1
|
Yang X, Liu C, Ren P. Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. J Chem Theory Comput 2024; 20:4065-4075. [PMID: 38742922 PMCID: PMC11187603 DOI: 10.1021/acs.jctc.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Conformational dynamics play a crucial role in determining the behavior of the biomolecules. Polarizable force fields, such as AMOEBA, can accurately capture electrostatic interactions underlying the conformational space. However, applying a polarizable force field in molecular dynamics (MD) simulations can be computationally expensive, especially in studying long-time-scale dynamics. To overcome this challenge, we incorporated the AMOEBA potential with Milestoning, an enhanced sampling method in this work. This integration allows us to efficiently sample the rare and important conformational states of a biomolecule by using many short and independent molecular dynamics trajectories with the AMOEBA force field. We applied this method to investigate the conformational dynamics of alanine dipeptide, DNA, and RNA A-B form conversion. Well-converged thermodynamic and kinetic properties were obtained, including the free energy difference, mean first passage time, and critical transitions between states. Our results demonstrate the power of integrating polarizable force fields with enhanced sampling methods in quantifying the thermodynamic and kinetic properties of biomolecules at the atomic level.
Collapse
Affiliation(s)
- Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
2
|
Winkler L, Galindo-Murillo R, Cheatham TE. Assessment of A- to B- DNA Transitions Utilizing the Drude Polarizable Force Field. J Chem Theory Comput 2023; 19:8955-8966. [PMID: 38014857 PMCID: PMC10720382 DOI: 10.1021/acs.jctc.3c01002] [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: 09/13/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
In addition to the well-characterized B-form of DNA, duplex DNA can adopt various conformations, such as A or Z-DNA. Though less common, these structures can be induced biologically through protein or ligand interactions or experimentally with niche environmental conditions, such as high salt concentrations or in mixed water-ethanol. Reproducing these alternate structures through molecular dynamics simulations in recent years has been quite challenging with the currently available force fields, simulation techniques, and time scales. In this study, the Drude polarizable force field is tested for its ability to facilitate transitions between A-DNA and B-DNA or maintain A-DNA. Though transitions away from B-DNA were observed in high concentrations of ethanol, the resulting structures had hybrid properties taken from both B-DNA and A-DNA structures. This was also true for A-DNA in ethanol, which lost some of the A-DNA properties that it was expected to maintain. When B-DNA was tested in high salt environments, the resulting B-DNA structures showed no distinguishable differences with the increasing salt concentrations tested. These results with the Drude FF and recent results with additive force fields suggest that at present the current additive and polarizable force fields do not facilitate a complete transition between B- to A-DNA conformations under the conditions simulated. At present, the Drude FF favors A-B DNA hybrid structures when simulated in nonphysiological conditions.
Collapse
Affiliation(s)
- Lauren Winkler
- Department
of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112,United States
| | - Rodrigo Galindo-Murillo
- Department
of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Thomas E. Cheatham
- Department
of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, Utah 84112,United States
| |
Collapse
|
3
|
Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | | |
Collapse
|
4
|
Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
Collapse
Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China
- Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| |
Collapse
|
5
|
Mo Y, Keller N, delToro D, Ananthaswamy N, Harvey SC, Rao VB, Smith DE. Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence. Nucleic Acids Res 2021; 48:11602-11614. [PMID: 33119757 PMCID: PMC7672480 DOI: 10.1093/nar/gkaa875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/20/2023] Open
Abstract
Many viruses employ ATP-powered motors during assembly to translocate DNA into procapsid shells. Previous reports raise the question if motor function is modulated by substrate DNA sequence: (i) the phage T4 motor exhibits large translocation rate fluctuations and pauses and slips; (ii) evidence suggests that the phage phi29 motor contacts DNA bases during translocation; and (iii) one theoretical model, the ‘B-A scrunchworm’, predicts that ‘A-philic’ sequences that transition more easily to A-form would alter motor function. Here, we use single-molecule optical tweezers measurements to compare translocation of phage, plasmid, and synthetic A-philic, GC rich sequences by the T4 motor. We observed no significant differences in motor velocities, even with A-philic sequences predicted to show higher translocation rate at high applied force. We also observed no significant changes in motor pausing and only modest changes in slipping. To more generally test for sequence dependence, we conducted correlation analyses across pairs of packaging events. No significant correlations in packaging rate, pausing or slipping versus sequence position were detected across repeated measurements with several different DNA sequences. These studies suggest that viral genome packaging is insensitive to DNA sequence and fluctuations in packaging motor velocity, pausing and slipping are primarily stochastic temporal events.
