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Peng HC, Mohan S, Huq MT, Bull JA, Michaud T, Piercy TC, Hilber S, Wettasinghe AP, Slinker JD, Kreutz C, Stelling AL. Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes. Anal Chem 2024; 96:8868-8874. [PMID: 38775341 DOI: 10.1021/acs.analchem.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.
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Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shrijaa Mohan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Muhammad T Huq
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Julie A Bull
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Troy Michaud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Turner C Piercy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Ashan P Wettasinghe
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jason D Slinker
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Vigna J, Mancini I, Mele A, Vacek J, Minofar B, Rossi B. Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents. Int J Biol Macromol 2024; 256:128443. [PMID: 38035952 DOI: 10.1016/j.ijbiomac.2023.128443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure. Multi-wavelength synchrotron UV Resonance Raman (UVRR) measurements indicate that the hydration shell of adenine-thymine pairs is strongly perturbed in the presence of DESs and that the preferential interaction between H-bond sites of guanine residues and DESs is significantly involved in the stabilization of the dsDNA. Finally, MD calculations show that the minor groove of DNA is significantly selective for the choline part of the investigated DESs compared to the major groove. This finding is likely to have a significant impact not only in terms of thermal stability but also in the modulation of ligand-DNA interactions.
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Affiliation(s)
- Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Mariagrazia Tortora
- Area Science Park, Padriciano, 99, 34149 Trieste, Italy; Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy
| | | | - Jacopo Vigna
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy
| | - Ines Mancini
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy
| | - Andrea Mele
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, S.S. 114 km 163.5, Basovizza, 34149 Trieste, Italy; Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive, 14, 38123 Povo Trento, Italy.
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3
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Barbero-Aparicio JA, Cuesta-Lopez S, García-Osorio CI, Pérez-Rodríguez J, García-Pedrajas N. Nonlinear physics opens a new paradigm for accurate transcription start site prediction. BMC Bioinformatics 2022; 23:565. [PMID: 36585618 PMCID: PMC9801560 DOI: 10.1186/s12859-022-05129-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learning (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors.
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Affiliation(s)
- José Antonio Barbero-Aparicio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Santiago Cuesta-Lopez
- grid.23520.360000 0000 8569 1592Universidad de Burgos, Hospital del Rey, s/n, 09001 Burgos, Spain ,ICAMCyL Foundation, Internacional Center for Advanced Materials and Raw Materials of Castilla y León, León Technology Park, main building, first floor, offices 106-108, C/Julia Morros s/n, Armunia, 24009 León, Spain
| | - César Ignacio García-Osorio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Javier Pérez-Rodríguez
- grid.449008.10000 0004 1795 4150Departamento de Métodos Cuantitativos, Universidad de Loyola Andalucía, Escritor Castilla Aguayo, 4, 14004 Córdoba, Spain
| | - Nicolás García-Pedrajas
- grid.411901.c0000 0001 2183 9102Department of Computing and Numerical Analysis, University of Córdoba, Edificio Albert Einstein, Campus de Rabanales, 14071 Córdoba, Spain
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4
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Fadaei F, Tortora M, Gessini A, Masciovecchio C, Catalini S, Vigna J, Mancini I, Mele A, Vacek J, Reha D, Minofar B, Rossi B. Structural specificity of groove binding mechanism between imidazolium-based ionic liquids and DNA revealed by synchrotron-UV Resonance Raman spectroscopy and molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Rossi B, Tortora M, Catalini S, Vigna J, Mancini I, Gessini A, Masciovecchio C, Mele A. Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments. Phys Chem Chem Phys 2021; 23:15980-15988. [PMID: 34313275 DOI: 10.1039/d1cp01970h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.
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Affiliation(s)
- Barbara Rossi
- Elettra-Sincrotrone Trieste, S. S. 114 km 163.5, Basovizza, 34149, Trieste, Italy.
