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Hadži S, Lah J. Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures. Methods Mol Biol 2022; 2516:239-257. [PMID: 35922630 DOI: 10.1007/978-1-0716-2413-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.
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Affiliation(s)
- San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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Lah J, Hadži S. Conditional Cooperativity in DNA Minor-Groove Recognition by Oligopeptides. Molecules 2021; 26:molecules26175188. [PMID: 34500619 PMCID: PMC8434113 DOI: 10.3390/molecules26175188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The recognition of specific DNA sequences in processes such as transcription is associated with a cooperative binding of proteins. Some transcription regulation mechanisms involve additional proteins that can influence the binding cooperativity by acting as corepressors or coactivators. In a conditional cooperativity mechanism, the same protein can induce binding cooperativity at one concentration and inhibit it at another. Here, we use calorimetric (ITC) and spectroscopic (UV, CD) experiments to show that such conditional cooperativity can also be achieved by the small DNA-directed oligopeptides distamycin and netropsin. Using a global thermodynamic analysis of the observed binding and (un)folding processes, we calculate the phase diagrams for this system, which show that distamycin binding cooperativity is more pronounced at lower temperatures and can be first induced and then reduced by increasing the netropsin or/and Na+ ion concentration. A molecular interpretation of this phenomenon is suggested.
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Hadži S, Lah J. Origin of heat capacity increment in DNA folding: The hydration effect. Biochim Biophys Acta Gen Subj 2020; 1865:129774. [PMID: 33164852 DOI: 10.1016/j.bbagen.2020.129774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/09/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Understanding DNA folding thermodynamics is crucial for prediction of DNA thermal stability. It is now well established that DNA folding is accompanied by a decrease of the heat capacity ∆cp, F, however its molecular origin is not understood. In analogy to protein folding it has been assumed that this is due to dehydration of DNA constituents, however no evidence exists to support this conclusion. METHODS Here we analyze partial molar heat capacity of nucleic bases and nucleosides in aqueous solutions obtained from calorimetric experiments and calculate the hydration heat capacity contribution ∆cphyd. RESULTS We present hydration heat capacity contributions of DNA constituents and show that they correlate with the solvent accessible surface area. The average contribution for nucleic base dehydration is +0.56 J mol-1 K-1 Å-2 and can be used to estimate the ∆cp, F contribution for DNA folding. CONCLUSIONS We show that dehydration is one of the major sources contributing to the observed ∆cp, F increment in DNA folding. Other possible sources contributing to the overall ∆cp, F should be significant but appear to compensate each other to high degree. The calculated ∆cphyd for duplexes and noncanonical DNA structures agree excellently with the overall experimental ∆cp, F values. By contrast, empirical parametrizations developed for proteins result in poor ∆cphyd predictions and should not be applied to DNA folding. GENERAL SIGNIFICANCE Heat capacity is one of the main thermodynamic quantities that strongly affects thermal stability of macromolecules. At the molecular level the heat capacity in DNA folding stems from removal of water from nucleobases.
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Affiliation(s)
- S Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
| | - J Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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Nguyen GTH, Leung WY, Tran TN, Wang H, Murray V, Donald WA. Mechanism for the Binding of Netropsin to Hairpin DNA Revealed Using Nanoscale Ion Emitters in Native Mass Spectrometry. Anal Chem 2019; 92:1130-1137. [PMID: 31778608 DOI: 10.1021/acs.analchem.9b04209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Netropsin is one of the first ligands to be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for developing potential anticancer and antibiotic agents. The mechanism by which netropsin binds to hairpin DNA remains controversial with two competing mechanisms having been proposed. In one mechanism, netropsin binding induces a hairpin-to-duplex DNA transition. Alternatively, netropsin binds in two thermodynamically different modes at a single duplexed AATT site. Here, results from native mass spectrometry (MS) with nanoscale ion emitters indicate that netropsin can simultaneously and sequentially bind to both hairpin and duplex DNA. Duplex DNA was not detected using conventional MS with larger emitters because nanoscale emitters significantly reduce the extent of salt adduction to ligand-DNA complex ions, including in the presence of relatively high concentrations of nonvolatile salts. Based on native MS and polyacrylamide gel electrophoresis results, the abundances of hairpin and duplex DNA are unaffected by the addition of netropsin. By native MS, the binding affinities for five ligand-DNA and DNA-DNA interactions can be rapidly obtained simultaneously. This research indicates a "simultaneous binding mechanism" for the interactions of netropsin with DNA.
