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Gheorghiu A, Coveney PV, Arabi AA. The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair. Phys Chem Chem Phys 2021; 23:6252-6265. [PMID: 33735350 PMCID: PMC8330266 DOI: 10.1039/d0cp06218a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/23/2021] [Indexed: 12/28/2022]
Abstract
The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.
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Affiliation(s)
- Alexander Gheorghiu
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK.
| | - Peter V Coveney
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and Informatics Institute, University of Amsterdam, P.O. Box 94323 1090 GH, Amsterdam, The Netherlands
| | - Alya A Arabi
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, AlAin, P. O. Box: 17666, United Arab Emirates.
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Garcia-Fernandez E, Paulo PMR, Costa SMB. Evaluation of electrostatic binding of PAMAM dendrimers and charged phthalocyanines by fluorescence correlation spectroscopy. Phys Chem Chem Phys 2015; 17:4319-27. [PMID: 25574969 DOI: 10.1039/c4cp05373g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have assessed host-guest interactions between PAMAM dendrimers and charged phthalocyanine probes by Fluorescence Correlation Spectroscopy (FCS). Our results show strong binding in water at low ionic strength with an affinity that decreases from KB ∼ 10(9) to 10(8) M(-1) upon decreasing the phthalocyanine charge of z = -4, -2 and -1. The binding affinity also decreases significantly upon salt addition leading to KB values of ca. 10(5)-10(6) M(-1). The changes of binding affinity probed by varying the phthalocyanine charge, and by changing the ionic strength or pH conditions, allowed us to evaluate the electrostatic contribution (Kel) in dendrimer-phthalocyanine interactions. In particular, this approach afforded values of electrostatic potential for PAMAM dendrimers in water at low ionic strength and at dendrimer concentrations in the nanomolar range. The electrostatic potential of PAMAM generations 4 and 7 are around 50 mV in close agreement with theoretical estimates using the Poisson-Boltzmann cell model. Interestingly, the nonelectrostatic binding is significant and contributes even more than electrostatic binding to dendrimer-phthalocyanine interactions. The nonelectrostatic binding contributes to an affinity of KB above 10(5) M(-1), as measured under conditions of low dendrimer charge and high ionic strength, which makes these dendrimers promising hosts as drug carriers.
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Affiliation(s)
- Emilio Garcia-Fernandez
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal.
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Sanchez F, Barrios A, Lopez-Lopez M, Lopez-Cornejo P, Bernal E, Sarrion B, Lebron J, Marchena M. A New Formulation for Quenching Processes under Restricted Geometry Conditions in the Slow Exchange Limit. PROGRESS IN REACTION KINETICS AND MECHANISM 2014. [DOI: 10.3184/146867814x13981545065017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A quantitative treatment of quenching processes under restricted geometry conditions in the Slow Exchange Limit is presented. The expressions for KSV have been obtained for this limit in some common situations that can arise in studies under restricted geometry conditions, such as an inhomogeneous quencher distribution in the solution, the presence of oxygen in solution, or the case of solutions containing a mixture of receptors. These situations have been considered and incorporated into the treatment.
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Affiliation(s)
- F. Sanchez
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - A. Barrios
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - M. Lopez-Lopez
- Department of Chemical Engineering, Physical Chemistry and Organic Chemistry, University of Huelva, Avenida de las Fuerzas Armadas s/n, Huelva, 21071, Spain
| | - P. Lopez-Cornejo
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - E. Bernal
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - B. Sarrion
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - J.A. Lebron
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
| | - M. Marchena
- The Department of Physical Chemistry, University of Sevilla, C/Profesor Garcia Gonzalez s/n, 41012 Sevilla, Spain
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Grueso E, Kuliszewska E, Prado-Gotor R, Perez-Tejeda P, Roldan E. Improving the understanding of DNA–propanediyl-1,3-bis(dodecyldimethylammonium) dibromide interaction using thermodynamic, structural and kinetic approaches. Phys Chem Chem Phys 2013; 15:20064-74. [DOI: 10.1039/c3cp53299b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bernal E, Sánchez F, Marchena M. On the meaning of parameters of the two state model in the case of photochemical reactions under restricted geometry conditions. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Marchena M, Sánchez F. A General Formulation Encompassing the Effects of Salts and Micelles (Direct and Reverse) on Ionic Reactions. J SOLUTION CHEM 2011. [DOI: 10.1007/s10953-011-9662-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bernal E, Marchena M, Sánchez F. Microheterogeneous catalysis. Molecules 2010; 15:4815-74. [PMID: 20657395 PMCID: PMC6257643 DOI: 10.3390/molecules15074815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 06/23/2010] [Accepted: 07/05/2010] [Indexed: 12/04/2022] Open
Abstract
The catalytic effect of micelles, polymers (such as DNA, polypeptides) and nanoparticles, saturable receptors (cyclodextrins and calixarenes) and more complex systems (mixing some of the above mentioned catalysts) have been reviewed. In these microheterogeneous systems the observed changes in the rate constants have been rationalized using the Pseudophase Model. This model produces equations that can be derived from the Brönsted equation, which is the basis for a more general formulation of catalytic effects, including electrocatalysis. When, in the catalyzed reaction one of the reactants is in the excited state, the applicability (at least formally) of the Pseudophase Model occurs only in two limiting situations: the lifetime of the fluorophore and the distributions of the quencher and the probe are the main properties that define the different situations.
