech Republic
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41
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Gresh N, Šponer JE, Špačková N, Leszczynski J, Šponer J. Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA. J Phys Chem B 2003. [DOI: 10.1021/jp022659s] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Judit E. Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Nad'a Špačková
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jerzy Leszczynski
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jiři Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
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Abstract
Hydrogen-bonded base pairs are an important determinant of nucleic acid structure and function. However, other interactions such as base-base stacking, base-backbone, and backbone-backbone interactions as well as effects exerted by the solvent and by metal or NH(4)(+) ions also have to be taken into account. In addition, hydrogen-bonded base complexes involving more than two bases can occur. With the rapidly increasing number and structural diversity of nucleic acid structures known at atomic detail higher-order hydrogen-bonded base complexes, base polyads, have attracted much interest. This review provides an overview on the occurrence of base polyads in nucleic acid structures and describes computational studies on these nucleic acid building blocks.
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Affiliation(s)
- J Sühnel
- Biocomputing Group, Institut für Molekulare Biotechnologie, Postfach 100813, D-07708 Jena, Germany
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Abstract
In the last five years we have witnessed a significant increase in the number publications describing accurate and reliable all-atom molecular dynamics simulations of nucleic acids. This increase has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions, the availability of faster parallel computers, and the development of well-validated empirical molecular mechanical force fields. With these technologies, it has been demonstrated that simulation is not only capable of consistently reproducing experimental observations of sequence specific fine structure of DNA, but also can give detailed insight into prevalent problems in nucleic acid structure, ion association and specific hydration of nucleic acids, polyadenine tract bending, and the subtle environmental dependence of the A-DNA-B-DNA duplex equilibrium. Despite the advances, there are still issues with the methods that need to be resolved through rigorous controlled testing. In general, these relate to deficiencies of the underlying molecular mechanical potentials or applied methods (such as the imposition of true periodicity in Ewald simulations and the need for energy conservation), and significant limits in effective conformational sampling. In this perspective, we provide an overview of our experiences, provide some cautionary notes, and provide recommendations for further study in molecular dynamics simulation of nucleic acids.
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Affiliation(s)
- T E Cheatham
- Department of Medicinal Chemistry, University of Utah, 30 South, 2000 East, Skaggs Hall 201, Salt Lake City, UT 84112-5820, USA.
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