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Affiliation(s)
- Giang T H Nguyen
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Wai Yu Leung
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Thinh N Tran
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Huixin Wang
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia.,Mark Wainwright Analytical Centre , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - William A Donald
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
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Song Y, Niederschulte J, Bales KN, Park AH, Bashkin JK, Dupureur CM. DNA binding thermodynamics and site stoichiometry as a function of polyamide size. Biochimie 2019; 165:170-178. [DOI: 10.1016/j.biochi.2019.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022]
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DNA recognition by linear indole-biphenyl DNA minor groove ligands. Biophys Chem 2018; 245:6-16. [PMID: 30513446 DOI: 10.1016/j.bpc.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 11/21/2022]
Abstract
Linear heterocyclic cations are interesting DNA minor groove ligands due to their lack of isohelical curvature classically associated with groove-binding compounds. We determined the DNA binding properties of four related dications harboring a linear indole-biphenyl core: the diamidine DB1883, a ditetrahydropyrimidine derivative (DB1804), and their monocationic counterparts (DB1944 and DB2627). These compounds exhibit heterogeneity in binding in accordance with their structures. Whereas the monocations exhibit salt-sensitive 1:1 binding to the duplex 5'-CGCGAATTCGCG-3' (A2T2), the dications show a marked preference for a salt-insensitive 2:1 complex. The two binding modes are differentially modulated by salt and specific non-ionic co-solutes. For both dications, 2-methyl-2,4-pentanediol enforces 1:1 binding as observed crystallographically. Fluorescence quenching studies show self-association without DNA in a relative order that is correlated with preference for the 2:1 complex. The data support a structure-binding relationship in which favorable cation-π interactions drive dimer formation via antiparallel stacking of the linear indole-biphenyl cation motif.
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Prusov AN, Kolomijtseva GY, Smirnova TA. Differential scanning calorimetric study of antibiotic distamycin A binding with chromatin within isolated rat liver nuclei. PHARMACEUTICAL BIOLOGY 2017; 55:687-690. [PMID: 27982735 PMCID: PMC6130587 DOI: 10.1080/13880209.2016.1258427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CONTEXT Natural oligopeptide antibiotic distamycin A (Dst) biosynthesized by Streptomyces distallicus is traditionally used in medical practice as an anti-inflammatory and antitumour drug. OBJECTIVE Dst was investigated for its effect on the structural components of native chromatin directly within isolated rat liver nuclei in the presence of physiologically significant cations (magnesium or spermine and spermidine). MATERIALS AND METHODS Differential scanning calorimetry (DSC) was used to study the Dst action at molar ratio Dst/DNA = 0.1 and 0.15 mM Dst on the melting profile of nuclei suspension in different conditions. RESULTS Results showed that the thermodynamic parameters of control nuclei in the presence of polyamines or Mg2+ were different. The incubation of nuclei with Dst raised transition temperatures of relaxed (peak II) and topologically constrained DNA (peak III) by 6-8 °C and decreased by 2-4 °C that of core-histones (peak I). The total excess transition enthalpy (ΔHexc) in buffer with polyamines (24.7 kJ/mol DNA nucleotides) increased by1.5 times versus control but in buffer with Mg2+, the value of ΔHexc (35.8 kJ/mol DNA nucleotides) remained unchanged. CONCLUSIONS The association of Dst with chromatin in the nucleus weakens histone-DNA contacts and causes additional strengthening of interaction between two complementary DNA chains. Our results contribute towards validation of DSC to test drug ability to modulate chromatin structure in the physiological environment and to clarify the mechanism of these modulations.