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6
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Bottari C, Catalini S, Foggi P, Mancini I, Mele A, Perinelli DR, Paciaroni A, Gessini A, Masciovecchio C, Rossi B. Base-specific pre-melting and melting transitions of DNA in presence of ionic liquids probed by synchrotron-based UV resonance Raman scattering. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Gupta MK, Madhanagopal BR, Ganesh KN. Peptide Nucleic Acid with Double Face: Homothymine–Homocytosine Bimodal Cα-PNA (bm-Cα-PNA) Forms a Double Duplex of the bm-PNA2:DNA Triplex. J Org Chem 2020; 86:414-428. [DOI: 10.1021/acs.joc.0c02158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Bharath Raj Madhanagopal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Krishna N. Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
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8
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Bhingardeve P, Madhanagopal BR, Ganesh KN. Cγ( S/ R)-Bimodal Peptide Nucleic Acids (Cγ- bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands. J Org Chem 2020; 85:13680-13693. [PMID: 32985197 DOI: 10.1021/acs.joc.0c01853] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ(S)-bm-PNA duplexes are more stable than Cγ(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.
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Affiliation(s)
- Pramod Bhingardeve
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Bharath Raj Madhanagopal
- Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
| | - Krishna N Ganesh
- Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pune 411008, India.,Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati 517507, India
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9
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Sanstead PJ, Ashwood B, Dai Q, He C, Tokmakoff A. Oxidized Derivatives of 5-Methylcytosine Alter the Stability and Dehybridization Dynamics of Duplex DNA. J Phys Chem B 2020; 124:1160-1174. [PMID: 31986043 PMCID: PMC7136776 DOI: 10.1021/acs.jpcb.9b11511] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The naturally occurring nucleobase 5-methylcytosine (mC) and its oxidized derivatives 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC) play important roles in epigenetic regulation and, along with cytosine (C), represent nucleobases currently implicated in the active cytosine demethylation pathway. Despite considerable interest in these modified bases, their impact on the thermodynamic stability of double-stranded DNA (dsDNA) remains ambiguous and their influence on hybridization kinetics and dynamics is even less well-understood. To address these unknowns, we employ steady-state and time-resolved infrared spectroscopy to measure the influence of cytosine modification on the thermodynamics and kinetics of hybridization by assessing the impact on local base pairing dynamics, shifts in the stability of the duplex state, and changes to the hybridization transition state. Modification with mC leads to more tightly bound base pairing below the melting transition and stabilizes the duplex relative to canonical DNA, but the free energy barrier to dehybridization at physiological temperature is nevertheless reduced slightly. Both hmC and fC lead to an increase in local base pair fluctuations, a reduction in the cooperativity of duplex melting, and a lowering of the dissociation barrier, but these effects are most pronounced when the 5-position is formylated. The caC nucleobase demonstrates little impact on dsDNA under neutral conditions, but we find that this modification can dynamically switch between C-like and fC-like behavior depending on the protonation state of the 5-position carboxyl group. Our results provide a consistent thermodynamic and kinetic framework with which to describe the modulation of the physical properties of double-stranded DNA containing these modified nucleobases.
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Affiliation(s)
- Paul J. Sanstead
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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10
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines. Biophys Chem 2018; 234:24-33. [PMID: 29407768 DOI: 10.1016/j.bpc.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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11
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Ramakers LAI, Hithell G, May JJ, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Hunt NT. 2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model. J Phys Chem B 2017; 121:1295-1303. [PMID: 28102674 DOI: 10.1021/acs.jpcb.7b00345] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced noncovalent interactions between the ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a suboptimal alternating A-T sequence. Results from two-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of the minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region. This induced fit maximizes favorable ligand-DNA enthalpic contributions in the optimal binding case and demonstrates that controlling the molecular details that induce subtle changes in DNA structure may hold the key to designing next-generation DNA-binding molecules.
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Affiliation(s)
- Lennart A I Ramakers
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
| | - John J May
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Harwell, Oxford OX11 0QX, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdon
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12
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Man VH, Pan F, Sagui C, Roland C. Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse. J Chem Phys 2016; 144:145101. [DOI: 10.1063/1.4945340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
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13
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Fakhfakh K, Hughesman CB, Louise Creagh A, Kao V, Haynes C. Calorimetric and Spectroscopic Analysis of the Thermal Stability of Short Duplex DNA-Containing Sugar and Base-Modified Nucleotides. Methods Enzymol 2015; 567:97-127. [PMID: 26794352 DOI: 10.1016/bs.mie.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Base- and sugar-modified analogs of DNA and RNA are finding ever expanding use in medicine and biotechnology as tools to better tailor structured oligonucleotides by altering their thermal stability, nuclease resistance, base-pairing specificity, antisense activity, or cellular uptake. Proper deployment of these chemical modifications generally requires knowledge of how each affects base-pairing properties and thermal stabilities. Here, we describe in detail how differential scanning calorimetry and UV spectroscopy may be used to quantify the melting thermodynamics of short dsDNA containing chemically modified nucleosides in one or both strands. Insights are provided into why and how the presence of highly stable base pairs containing modified nucleosides can alter the nature of calorimetry or melting spectroscopy data, and how each experiment must therefore be conducted to ensure high-quality melting thermodynamics data are obtained. Strengths and weaknesses of the two methods when applied to chemically modified duplexes are also addressed.