Collapse
Affiliation(s)
- Youbin Mo
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Keller
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Damian delToro
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neeti Ananthaswamy
- Department of Biology, The Catholic University of America, District of Columbia, 20064, USA
| | - Stephen C Harvey
- Department of Biochemistry and Biophysics, Univ. of Pennsylvania, Philadelphia, PA 19104, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, District of Columbia, 20064, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
6
|
Kovaleva N, Strelnikov IA, Zubova EA. Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer. ACS OMEGA 2020; 5:32995-33006. [PMID: 33403261 PMCID: PMC7774075 DOI: 10.1021/acsomega.0c04247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.
Collapse
|
7
|
Ghoshdastidar D, Senapati S. Dehydrated DNA in B-form: ionic liquids in rescue. Nucleic Acids Res 2019; 46:4344-4353. [PMID: 29669113 PMCID: PMC5961314 DOI: 10.1093/nar/gky253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 04/10/2018] [Indexed: 12/19/2022] Open
Abstract
The functional B-conformation of DNA succumbs to the A-form at low water activity. Methods for room temperature DNA storage that rely upon ‘anhydrobiosis’, thus, often encounter the loss of DNA activity due to the B→A-DNA transition. Here, we show that ionic liquids, an emerging class of green solvents, can induce conformational transitions in DNA and even rescue the dehydrated DNA in the functional B-form. CD spectroscopic analyses not only reveal rapid transition of A-DNA in 78% ethanol medium to B-conformation in presence of ILs, but also the high resistance of IL-bound B-form to transit to A-DNA under dehydration. Molecular dynamics simulations show the unique ability of ILs to disrupt Na+ ion condensation and form ‘IL spine’ in DNA minor groove to drive the A→B transition. Implications of these findings range from the plausible use of ILs as novel anhydrobiotic DNA storage medium to a switch for modulating DNA conformational transitions.
Collapse
Affiliation(s)
- Debostuti Ghoshdastidar
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| |
Collapse
|
8
|
Zhang H, Fu H, Shao X, Dehez F, Chipot C, Cai W. Changes in Microenvironment Modulate the B- to A-DNA Transition. J Chem Inf Model 2019; 59:2324-2330. [PMID: 30767527 DOI: 10.1021/acs.jcim.8b00885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.
Collapse
Affiliation(s)
- Hong Zhang
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,State Key Laboratory of Medicinal Chemical Biology , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| | - François Dehez
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , Vandoeuvre-lès-Nancy F-54506 , France.,LPCT, UMR 7019 Université de Lorraine CNRS , Vandoeuvre-lès-Nancy F-54500 , France.,Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry , Nankai University, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
| |
Collapse
|
9
|
Porschke D. Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:325-332. [PMID: 29404661 PMCID: PMC5982448 DOI: 10.1007/s00249-018-1276-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/21/2017] [Accepted: 01/02/2018] [Indexed: 11/28/2022]
Abstract
Because of open problems in the relation between results obtained by relaxation experiments and molecular dynamics simulations on the B-A transition of DNA, relaxation measurements of the B-A dynamics have been extended to a wider range of conditions. Field-induced reaction effects are measured selectively by the magic angle technique using a novel cell construction preventing perturbations from cell window anisotropy. The kinetics was recorded for the case of poly[d(AT)] up to the salt concentration limit of 4.4 mM, where aggregation does not yet interfere. Now experimental data on the B-A dynamics are available for poly[d(AT)] at salt concentrations of 0.18, 0.73, 2.44 and 4.4 mM. In all cases, a spectrum of time constants is found, ranging from ~ 10 μs up to components approaching ~ 1 ms. The relatively small dependence of these data on the salt concentration indicates that electrostatic effects on the kinetics are not as strong as may be expected. The ethanol content at the transition center is a linear function of the logarithm of the salt concentration, and the slope is close to that expected from polyelectrolyte theory. The B-A transition dynamics was also measured in D2O at a salt concentration of 2.4 mM: the center of the transition is found at 20.0 mol/l H2O and at 20.1 mol/l D2O with an estimated accuracy of ± 0.1 mol/l; the spectrum of time constants at the respective transition centers is very similar. The experimental results are discussed regarding the data obtained by molecular dynamics simulations.