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Affiliation(s)
- Andrey N. Prusov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- CONTACT Andrey N. PrusovM.V. Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-Chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow119991, Russia
| | - Galina Ya. Kolomijtseva
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana A. Smirnova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Jabasini M, Ewis A, Sato Y, Nakahori Y, Baba Y. Anomalous Separation of Small Y-Chromosomal DNA Fragments on Microchip Electrophoresis. Sci Pharm 2016; 84:507-513. [PMID: 28117316 PMCID: PMC5064241 DOI: 10.3390/scipharm84030507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/13/2016] [Indexed: 11/16/2022] Open
Abstract
We investigated an anomalous DNA separation where two DNA fragments from the human Y-chromosome sY638 (64 bp) and sY592 (65 bp), with only one base pair difference, were separated. This result is abnormal since in a previous study, we found that 5 bp was the minimum difference between two DNA fragments that the microchip electrophoresis system can separate. The formation of a mini-loop in the structure of the DNA fragment of sY638 (64 bp) was strongly expected to be the reason. To investigate this, we synthesized three modified DNA fragments for sY638 (64 bp), and the modifications were in two expected locations for possible mini-loop formation. Later, the separation between sY592 (65 bp) and the three modified fragments of sY638 (64 bp) was not possible. Thus, we conclude that the formation of a mini-loop in the structure of the DNA is the reason behind this anomalous separation.
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Affiliation(s)
- Mohammad Jabasini
- Department of Pharmaceutical Information Science, Institute of Health Biosciences, The University of Tokushima, 1-78-1 Sho-machi, 770-8505 Tokushima, Japan.
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, 464-8603 Nagoya, Japan.
| | - Ashraf Ewis
- Department of Human Genetics Public Health, School of Medicine, The University of Tokushima, 3-18-15 Kuramoto-cho, 770-8503 Tokushima, Japan.
| | - Youichi Sato
- Department of Pharmaceutical Information Science, Institute of Health Biosciences, The University of Tokushima, 1-78-1 Sho-machi, 770-8505 Tokushima, Japan.
| | - Yutaka Nakahori
- Department of Human Genetics Public Health, School of Medicine, The University of Tokushima, 3-18-15 Kuramoto-cho, 770-8503 Tokushima, Japan.
| | - Yoshinobu Baba
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, 464-8603 Nagoya, Japan.
- ImPACT Research Center for Advanced Nanobiodevices., Nagoya University, Furo-cho, Chikusa-ku, 464-8603 Nagoya, Japan.
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hayashi-cho 2217-14, 761-0395 Takamatsu, Japan.
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Bončina M, Hamon F, Islam B, Teulade-Fichou MP, Vesnaver G, Haider S, Lah J. Dominant Driving Forces in Human Telomere Quadruplex Binding-Induced Structural Alterations. Biophys J 2016; 108:2903-11. [PMID: 26083930 DOI: 10.1016/j.bpj.2015.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/07/2015] [Accepted: 05/03/2015] [Indexed: 01/23/2023] Open
Abstract
Recently various pathways of human telomere (ht) DNA folding into G-quadruplexes and of ligand binding to these structures have been proposed. However, the key issue as to the nature of forces driving the folding and recognition processes remains unanswered. In this study, structural changes of 22-mer ht-DNA fragment (Tel22), induced by binding of ions (K(+), Na(+)) and specific bisquinolinium ligands, were monitored by calorimetric and spectroscopic methods and by gel electrophoresis. Using the global model analysis of a wide variety of experimental data, we were able to characterize the thermodynamic forces that govern the formation of stable Tel22 G-quadruplexes, folding intermediates, and ligand-quadruplex complexes, and then predict Tel22 behavior in aqueous solutions as a function of temperature, salt concentration, and ligand concentration. On the basis of the above, we believe that our work sets the framework for better understanding the heterogeneity of ht-DNA folding and binding pathways, and its structural polymorphism.