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Affiliation(s)
- Kareem Fakhfakh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis B Hughesman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vincent Kao
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada; RES'EAU Water Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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14
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Solovyev AY, Tarnovskaya SI, Chernova IA, Shataeva LK, Skorik YA. The interaction of amino acids, peptides, and proteins with DNA. Int J Biol Macromol 2015; 78:39-45. [PMID: 25841380 DOI: 10.1016/j.ijbiomac.2015.03.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 10/23/2022]
Abstract
Amino acids that carry charges on their side groups can bind to double stranded DNA (dsDNA) and change the strength of the double helix. Measurement of the DNA melting temperature (Tm) confirmed that acidic amino acids (Glu, Asp) weaken the H-bonds between DNA strands, whereas basic amino acids (Arg, Lys) strengthen the interaction between the strands. A rank correlation exists between the amino acid isoelectric points and the observed changes in Tm. A similar dependence of the hyperchromic effect on the isoelectric point of a protein (pepsin, insulin, cortexin, and protamine) was observed for DNA-protein complexes at room temperature. Short peptides (KE, AEDG, and KEDP) containing a mixture of acidic and basic amino acid residues also affect Tm and the stability of the double helix. A model for binding Glu and Lys to dsDNA was explored by a docking simulation. The model shows that Glu, in an untwisted shape, binds to dsDNA in its major groove and disrupts three H-bonds between the strands, thereby destabilizing the double helix. Lys, in an untwisted shape, binds to the external side of the dsDNA and forms two bonds with O atoms of neighboring phosphodiester groups, thereby strengthening the DNA helix.
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Affiliation(s)
- Andrey Y Solovyev
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation
| | - Svetlana I Tarnovskaya
- St. Petersburg State Polytechnical University, Polytekhnicheskaya ul. 29, St. Petersburg 195251, Russian Federation
| | - Irina A Chernova
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation
| | - Larisa K Shataeva
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation
| | - Yury A Skorik
- Institute of Macromolecular Compounds of the Russian Academy of Sciences, Bolshoy pr. VO 31, St. Petersburg 199004, Russian Federation; St. Petersburg State Chemical Pharmaceutical Academy, ul. Prof. Popova 14, St. Petersburg 197022, Russian Federation.
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15
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Cheneke B, van den Berg B, Movileanu L. Quasithermodynamic contributions to the fluctuations of a protein nanopore. ACS Chem Biol 2015; 10:784-94. [PMID: 25479108 PMCID: PMC4372101 DOI: 10.1021/cb5008025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Proteins undergo thermally activated conformational fluctuations among two or more substates, but a quantitative inquiry on their kinetics is persistently challenged by numerous factors, including the complexity and dynamics of various interactions, along with the inability to detect functional substates within a resolvable time scale. Here, we analyzed in detail the current fluctuations of a monomeric β-barrel protein nanopore of known high-resolution X-ray crystal structure. We demonstrated that targeted perturbations of the protein nanopore system, in the form of loop-deletion mutagenesis, accompanying alterations of electrostatic interactions between long extracellular loops, produced modest changes of the differential activation free energies calculated at 25 °C, ΔΔG(⧧), in the range near the thermal energy but substantial and correlated modifications of the differential activation enthalpies, ΔΔH(⧧), and entropies, ΔΔS(⧧). This finding indicates that the local conformational reorganizations of the packing and flexibility of the fluctuating loops lining the central constriction of this protein nanopore were supplemented by changes in the single-channel kinetics. These changes were reflected in the enthalpy-entropy reconversions of the interactions between the loop partners with a compensating temperature, TC, of ∼300 K, and an activation free energy constant of ∼41 kJ/mol. We also determined that temperature has a much greater effect on the energetics of the equilibrium gating fluctuations of a protein nanopore than other environmental parameters, such as the ionic strength of the aqueous phase as well as the applied transmembrane potential, likely due to ample changes in the solvation activation enthalpies. There is no fundamental limitation for applying this approach to other complex, multistate membrane protein systems. Therefore, this methodology has major implications in the area of membrane protein design and dynamics, primarily by revealing a better quantitative assessment on the equilibrium transitions among multiple well-defined and functionally distinct substates of protein channels and pores.