Collapse
Affiliation(s)
- Dietmar Porschke
- Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| |
Collapse
|
10
|
Abstract
The complex conformational change from B-DNA to Z-DNA requires inversion of helix-handedness. Multiple degrees of freedom are intricately coupled during this transition, and formulating an appropriate reaction coordinate that captures the underlying complexity would be problematic. In this contribution, we adopt an alternative approach, based on the potential energy landscape perspective, to construct a kinetic transition network. Microscopic insight into the B → Z transition is provided in terms of geometrically defined discrete paths consisting of local minima and the transition states that connect them. We find that the inversion of handedness can occur via two competing mechanisms, either involving stretched intermediates, or a B-Z junction, in agreement with previous predictions. The organisation of the free energy landscape further suggests that this process is likely to be slow under physiological conditions. Our results represent a key step towards decoding the more intriguing features of the B → Z transition, such as the role of ionic strength and negative supercoiling in reshaping the landscape.
Collapse
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| |
Collapse
|
11
|
Szymborska-Małek K, Komorowska M, Gąsior-Głogowska M. Effects of Near Infrared Radiation on DNA. DLS and ATR-FTIR Study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:258-267. [PMID: 28723592 DOI: 10.1016/j.saa.2017.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/13/2017] [Accepted: 07/07/2017] [Indexed: 06/07/2023]
Abstract
We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100nm) for 5, 10, and 20min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation. For the NIR-treated samples (at room temperature) the B form was better conserved than in the control sample independently of the irradiation period. Above 50°C a considerable increase in the A form was only observed for 10min NIR exposed samples. The hydrodynamic radius, (Rh), studied by the dynamic light scattering, showed drastic decrease with the increasing irradiation time. Principal components analysis (PCA) allowed to detect the spectral features correlated with the NIR effect and thermal stability of the DNA films. Obtained results strongly support the idea that the photoionization of water by NIR radiation in presence of DNA molecules is the main factor influencing on its physicochemical properties.
Collapse
Affiliation(s)
- Katarzyna Szymborska-Małek
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Box 1410, 50-950 Wroclaw 2, Poland
| | - Małgorzata Komorowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland.
| | - Marlena Gąsior-Głogowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland
| |
Collapse
|
12
|
Zgarbová M, Jurečka P, Šponer J, Otyepka M. A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker. J Chem Theory Comput 2017; 14:319-328. [DOI: 10.1021/acs.jctc.7b00926] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| |
Collapse
|
13
|
Geng J, Aioub M, El-Sayed MA, Barry BA. An Ultraviolet Resonance Raman Spectroscopic Study of Cisplatin and Transplatin Interactions with Genomic DNA. J Phys Chem B 2017; 121:8975-8983. [PMID: 28925698 DOI: 10.1021/acs.jpcb.7b08156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet resonance Raman (UVRR) spectroscopy is a label-free method to define biomacromolecular interactions with anticancer compounds. Using UVRR, we describe the binding interactions of two Pt(II) compounds, cisplatin (cis-diamminedichloroplatinum(II)) and its isomer, transplatin, with nucleotides and genomic DNA. Cisplatin binds to DNA and other cellular components and triggers apoptosis, whereas transplatin is clinically ineffective. Here, a 244 nm UVRR study shows that purine UVRR bands are altered in frequency and intensity when mononucleotides are treated with cisplatin. This result is consistent with previous suggestions that purine N7 provides the cisplatin-binding site. The addition of cisplatin to DNA also causes changes in the UVRR spectrum, consistent with binding of platinum to purine N7 and disruption of hydrogen-bonding interactions between base pairs. Equally important is that transplatin treatment of DNA generates similar UVRR spectral changes, when compared to cisplatin-treated samples. Kinetic analysis, performed by monitoring decreases of the 1492 cm-1 band, reveals biphasic kinetics and is consistent with a two-step binding mechanism for both platinum compounds. For cisplatin-DNA, the rate constants (6.8 × 10-5 and 6.5 × 10-6 s-1) are assigned to the formation of monofunctional adducts and to bifunctional, intrastrand cross-linking, respectively. In transplatin-DNA, there is a 3.4-fold decrease in the rate constant of the slow phase, compared with the cisplatin samples. This change is attributed to generation of interstrand, rather than intrastrand, adducts. This longer reaction time may result in increased competition in the cellular environment and account, at least in part, for the lower pharmacological efficacy of transplatin.