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Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Florian Hamon
- Institut Curie, Centre National de la Recherche Scientifique UMR-176, Centre Universitaire d'Orsay, Orsay, France
| | - Barira Islam
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Centre National de la Recherche Scientifique UMR-176, Centre Universitaire d'Orsay, Orsay, France
| | - Gorazd Vesnaver
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Shozeb Haider
- Centre for Cancer Research and Cell Biology, Queen's University of Belfast, Belfast, UK; University College London School of Pharmacy, Bloomsbury, London, UK
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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Hostnik G, Bončina M, Dolce C, Mériguet G, Rollet AL, Cerar J. Influence of counterions on the conformation of conjugated polyelectrolytes: the case of poly(thiophen-3-ylacetic acid). Phys Chem Chem Phys 2016; 18:25036-25047. [DOI: 10.1039/c6cp04193k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Binding of large hydrophobic counterions to poly(thiophen-3-ylacetate) provokes the conformational change of this conjugated polyelectrolyte.
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Affiliation(s)
- Gregor Hostnik
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Matjaž Bončina
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Caterina Dolce
- Sorbonne Universités
- UPMC Univ Paris 06
- CNRS
- Laboratoire PHENIX
- Paris
| | | | | | - Janez Cerar
- Faculty of Chemistry and Chemical Technology
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
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Bončina M, Podlipnik Č, Piantanida I, Eilmes J, Teulade-Fichou MP, Vesnaver G, Lah J. Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes. Nucleic Acids Res 2015; 43:10376-86. [PMID: 26546516 PMCID: PMC4666371 DOI: 10.1093/nar/gkv1167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/21/2015] [Indexed: 01/13/2023] Open
Abstract
Thermodynamic studies of ligand binding to human telomere (ht) DNA quadruplexes, as a rule, neglect the involvement of various ht-DNA conformations in the binding process. Therefore, the thermodynamic driving forces and the mechanisms of ht-DNA G-quadruplex-ligand recognition remain poorly understood. In this work we characterize thermodynamically and structurally binding of netropsin (Net), dibenzotetraaza[14]annulene derivatives (DP77, DP78), cationic porphyrin (TMPyP4) and two bisquinolinium ligands (Phen-DC3, 360A-Br) to the ht-DNA fragment (Tel22) AGGG(TTAGGG)3 using isothermal titration calorimetry, CD and fluorescence spectroscopy, gel electrophoresis and molecular modeling. By global thermodynamic analysis of experimental data we show that the driving forces characterized by contributions of specific interactions, changes in solvation and conformation differ significantly for binding of ligands with low quadruplex selectivity over duplexes (Net, DP77, DP78, TMPyP4; KTel22 ≈ <KdsDNA) and for highly selective quadruplex-specific ligands (Phen-DC3, 360A-Br; KTel22 > KdsDNA). These contributions are in accordance with the observed structural features (changes) and suggest that upon binding Net, DP77, DP78 and TMPyP4 select hybrid-1 and/or hybrid-2 conformation while Phen-DC3 and 360A-Br induce the transition of hybrid-1 and hybrid-2 to the structure with characteristics of antiparallel or hybrid-3 type conformation.
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Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Julita Eilmes
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | | | - Gorazd Vesnaver
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
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Bončina M, Lukšič M, Seručnik M, Vlachy V. Thermodynamic analysis of the interaction of partially hydrophobic cationic polyelectrolytes with sodium halide salts in water. Mol Phys 2014. [DOI: 10.1080/00268976.2013.871365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Xu Z, Brodbelt JS. Differentiation and distributions of DNA/cisplatin crosslinks by liquid chromatography-electrospray ionization-infrared multiphoton dissociation mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:71-79. [PMID: 24135806 PMCID: PMC3880628 DOI: 10.1007/s13361-013-0755-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/08/2013] [Accepted: 09/17/2013] [Indexed: 06/02/2023]
Abstract
Liquid chromatography-electrospray ionization-infrared multiphoton dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), which have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared with the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink.