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Affiliation(s)
- Belete
R. Cheneke
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Bert van den Berg
- Institute
for Cellular and Molecular Biosciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Structural
Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, United States
- Syracuse
Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, New York 13244, United States
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16
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Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. Nucleic Acids Res 2013; 41:1005-16. [PMID: 23193257 PMCID: PMC3553954 DOI: 10.1093/nar/gks1135] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/22/2012] [Indexed: 01/16/2023] Open
Abstract
DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K(+)-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. As Raman spectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G(3)(TTAG(3))(3) in the presence of K(+) and Na(+) ions throughout wide range of DNA concentrations. We demonstrate that the K(+)-structure of G(3)(TTAG(3))(3) at low DNA concentration is close to the antiparallel fold of Na(+)-stabilized quadruplex. On the increase of G(3)(TTAG(3))(3) concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K(+)-stabilized samples. The transition is synergically supported by increased K(+) concentration. However, even for extremely high G(3)(TTAG(3))(3) and K(+) concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K(+) ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na(+)-stabilized G(3)(TTAG(3))(3) retains its antiparallel folding regardless of the extremely high DNA and/or Na(+) concentrations, thermal destabilization or annealing.
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Affiliation(s)
- Jan Palacký
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Iva Kejnovská
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Peter Mojzeš
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
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17
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Movileanu L, Schiff EA. Entropy-enthalpy Compensation of Biomolecular Systems in Aqueous Phase: a Dry Perspective. MONATSHEFTE FUR CHEMIE 2012; 144:59-65. [PMID: 23976794 DOI: 10.1007/s00706-012-0839-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We survey thermodynamic measurements on processes involving biological macromolecules in aqueous solution, which illustrate well the ubiquitous phenomenon of entropy-enthalpy compensation. The processes include protein folding/unfolding and ligand binding/unbinding, with compensation temperatures varying by about 50 K around an average near 293 K. We show that incorporating both near-exact entropy-enthalpy compensation (due to solvent relaxation) and multi-excitation entropy (from vibrational quanta) leads to a compensation temperature in water of about 230 K. We illustrate a general procedure for subtracting solvent and environment-related terms to determine the bare Gibbs free energy changes of chemical processes.
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Affiliation(s)
- Liviu Movileanu
- Department of Physics, Syracuse University, Syracuse, New York USA
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18
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Cheneke BR, Indic M, van den Berg B, Movileanu L. An outer membrane protein undergoes enthalpy- and entropy-driven transitions. Biochemistry 2012; 51:5348-58. [PMID: 22680931 DOI: 10.1021/bi300332z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
β-Barrel membrane proteins often fluctuate among various open substates, yet the nature of these transitions is not fully understood. Using temperature-dependent, single-molecule electrophysiology analysis, along with rational protein design, we show that OccK1, a member of the outer membrane carboxylate channel from Pseudomonas aeruginosa, features a discrete gating dynamics comprising both enthalpy-driven and entropy-driven current transitions. OccK1 was chosen for the analysis of these transitions, because it is a monomeric transmembrane β-barrel of a known high-resolution crystal structure and displays three distinguishable, time-resolvable open substates. Native and loop-deletion OccK1 proteins showed substantial changes in the activation enthalpies and entropies of the channel transitions, but modest alterations in the equilibrium free energies, confirming that the system never departs from equilibrium. Moreover, some current fluctuations of OccK1 indicated a counterintuitive, negative activation enthalpy, which was compensated by a significant decrease in the activation entropy. Temperature scanning of the single-channel properties of OccK1 exhibited a thermally induced switch of the energetically most favorable open substate at the lowest examined temperature of 4 °C. Therefore, such a semiquantitative assessment of the current fluctuation dynamics not only demonstrates the complexity of channel gating but also reveals distinct functional traits of a β-barrel outer membrane protein under different temperature circumstances.