Collapse
Affiliation(s)
- Jiafeng Geng
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Mena Aioub
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Mostafa A El-Sayed
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, ‡Parker H. Petit Institute of Bioengineering and Bioscience, and §Laser Dynamics Laboratory, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| |
Collapse
|
14
|
Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:63-73. [DOI: 10.1016/j.pbiomolbio.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 04/16/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
|
15
|
Muntean CM, Bratu I, Hernanz A. Vibrational Relaxation of the Backbone and Base Modes in LacDNA Complexes by UV Resonance Raman Spectroscopy. J Phys Chem B 2017. [PMID: 28650655 DOI: 10.1021/acs.jpcb.7b04271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrational band shape analysis through time correlation function concept is widely used to obtain experimental information on the molecular dynamics of medium-size molecules in different environments. Interesting details are revealed by extending this technique to biomolecules such as functional groups of the nucleic acids in media approaching the physiological conditions. In this work a study into the UV resonance Raman (UVRR) vibrational half bandwidths of functional groups in LacDNA, upon lowering the pH (pH 6.4, pH 3.45) and in the presence of Mn2+ and Ca2+ ions, respectively, was of interest. The corresponding global relaxation times have been derived. Also, the 793 cm-1 UVRR band, corresponding to ν (backbone O-P-O, dT) oscillator of LacDNA in aqueous solutions, was selected for band shape-analysis. Vibrational relaxation appears as the dominant relaxation process for this mode, with vibrational dephasing being the most efficient for this oscillator. Current theories developed for vibrational dephasing have been applied to this profile, and relevant relaxation parameters have been obtained and discussed. To our knowledge this is the first study on DNA oligomers vibrational band shape analysis through time correlation function concept.
Collapse
Affiliation(s)
- Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies , 67-103 Donat Street, RO-400293 Cluj-Napoca, Romania
| | - Ioan Bratu
- National Institute for Research & Development of Isotopic and Molecular Technologies , 67-103 Donat Street, RO-400293 Cluj-Napoca, Romania
| | - Antonio Hernanz
- UNED , Departamento de Ciencias y Técnicas Fisicoquímicas, Paseo de la Senda del Rey, 9, E-28040 Madrid, Spain
| |
Collapse
|
16
|
Porschke D. Boundary conditions for free A-DNA in solution and the relation of local to global DNA structures at reduced water activity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:413-21. [PMID: 26872482 PMCID: PMC4901124 DOI: 10.1007/s00249-015-1110-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/30/2015] [Accepted: 12/17/2015] [Indexed: 11/05/2022]
Abstract
Because of repeated claims that A-DNA cannot exist without aggregation or condensation, the state of DNA restriction fragments with 84–859 bp has been analyzed in aqueous solutions upon reduction of the water activity. Rotational diffusion times τd measured by electric dichroism at different water activities with a wide variation of viscosities are normalized to values τc at the viscosity of water, which indicate DNA structures at a high sensitivity. For short helices (chain lengths \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ {\ell} $$\end{document}ℓ ≤ persistence length p), cooperative formation of A-DNA is reflected by the expected reduction of the hydrodynamic length; the transition to the A-form is without aggregation or condensation upon addition of ethanol at monovalent salt ≤1 mM. The aggregation boundary, indicated by a strong increase of τc, is shifted to higher monovalent salt (≥4 mM) when ethanol is replaced by trifluoroethanol. The BA transition is not indicated anymore by a cooperative change of τc for \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ {\ell} $$\end{document}ℓ » p; τc values for these long chains decrease upon reduction of the water activity continuously over the full range, including the BA transition interval. This suggests a non-cooperative BC transition, which induces DNA curvature. The resulting wide distribution of global structures hides changes of local length during the BA transition. Free A-DNA without aggregation/condensation is found at low-salt concentrations where aggregation is inhibited and/or very slow. In an intermediate range of solvent conditions, where the A-form starts to aggregate, a time window remains that can be used for analysis of free A-DNA in a quasi-equilibrium state.