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Cao J, Wei Y, Cheng Y, Guo LH. Study on the binding interaction between perfluoroalkyl acids and DNA. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:8355-8363. [PMID: 23645002 DOI: 10.1007/s11356-013-1760-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 04/22/2013] [Indexed: 06/02/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are carcinogens, and elucidating their DNA binding properties is crucial for understanding PFAA genotoxicity. We have investigated the binding mode and affinity of five PFAAs to seven DNA molecules using fluorescence displacement and molecular docking analysis. DNA conformational changes upon PFAA binding were also examined by circular dichroism (CD). The data revealed that DNA intercalation was the dominant interaction mode of the PFAAs; however, these molecules also bound to grooves. The dissociation constants for the PFAAs ranged between 0.11 and 1,217.14 μM, and between 3.46 and 2,141.21 μM for DNA intercalation and groove binding, respectively. PFAAs that contain longer carbon chains had stronger DNA intercalation affinities. Binding to DNA was stronger for perfluoroalkyl sulfonates than for perfluorcarboxyl acids that contain the same number of carbons. This observation is postulated to arise from the presence of more fluorine and oxygen atoms in perfluoroalkyl sulfonates acting as hydrogen bond donors that facilitate stronger DNA intercalation. The binding of the PFAAs to DNA showed some CT-DNA sequence selectivity. Molecular docking analysis confirmed the DNA binding mode and affinities of the PFAAs. CD analysis revealed that the PFAAs weakened DNA base stacking and loosened DNA helicity. The present study has improved our understanding of the formation of PFAA-DNA adducts.
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Affiliation(s)
- Jie Cao
- AQSIQ Key Laboratory of Drug Detection, Fujian International Travel Healthcare Center, Fujian Entry-Exit Inspection and Quarantine Bureau of P.R.C., Fujian, 350001, China
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Bončina M, Lah J, Prislan I, Vesnaver G. Energetic basis of human telomeric DNA folding into G-quadruplex structures. J Am Chem Soc 2012; 134:9657-63. [PMID: 22594380 DOI: 10.1021/ja300605n] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent theoretical studies performed on the folding/unfolding mechanism of the model telomeric human DNA, 5'-AGGGTTAGGGTTAGGGTTAGGG-3' (Tel22), have indicated that in the presence of K(+) ions Tel22 folds into two hybrid G-quadruplex structures characterized by one double and two reversal TTA loops arranged in a different way. They predicted a new unfolding pathway from the initial mixture of hybrid G-quadruplexes via the corresponding intermediate triplex structures into the final, fully unfolded state. Significantly, no experimental evidence supporting the suggested pathway has been reported. In the current work, we performed a comprehensive global thermodynamic analysis of calorimetric (DSC, ITC) and spectroscopic (CD) data obtained on monitoring the folding/unfolding of Tel22 induced by changes of temperature and K(+) concentration. We show that unfolding of Tel22 may be described as a monomolecular equilibrium three-state process that involves thermodynamically distinguishable folded (F), intermediate (I), and unfolded (U) state. Considering that calorimetric methods cannot distinguish between energetically similar G-quadruplex or triplex conformations predicted by the theoretical model one can conclude that our results represent the first experimental support of the suggested unfolding/folding mechanism of Tel22. This conclusion is confirmed by the fact that the estimated number of K(+) ions released upon each unfolding step in our thermodynamic model agrees well with the corresponding values predicted by the theoretical model and that the observed changes in enthalpy, entropy, and heat capacity accompanying the F → I and I → U transitions can be reasonably explained only if the intermediate state I is considered to be a triplex structural conformation.
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Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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De Jonge N, Simic M, Buts L, Haesaerts S, Roelants K, Garcia-Pino A, Sterckx Y, De Greve H, Lah J, Loris R. Alternative interactions define gyrase specificity in the CcdB family. Mol Microbiol 2012; 84:965-78. [DOI: 10.1111/j.1365-2958.2012.08069.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Melting behavior and ligand binding of DNA intramolecular secondary structures. Biophys Chem 2011; 159:162-71. [DOI: 10.1016/j.bpc.2011.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/23/2022]
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Lewis EA, Munde M, Wang S, Rettig M, Le V, Machha V, Wilson WD. Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site. Nucleic Acids Res 2011; 39:9649-58. [PMID: 21890907 PMCID: PMC3239193 DOI: 10.1093/nar/gkr699] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Structural results with minor groove binding agents, such as netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.