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Affiliation(s)
- Belete R Cheneke
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
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19
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Cuesta-López S, Menoni H, Angelov D, Peyrard M. Guanine radical chemistry reveals the effect of thermal fluctuations in gene promoter regions. Nucleic Acids Res 2011; 39:5276-83. [PMID: 21398632 PMCID: PMC3130270 DOI: 10.1093/nar/gkr096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/24/2022] Open
Abstract
DNA is not the static entity that structural pictures suggest. It has been longly known that it 'breathes' and fluctuates by local opening of the bases. Here we show that the effect of structural fluctuations, exhibited by AT-rich low stability regions present in some common transcription initiation regions, influences the properties of DNA in a distant range of at least 10 bp. This observation is confirmed by experiments on genuine gene promoter regions of DNA. The spatial correlations revealed by these experiments throw a new light on the physics of DNA and could have biological implications, for instance by contributing to the cooperative effects needed to assemble the molecular machinery that forms the transcription complex.
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Affiliation(s)
- Santiago Cuesta-López
- Université de Lyon, Laboratoire de Physique CNRS UMR 5672 and Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Hervé Menoni
- Université de Lyon, Laboratoire de Physique CNRS UMR 5672 and Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Dimitar Angelov
- Université de Lyon, Laboratoire de Physique CNRS UMR 5672 and Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 7, France
| | - Michel Peyrard
- Université de Lyon, Laboratoire de Physique CNRS UMR 5672 and Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 7, France
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20
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Cheneke BR, van den Berg B, Movileanu L. Analysis of gating transitions among the three major open states of the OpdK channel. Biochemistry 2011; 50:4987-97. [PMID: 21548584 PMCID: PMC3107985 DOI: 10.1021/bi200454j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OpdK is an outer membrane protein of the pathogenic bacterium Pseudomonas aeruginosa. The recent crystal structure of this protein revealed a monomeric, 18-stranded β-barrel with a kidney-shaped pore, whose constriction features a diameter of 8 Å. Using systematic single-channel electrical recordings of this protein pore reconstituted into planar lipid bilayers under a broad range of ion concentrations, we were able to probe its discrete gating kinetics involving three major and functionally distinct conformations, in which a dominant open substate O(2) is accompanied by less thermodynamically stable substates O(1) and O(3). Single-channel electrical data enabled us to determine the alterations in the energetics and kinetics of the OpdK protein when experimental conditions were changed. In the future, such a semiquantitative analysis might provide a better understanding on the dynamics of current fluctuations of other β-barrel membrane protein channels.
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Affiliation(s)
- Belete R. Cheneke
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Bert van den Berg
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Syracuse Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, New York 13244, USA
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21
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Khandelwal G, Bhyravabhotla J. A phenomenological model for predicting melting temperatures of DNA sequences. PLoS One 2010; 5:e12433. [PMID: 20865157 PMCID: PMC2928768 DOI: 10.1371/journal.pone.0012433] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/02/2010] [Indexed: 11/29/2022] Open
Abstract
We report here a novel method for predicting melting temperatures of DNA sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of DNA. The model presented here attempts to quantify the energetic components stabilizing the structure of DNA such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. The model gives a Pearson product-moment correlation coefficient (r) of approximately 0.98 between experimental and predicted melting temperatures for over 300 sequences of varying lengths ranging from 15-mers to genomic level and at different salt concentrations. The approach is implemented as a web tool (www.scfbio-iitd.res.in/chemgenome/Tm_predictor.jsp) for the prediction of melting temperatures of DNA sequences.
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Affiliation(s)
- Garima Khandelwal
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, India
| | - Jayaram Bhyravabhotla
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, India
- School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
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22
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Kratochvílová I, Todorciuc T, Král K, Nemec H, Buncek M, Sebera J, Zális S, Vokácová Z, Sychrovský V, Bednárová L, Mojzes P, Schneider B. Charge transport in DNA oligonucleotides with various base-pairing patterns. J Phys Chem B 2010; 114:5196-205. [PMID: 20353252 DOI: 10.1021/jp100264v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.
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Affiliation(s)
- Irena Kratochvílová
- Institute of Physics AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8, Czech Republic.