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Affiliation(s)
- Eva Bernal
- Department of Physical Chemistry, University of Seville, C/Profesor García González, s/n, 41012, Seville, Spain.
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Lopes-Costa T, Sanchez F, Lopez-Cornejo P. Cooperative and noncooperative binding of *Ru(bpy)3(2+) to DNA and SB4.5G dendrimers. J Phys Chem B 2009; 113:9373-8. [PMID: 19537733 DOI: 10.1021/jp902110x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The process *Ru(bpy)(3)(2+) + S(2)O(8)(2-) in two different reaction media, the SB4.5G dendrimer and DNA solutions, was studied. In both media, the receptors have anionic characteristics. This fact will produce a binding of the ruthenium complex to the two receptors by attractive electrostatic interactions. On the contrary, the peroxodisulfate ions will be preferentially located in the aqueous solution due to electrostatic repulsions with the receptors. Despite the similarities of the receptors, some differences are observed in these two reaction media. These differences arise from the fact that the binding of the *Ru(bpy)(3)(2+) complex to DNA shows a negative cooperativity, whereas the binding to the dendrimer is noncooperative in character. The anticooperative character of the binding that happens in DNA solutions becomes noncooperative when an electrolyte, NaNO(3), is added to the medium. This is related to a condensation of the salt's counterions on the surface of the DNA which produces a decrease of the equilibrium constant corresponding to the binding of the complex to the receptor. Therefore, it is shown that the ionic strength of the reaction medium exerts a great influence on the cooperative nature of the ligand/receptor binding. This also explains the different behavior observed in DNA and dendrimer solutions.
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Affiliation(s)
- T Lopes-Costa
- Departamento de Quimica Fisica, Universidad de Sevilla, Sevilla, Spain
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Grueso E, Roldan E, Sanchez F. Kinetic Study of the Cetyltrimethylammonium/DNA Interaction. J Phys Chem B 2009; 113:8319-23. [DOI: 10.1021/jp810966n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. Grueso
- The Department of Physical Chemistry, University of Seville, C/Profesor García González s/n, 41012 Seville, Spain
| | - E. Roldan
- The Department of Physical Chemistry, University of Seville, C/Profesor García González s/n, 41012 Seville, Spain
| | - F. Sanchez
- The Department of Physical Chemistry, University of Seville, C/Profesor García González s/n, 41012 Seville, Spain
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Silverman LN, Pitzer ME, Ankomah PO, Boxer SG, Fenlon EE. Vibrational stark effect probes for nucleic acids. J Phys Chem B 2007; 111:11611-3. [PMID: 17877390 PMCID: PMC2546494 DOI: 10.1021/jp0750912] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. To explore the use of VSE in nucleic acids, we investigated the Stark spectroscopy of nine structurally diverse nucleosides. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; that is, from 2253 cm-1 for 2'-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm(-1) for a 13C-labeled 5-thiocyanatomethyl-2'-deoxyuridine 3c. The largest Stark tuning rate observed was |Deltamu| = 1.1 cm(-1)/(MV/cm) for both 5-cyano-2'-deoxyuridine 1 and N2-nitrile-2'-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (epsilon = 412 M-1cm-1) and ease of incorporation into oligomers.
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Affiliation(s)
- Lisa N. Silverman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
| | - Michael E. Pitzer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
| | - Peter O. Ankomah
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
- To whom correspondence should be addressed. Stark Spectroscopy: E-mail: . Telephone: 650-723-4482. Fax: 650-723-4817. Synthesis: E-mail: . Telephone: 717-291-4201. Fax: 717-291-4343
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
- To whom correspondence should be addressed. Stark Spectroscopy: E-mail: . Telephone: 650-723-4482. Fax: 650-723-4817. Synthesis: E-mail: . Telephone: 717-291-4201. Fax: 717-291-4343
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