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Affiliation(s)
- Edwin A Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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Lah J, Seručnik M, Vesnaver G. Influence of a hairpin loop on the thermodynamic stability of a DNA oligomer. J Nucleic Acids 2011; 2011:513910. [PMID: 21904665 PMCID: PMC3166569 DOI: 10.4061/2011/513910] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/16/2011] [Indexed: 11/23/2022] Open
Abstract
DSC was used to evaluate the mechanism of the thermally induced unfolding of the single-stranded hairpin HP = 5′-CGGAATTCCGTCTCCGGAATTCCG-3′ and its core duplex D (5′-CGGAATTCCG-3′)2. The DSC melting experiments performed at several salt concentrations were successfully described for HP and D in terms of a three-state transition model HP↔I (intermediate state) ↔ S (unfolded single-stranded state) and two state transition model D↔2S, respectively. Comparison of the model-based thermodynamic parameters obtained for each HP and D transition shows that in unfolding of HP only the HP↔I transition is affected by the TCTC loop. This observation suggests that in the intermediate state its TCTC loop part exhibits significantly more flexible structure than in the folded state while its duplex part remains pretty much unchanged.
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Affiliation(s)
- Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia
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Zhang YL, Zhang X, Fei XC, Wang SL, Gao HW. Binding of bisphenol A and acrylamide to BSA and DNA: insights into the comparative interactions of harmful chemicals with functional biomacromolecules. JOURNAL OF HAZARDOUS MATERIALS 2010; 182:877-885. [PMID: 20673609 DOI: 10.1016/j.jhazmat.2010.06.131] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/21/2010] [Accepted: 06/30/2010] [Indexed: 05/29/2023]
Abstract
The interactions between bisphenol A (BPA)/acrylamide (AA) and bovine serum albumin (BSA)/deoxyribonucleic acid (DNA) was investigated by the equilibrium dialysis, fluorophotometry, isothermal titration calorimetry (ITC) and circular dichroism (CD). The bindings of BPA and AA to BSA and DNA responded to the partition law and Langmuir isothermal model, respectively. The saturation mole number of AA was calculated to be 24 per mol BSA and 0.26 per mol DNA-P. All the reactions were spontaneous driven by entropy change. BPA stacked into the aromatic hydrocarbon groups of BSA and between adjacent basepairs of DNA via the hydrophobic effect. The interactions of AA with BSA and DNA induced the formation of hydrogen bond and caused changes of their secondary structures. At normal physiological condition, 0.100 mmol/l BPA reduced the binding of vitamin B(2) to BSA by more than 70%, and 2.8 mmol/l AA by almost one half. This work provides an insight into non-covalent intermolecular interaction between organic contaminant and biomolecule, helping to elucidate the toxic mechanism of harmful chemicals.
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Affiliation(s)
- Ya-Lei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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Bončina M, Lah J, Reščič J, Vlachy V. Thermodynamics of the Lysozyme−Salt Interaction from Calorimetric Titrations. J Phys Chem B 2010; 114:4313-9. [DOI: 10.1021/jp9071845] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Vojko Vlachy
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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Bren U, Lah J, Bren M, Martínek V, Florián J. DNA duplex stability: the role of preorganized electrostatics. J Phys Chem B 2010; 114:2876-85. [PMID: 20131770 PMCID: PMC2841231 DOI: 10.1021/jp9064246] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The insertion of a DNA base moiety at the end of a DNA duplex to form a Watson-Crick or wobble pair during DNA annealing or replication is a step of fundamental biological importance. Therefore, we investigated the energetics of a formation of the terminal G x C, G x T, and G x A base pairs in DNA containing a 5'-dangling G adjacent to the base insertion point using differential scanning calorimetry and computer simulations. The energies calculated along classical molecular dynamics trajectories in aqueous solution were analyzed in the framework of linear-response approximation (LRA) to obtain relative free energies for the base insertion and their electrostatic, van der Waals, and preorganization components. Using the generic set of LRA parameters, the calculated free energies disfavored the mispair formation by 2.5 (G x C --> G x T) and 1.7 (G x C --> G x A) kcal/mol, in reasonable agreement with the experimental free energy differences of 1.8 and 1.4 kcal/mol, respectively. The calculated preorganization components of these free energies of 0.6 (G x C --> G x T) and -0.1 (G x C --> G x A) kcal/mol show that electrostatic preorganization, which is an important source of DNA replication fidelity, plays a lesser role in the mispair destabilization in the absence of DNA polymerase.