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23
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Shaw CP, Jirasek A. The use of ultraviolet resonance Raman spectroscopy in the analysis of ionizing-radiation-induced damage in DNA. APPLIED SPECTROSCOPY 2009; 63:412-422. [PMID: 19366507 DOI: 10.1366/000370209787944325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ultraviolet resonance Raman spectroscopy (UVRRS) was used to determine damage done in both calf-thymus DNA (CT-DNA) and a short stranded DNA oligomer (SS-DNA) due to ionizing radiation from a medical (60)Co radiation therapy unit used in the treatment of cancer. Spectra were acquired at incident UV wavelengths of 248, 257, and 264 nm in order to utilize the differences in UVRR cross-sections of the bases with wavelength. Through the analysis of difference spectra between irradiated and unirradiated DNA at each of the incident UV wavelengths, damage to CT- and SS-DNA was observed and identified. Significant radiation-induced increases in the difference spectra of the CT-DNA indicated disruption of the stable, stacked structure of its bases, as well as the disruption of Watson-Crick hydrogen bonds between the base pairs. Base unstacking was not as evident in the SS-DNA, while radiation-induced spectral decreases suggest disruption of the structure of the nucleotides. As demonstrated, UVRRS has the ability to highlight contributions from specific moieties with the use of varying incident UV wavelengths, thus enhancing the already information-rich content of the Raman spectra.
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Affiliation(s)
- C P Shaw
- Department of Physics and Astronomy, University of Victoria, Victoria, B.C., Canada
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24
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Peyrard M, Cuesta-López S, Angelov D. Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:034103. [PMID: 21817248 DOI: 10.1088/0953-8984/21/3/034103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the timescales associated with the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available (Montrichok et al 2003 Europhys. Lett. 62 452), we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.
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Affiliation(s)
- M Peyrard
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS UMR 5672, 46 allée d'Italie, F-69364 Lyon Cedex 07, France
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25
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Abstract
We have measured temperature-dependent (between 20 and80∘C) electrical conductivity and molecular structure (Raman spectroscopy) of DNA-lipid cast film. Our findings show that the conductivity is strongly influenced by premelting effects in the molecular structure starting near physiological temperatures (∼40∘C), prior to the global DNA denaturation.
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26
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Stepanek J, Vincent M, Turpin PY, Paulin D, Fermandjian S, Alpert B, Zentz C. C-->G base mutations in the CArG box of c-fos serum response element alter its bending flexibility. Consequences for core-SRF recognition. FEBS J 2007; 274:2333-48. [PMID: 17403043 DOI: 10.1111/j.1742-4658.2007.05768.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
By binding to the CArG box sequence, the serum response factor (SRF) activates several muscle-specific genes, as well as genes that respond to mitogens. The core domain of the SRF (core-SRF) binds as a dimer to the CArG box C-5C-4A-3T-2A-1T+1T+2A+3G+4G+5 of the c-fos serum response element (SREfos). However, previous studies using 20-mer DNAs have shown that the binding stoichiometry of core-SRF is significantly altered by mutations C-5-->G (SREGfos) and C-5C-4-->GG (SREGGfos) of the CArG box [A Huet, A Parlakian, M-C Arnaud, J-M Glandières, P Valat, S Fermandjian, D Paulin, B Alpert & C Zentz (2005) FEBS J272, 3105-3119]. To understand these effects, we carried out a comparative analysis of the three 20-mer DNAs SREfos, SREGfos and SREGGfos in aqueous solution. Their CD spectra were of the B-DNA type with small differences generated by variations in the mutual arrangement of the base pairs. Analysis by singular value decomposition of a set of Raman spectra recorded as a function of temperature, revealed a premelting transition associated with a conformational shift in the DNA double helices from a bent to a linear form. Time-resolved fluorescence anisotropy shows that the fluorescein reporter linked to the oligonucleotide 5'-ends experiences twisting motions of the double helices related to the interconversion between bent and linear conformers. The three SREs present various bent populations submitted, however, to particular internal dynamics, decisive for the mutual adjustment of binding partners and therefore specific complex formation.