Collapse
Affiliation(s)
- Dietmar Porschke
- Max Planck Institut für biophysikalische Chemie, 37077, Göttingen, Germany.
| |
Collapse
|
17
|
Yamaguchi N, Zouzumi YK, Shimada N, Nakano SI, Sugimoto N, Maruyama A, Miyoshi D. A reversible B–A transition of DNA duplexes induced by synthetic cationic copolymers. Chem Commun (Camb) 2016; 52:7446-9. [DOI: 10.1039/c6cc02237e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible B–A transitions of DNA duplexes were induced by synthetic cationic and anionic polymers.
Collapse
Affiliation(s)
- Nonoka Yamaguchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe 650-0047
- Japan
| | - Yu-ki Zouzumi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe 650-0047
- Japan
| | - Naohiko Shimada
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe 650-0047
- Japan
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe 650-0047
- Japan
- Frontier Institute for Biomolecular Engineering Research (FIBER)
| | - Atsushi Maruyama
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Konan University
- Kobe 650-0047
- Japan
| |
Collapse
|
18
|
The Influence of DNA Configuration on the Direct Strand Break Yield. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:417501. [PMID: 26124855 PMCID: PMC4466367 DOI: 10.1155/2015/417501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/11/2015] [Accepted: 01/28/2015] [Indexed: 11/24/2022]
Abstract
Purpose. To study the influence of DNA configuration on the direct damage yield. No indirect effect has been accounted for. Methods. The GEANT4-DNA code was used to simulate the interactions of protons and alpha particles with geometrical models of the A-, B-, and Z-DNA configurations. The direct total, single, and double strand break yields and site-hit probabilities were determined. Certain features of the energy deposition process were also studied. Results. A slight increase of the site-hit probability as a function of the incident particle linear energy transfer was found for each DNA configuration. Each DNA form presents a well-defined site-hit probability, independently of the particle linear energy transfer. Approximately 70% of the inelastic collisions and ~60% of the absorbed dose are due to secondary electrons. These fractions are slightly higher for protons than for alpha particles at the same incident energy. Conclusions. The total direct strand break yield for a given DNA form depends weakly on DNA conformation topology. This yield is practically determined by the target volume of the DNA configuration. However, the double strand break yield increases with the packing ratio of the DNA double helix; thus, it depends on the DNA conformation.
Collapse
|
19
|
Chandra GK, Eklouh-Molinier C, Fere M, Angiboust JF, Gobinet C, Van-Gulick L, Jeannesson P, Piot O. Probing in Vitro Ribose Induced DNA-Glycation Using Raman Microspectroscopy. Anal Chem 2015; 87:2655-64. [DOI: 10.1021/acs.analchem.5b00182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Goutam Kumar Chandra
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Christophe Eklouh-Molinier
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Michael Fere
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Jean-François Angiboust
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Cyril Gobinet
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Laurence Van-Gulick
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Pierre Jeannesson
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Olivier Piot
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| |
Collapse
|
20
|
Kulkarni M, Mukherjee A. Sequence dependent free energy profiles of localized B- to A-form transition of DNA in water. J Chem Phys 2014; 139:155102. [PMID: 24160545 DOI: 10.1063/1.4825175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
DNA carries an inherent polymorphism, which surfaces under various external conditions. While B-form remains predominant under normal physiological conditions for most of the DNA sequences, low humidity and increased ion concentration cause B- to A-form transition. Certain proteins and molecules also sometimes cause local deformation of the DNA to the specific A-form. Previous experimental and computational studies focused on the overall B- to A-form transition. Here for the first time we investigated thermodynamics and mechanism of B- to A-form transition in water for various DNA sequences at a local dinucleotide base pair level. We introduced a new reaction coordinate Zp', based on the unique order parameter Zp, to drive B- to A-form transition locally and thereby calculate free energy profiles for the same for all the ten different dinucleotide steps embedded in a twelve base pair DNA. Results show that the trend of "A" and "B" philicity observed in experiment is preserved even at this local dinucleotide level, indicating its localized origin. Higher free energy cost obtained here is attributed to the cost of creating B∕A junctions along with formation of B->A transition at dimer level. We find that while water energetically stabilizes A-form for all the ten different dinucleotide steps to various extents, entropy acts against it. Therefore, we find that the stability of B-form DNA in water is entropic in origin. Mechanism of the conversion appears to be triggered by Slide; however, backbone parameters change concertedly.