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Affiliation(s)
- Urban Bren
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Matevž Bren
- Institute of Mathematics, Physics and Mechanics, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Václav Martínek
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
| | - Jan Florián
- Department of Chemistry, Loyola University Chicago, Chicago, IL 60626, USA
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Simic M, De Jonge N, Loris R, Vesnaver G, Lah J. Driving forces of gyrase recognition by the addiction toxin CcdB. J Biol Chem 2009; 284:20002-10. [PMID: 19465484 DOI: 10.1074/jbc.m109.014035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gyrase, an essential bacterial topoisomerase, is the target of several antibiotics (e.g. quinolones) as well as of bacterial toxin CcdB. This toxin, encoded by Escherichia coli toxin-antitoxin module ccd, poisons gyrase by causing inhibition of both transcription and replication. Because the molecular driving forces of gyrase unfolding and CcdB-gyrase binding were unknown, the nature of the CcdB-gyrase recognition remained elusive. Therefore, we performed a detailed thermodynamic analysis of CcdB binding to several fragments of gyrase A subunit (GyrA) that contain the CcdB-binding site. Binding of CcdB to the shorter fragments was studied directly by isothermal titration calorimetry. Its binding to the longer GyrA59 fragment in solution is kinetically limited and was therefore investigated via urea induced unfolding of the GyrA59-CcdB complex and unbound GyrA59 and CcdB, monitored by circular dichroism spectroscopy. Model analysis of experimental data, in combination with the relevant structural information, indicates that CcdB binding to gyrase is an enthalpic process driven mainly by specific interactions between CcdB and the highly stable dimerization domain of the GyrA. The dissection of binding energetics indicates that CcdB-gyrase recognition is accompanied by opening of the tower and catalytic domain of GyrA. Such extensive structural rearrangements appear to be crucial driving forces for the functioning of the ccd toxin-antitoxin module.
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Affiliation(s)
- Mario Simic
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, 1000 Ljubljana, Slovenia
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Zhang X, Chen L, Fei XC, Ma YS, Gao HW. Binding of PFOS to serum albumin and DNA: insight into the molecular toxicity of perfluorochemicals. BMC Mol Biol 2009; 10:16. [PMID: 19239717 PMCID: PMC2656506 DOI: 10.1186/1471-2199-10-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 02/25/2009] [Indexed: 11/12/2022] Open
Abstract
Background Health risk from exposure of perfluorochemicals (PFCs) to wildlife and human has been a subject of great interest for understanding their molecular mechanism of toxicity. Although much work has been done, the toxigenicity of PFCs remains largely unknown. In this work, the non-covalent interactions between perfluorooctane sulfonate (PFOS) and serum albumin (SA) and DNA were investigated under normal physiological conditions, aiming to elucidate the toxigenicity of PFCs. Results In equilibrium dialysis assay, the bindings of PFOS to SA correspond to the Langmuir isothermal model with two-step sequence model. The saturation binding number of PFOS was 45 per molecule of SA and 1 per three base-pairs of DNA, respectively. ITC results showed that all the interactions were spontaneous driven by entropy change. Static quenching of the fluorescence of SA was observed when interacting with PFOS, indicating PFOS bound Trp residue of SA. CD spectra of SA and DNA changed obviously in the presence of PFOS. At normal physiological conditions, 1.2 mmol/l PFOS reduces the binding ratio of Vitamin B2 to SA by more than 30%. Conclusion The ion bond, van der Waals force and hydrophobic interaction contributed to PFOS binding to peptide chain of SA and to the groove bases of DNA duplex. The non-covalent interactions of PFOS with SA and DNA alter their secondary conformations, with the physiological function of SA to transport Vitamin B2 being inhibited consequently. This work provides a useful experimental method for further studying the toxigenicity of PFCs.
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Affiliation(s)
- Xian Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China.
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Prislan I, Lah J, Vesnaver G. Diverse Polymorphism of G-Quadruplexes as a Kinetic Phenomenon. J Am Chem Soc 2008; 130:14161-9. [DOI: 10.1021/ja8026604] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Iztok Prislan
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Gorazd Vesnaver
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Aškerčeva 5, 1000 Ljubljana, Slovenia
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