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Affiliation(s)
- Josef Stepanek
- Laboratoire de Biophysique Moléculaire Cellulaire & Tissulaire, Université Pierre et Marie Curie, Evry, France
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27
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Patel MM, Anchordoquy TJ. Ability of spermine to differentiate between DNA sequences--preferential stabilization of A-tracts. Biophys Chem 2006; 122:5-15. [PMID: 16504371 DOI: 10.1016/j.bpc.2006.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 02/07/2006] [Accepted: 02/07/2006] [Indexed: 11/16/2022]
Abstract
The regulatory roles fulfilled by polyamines by governance of chromatin structure are made possible by their strong association with cellular DNA, and hence by their ability to modulate DNA structure and function. Towards this end, it is crucial to understand the manifestation of sequence-dependent polyamine binding at the secondary and tertiary structural levels of DNA. This study utilizes circular dichroism (CD) and isothermal titration calorimetry (ITC) to address this relationship by using 20bp oligonucleotides with sequences-poly(dA):poly(dT), poly(dAdT):poly(dAdT), poly(dG):poly(dC), poly(dGdC):poly(dGdC)-that yield physiologically relevant structures, and poly(dIdC):poly(dIdC). CD studies show that at physiological ionic strength (150mM NaCl), spermine preferentially stabilizes A-tracts, and increases flexibility of the G-tract oligomer; the latter is also suggested by the larger change in entropy (DeltaS) of spermine binding to G-tracts. Given the chromatin destabilizing property of these sequences, these findings suggest a role for spermine in stabilization of non-nucleosomal A-tracts, and a compensating mechanism for incorporation of G-tracts in the chromatin structure. Other implications of these findings in sequence dependent DNA packaging are discussed.
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Affiliation(s)
- Mayank M Patel
- Department of Pharmaceutical Sciences, School of Pharmacy--C238, University of Colorado Health Sciences Center, 4200 E. Ninth Avenue, Denver, CO 80262, USA.
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28
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Abstract
T(m) is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. Beyond a simple numerical value (the T(m)), a thermal denaturation experiment, in which the folded fraction of a structure is plotted vs. temperature, yields important thermodynamic information. We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves.
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Affiliation(s)
- Jean-Louis Mergny
- Laboratoire de Biophysique, INSERM UR565, CNRS UMR 5153, Muséum National d'Histoire Naturelle, 75231 Paris, France.
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29
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De Luchi D, Gouyette C, Subirana JA. The influence of size on the thermal stability of oligonucleotides: the case of AT sequences. Anal Biochem 2004; 322:279-82. [PMID: 14596840 DOI: 10.1016/j.ab.2003.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Daniela De Luchi
- Department d'Enginyeria Quimica, ETSEIB, Universitat Politècnica de Catalunya, Av Diagonal 647, E-08028, Barcelona, Spain
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Zozulya VN, Nesterov AB, Ryazanova OA, Blagoi YP. Conformational transitions and aggregation in poly(dA)-poly(dT) system induced by Na+ and Mg2+ ions. Int J Biol Macromol 2004; 33:183-91. [PMID: 14607363 DOI: 10.1016/j.ijbiomac.2003.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Effects of Mg(2+) ions on thermally induced conformational transitions in the synthetic poly(dA).poly(dT) and poly(dA).2poly(dT) were studied in the buffered solutions (pH 6.9), containing 0.1 or 1M NaCl at polynucleotide concentration of 0.1-0.3mM (in nucleic bases). The experiments consist of measurements of the UV absorption and intensity of conventional visible static light scattering. The diagram of conformational transitions in the poly(dA)-poly(dT)-Mg(2+) system was constructed on a basis of experimental data obtained. Anomalously strong light scattering, like critical opalescence, has been revealed at 0.1M NaCl and [Mg(2+)]>/=20mM in the melting range of both polynucleotides, which eventually disappeared after the completion of polymer strands separation. The effect presumably is caused by a fluctuation process of polymer strands complexing which arises at a certain concentration of Mg(2+) ions.
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Affiliation(s)
- V N Zozulya
- Institute for Low Temperature Physics and Engineering of National Academy of Sciences of Ukraine, 47 Lenin Ave., 61103 Kharkov, Ukraine.
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Dong R, Yan X, Pang X, Liu S. Temperature-dependent Raman spectra of collagen and DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:557-561. [PMID: 14747079 DOI: 10.1016/s1386-1425(03)00262-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Raman spectra of collagen and DNA were discussed at different temperatures. The temperature-dependence of Raman intensity was obtained in the region from -150 to 200 degrees C. Four denaturation points at 0, 40, 68 and 90 degrees C of collagen and two peaks at 38 and 82 degrees C for DNA were obtained. The wavenumbers of many vibrational modes were found to increase for lower temperature, but the peak at 1302 cm(-1) of collagen and the peak at 1101 cm(-1) of DNA showed the opposite trend. In all of the vibrational modes of DNA, the bases showed the most sensitive to different temperatures and there is a pronounced shift of bands at 70 degrees C, the starting point of denaturation.
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Affiliation(s)
- Ruixin Dong
- School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China.
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