Collapse
Affiliation(s)
- Mandar Kulkarni
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | | |
Collapse
|
21
|
Sun S, Liu M, Dong F, Fan S, Yao Y. A histone-like protein induces plasmid DNA to form liquid crystals in vitro and gene compaction in vivo. Int J Mol Sci 2013; 14:23842-57. [PMID: 24322443 PMCID: PMC3876081 DOI: 10.3390/ijms141223842] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/17/2013] [Accepted: 11/21/2013] [Indexed: 12/15/2022] Open
Abstract
The liquid crystalline state is a universal phenomenon involving the formation of an ordered structure via a self-assembly process that has attracted attention from numerous scientists. In this study, the dinoflagellate histone-like protein HCcp3 is shown to induce super-coiled pUC18 plasmid DNA to enter a liquid crystalline state in vitro, and the role of HCcp3 in gene condensation in vivo is also presented. The plasmid DNA (pDNA)-HCcp3 complex formed birefringent spherical particles with a semi-crystalline selected area electronic diffraction (SAED) pattern. Circular dichroism (CD) titrations of pDNA and HCcp3 were performed. Without HCcp3, pUC18 showed the characteristic B conformation. As the HCcp3 concentration increased, the 273 nm band sharply shifted to 282 nm. When the HCcp3 concentration became high, the base pair (bp)/dimer ratio fell below 42/1, and the CD spectra of the pDNA-HCcp3 complexes became similar to that of dehydrated A-form DNA. Microscopy results showed that HCcp3 compacted the super-coiled gene into a condensed state and that inclusion bodies were formed. Our results indicated that HCcp3 has significant roles in gene condensation both in vitro and in histone-less eukaryotes in vivo. The present study indicates that HCcp3 has great potential for applications in non-viral gene delivery systems, where HCcp3 may compact genetic material to form liquid crystals.
Collapse
Affiliation(s)
- Shiyong Sun
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (F.D.); Tel./Fax: +86-816-2419569 (S.S.)
| | - Mingxue Liu
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
| | - Faqin Dong
- Key Laboratory of Solid Waste Treatment and Resource Recycle & Fundamental Science on Nuclear Waste and Environmental Security Laboratory, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (F.D.); Tel./Fax: +86-816-2419569 (S.S.)
| | - Shenglan Fan
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
| | - Yanchen Yao
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China; E-Mails: (S.F.); (Y.Y.)
| |
Collapse
|
22
|
Foloppe N, Guéroult M, Hartmann B. Simulating DNA by molecular dynamics: aims, methods, and validation. Methods Mol Biol 2013; 924:445-468. [PMID: 23034759 DOI: 10.1007/978-1-62703-017-5_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.
Collapse
|
23
|
Perry CC, Urata SM, Lee M, Aguilera JA, Milligan JR. Radioprotective effects produced by the condensation of plasmid DNA with avidin and biotinylated gold nanoparticles. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2012; 51:457-468. [PMID: 22825766 DOI: 10.1007/s00411-012-0429-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/28/2012] [Indexed: 06/01/2023]
Abstract
The treatment of aqueous solutions of plasmid DNA with the protein avidin results in significant changes in physical, chemical, and biochemical properties. These effects include increased light scattering, formation of micron-sized particles containing both DNA and protein, and plasmid protection against thermal denaturation, radical attack, and nuclease digestion. All of these changes are consistent with condensation of the plasmid by avidin. Avidin can be displaced from the plasmid at higher ionic strengths. Avidin is not displaced from the plasmid by an excess of a tetra-arginine ligand, nor by the presence of biotin. Therefore, this system offers the opportunity to reversibly bind biotin-labeled species to a condensed DNA-protein complex. An example application is the use of biotinylated gold nanoparticles. This system offers the ability to examine in better detail the chemical mechanisms involved in important radiobiological effects. Examples include protein modulation of radiation damage to DNA, and radiosensitization by gold nanoparticles.
Collapse
Affiliation(s)
- Christopher C Perry
- Department of Biochemistry, Loma Linda University, 11085 Campus Street, Loma Linda, CA, 92350, USA
| | | | | | | | | |
Collapse
|
24
|
Dixit SB, Mezei M, Beveridge DL. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. J Biosci 2012; 37:399-421. [PMID: 22750979 DOI: 10.1007/s12038-012-9223-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the observed water and ion atmosphere around the DNA sequences is the MD simulation is in good agreement with experimental observations.
Collapse
Affiliation(s)
- Surjit B Dixit
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06457, USA
| | | | | |
Collapse
|
25
|
Abstract
This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50-100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation.
Collapse
Affiliation(s)
- David L Beveridge
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University Middletown, CT 06459, USA.
| | | | | |
Collapse
|
26
|
Lee OS, Cho VY, Schatz GC. A- to B-Form Transition in DNA Between Gold Surfaces. J Phys Chem B 2012; 116:7000-5. [DOI: 10.1021/jp300877e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- One-Sun Lee
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Vince Y. Cho
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| |
Collapse
|
27
|
Shen X, Gu B, Che SA, Zhang FS. Solvent effects on the conformation of DNA dodecamer segment: A simulation study. J Chem Phys 2011; 135:034509. [DOI: 10.1063/1.3610549] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
|
28
|
Krishnan R, Oh DH. Structural determinants of photoreactivity of triplex forming oligonucleotides conjugated to psoralens. J Nucleic Acids 2010; 2010. [PMID: 20725628 PMCID: PMC2915845 DOI: 10.4061/2010/523498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Accepted: 06/03/2010] [Indexed: 11/23/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) with both DNA and 2′-O-methyl RNA backbones can direct psoralen photoadducts to specific DNA sequences. However, the functional consequences of these differing structures on psoralen photoreactivity are unknown. We designed TFO sequences with DNA and 2′-O-methyl RNA backbones conjugated to psoralen by 2-carbon linkers and examined their ability to bind and target damage to model DNA duplexes corresponding to sequences within the human HPRT gene. While TFO binding affinity was not dramatically affected by the type of backbone, psoralen photoreactivity was completely abrogated by the 2′-O-methyl RNA backbone. Photoreactivity was restored when the psoralen was conjugated to the RNA TFO via a 6-carbon linker. In contrast to the B-form DNA of triplexes formed by DNA TFOs, the CD spectra of triplexes formed with 2′-O-methyl RNA TFOs exhibited features of A-form DNA. These results indicate that 2′-O-methyl RNA TFOs induce a partial B-to-A transition in their target DNA sequences which may impair the photoreactivity of a conjugated psoralen and suggest that optimal design of TFOs to target DNA damage may require a balance between binding ability and drug reactivity.
Collapse
Affiliation(s)
- Rajagopal Krishnan
- Department of Dermatology, University of California at San Francisco, San Francisco, CA 94121, USA
| | | |
Collapse
|
29
|
Borkar A, Ghosh I, Bhattacharyya D. Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. J Biomol Struct Dyn 2010; 27:695-712. [DOI: 10.1080/07391102.2010.10508582] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
30
|
MacKerell AD. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B 2009; 113:3235-44. [PMID: 19708270 PMCID: PMC2784611 DOI: 10.1021/jp8102782] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Canonical forms of duplex DNA are known to sample well-defined regions of the alpha, beta, gamma, epsilon, and zeta dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, B1, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the alpha, beta, gamma, epsilon, and zeta dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of alpha, beta, gamma, epsilon, and zeta dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.
Collapse
Affiliation(s)
- Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
| |
Collapse
|