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Lah J, Hadži S. Thermodynamic Origin of the Linear Pressure Dependence of DNA Thermal Stability. J Phys Chem Lett 2024; 15:9064-9069. [PMID: 39194396 PMCID: PMC11382263 DOI: 10.1021/acs.jpclett.4c01563] [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: 08/29/2024]
Abstract
High pressure affects the structure and function of DNA and is a key parameter for studying the origin and physical limits of life. Different types of DNA structures systematically show a linear pressure dependence of thermal stability (up to ∼200 MPa), which is maintained even when the solution composition is changed. The reasons behind the linear pressure dependence are not understood. We have performed a thermodynamic analysis of the pressure-, temperature- and composition-dependent (un)folding of various polynucleotide duplexes and G-quadruplexes. We demonstrate that the reason for the observed linearity is the link between compressibility and expansibility, both of which largely depend on DNA hydration. We predicted the temperature and pressure dependence of compressibility and expansibility of (un)folding and explain how they affect the corresponding volume change and thermodynamic stability parameters. These predictions indicate the existence of a convergence temperature at which compressibility and volume of (un)folding simultaneously become equal to zero.
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Affiliation(s)
- Jurij Lah
- Faculty of Chemistry and Chemical technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - San Hadži
- Faculty of Chemistry and Chemical technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
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2
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Rissone P, Severino A, Pastor I, Ritort F. Universal cold RNA phase transitions. Proc Natl Acad Sci U S A 2024; 121:e2408313121. [PMID: 39150781 PMCID: PMC11348302 DOI: 10.1073/pnas.2408313121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/12/2024] [Indexed: 08/18/2024] Open
Abstract
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick RNA hairpins, the most basic secondary structure elements, undergo a glass-like transition below [Formula: see text]C where the heat capacity abruptly changes and the RNA folds into a diversity of misfolded structures. We hypothesize that an altered RNA biochemistry, determined by sequence-independent ribose-water interactions, outweighs sequence-dependent base pairing. The ubiquitous ribose-water interactions lead to universal RNA phase transitions below TG, such as maximum stability at [Formula: see text]C where water density is maximum, and cold denaturation at [Formula: see text]C. RNA cold biochemistry may have a profound impact on RNA function and evolution.
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Affiliation(s)
- Paolo Rissone
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Barcelona 08028, Spain
| | - Aurélien Severino
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Barcelona 08028, Spain
| | - Isabel Pastor
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Barcelona 08028, Spain
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Barcelona 08028, Spain
- Institut de Nanociència i Nanotecnologia, Universitat de Barcelona, Barcelona 08028, Spain
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3
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Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
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4
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Perin N, Gulin M, Kos M, Persoons L, Daelemans D, Fabijanić I, Stojković MR, Hranjec M. Synthesis and Biological Evaluation of Novel Amino and Amido Substituted Pentacyclic Benzimidazole Derivatives as Antiproliferative Agents. Int J Mol Sci 2024; 25:2288. [PMID: 38396966 PMCID: PMC10889688 DOI: 10.3390/ijms25042288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Newly designed pentacyclic benzimidazole derivatives featuring amino or amido side chains were synthesized to assess their in vitro antiproliferative activity. Additionally, we investigated their direct interaction with nucleic acids, aiming to uncover potential mechanisms of biological action. These compounds were prepared using conventional organic synthesis methodologies alongside photochemical and microwave-assisted reactions. Upon synthesis, the newly derived compounds underwent in vitro testing for their antiproliferative effects on various human cancer cell lines. Notably, derivatives 6 and 9 exhibited significant antiproliferative activity within the submicromolar concentration range. The biological activity was strongly influenced by the N atom's position on the quinoline moiety and the position and nature of the side chain on the pentacyclic skeleton. Findings from fluorescence, circular dichroism spectroscopy, and thermal melting assays pointed toward a mixed binding mode-comprising intercalation and the binding of aggregated compounds along the polynucleotide backbone-of these pentacyclic benzimidazoles with DNA and RNA.
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Affiliation(s)
- Nataša Perin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; (N.P.); (M.G.); (M.K.)
| | - Marjana Gulin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; (N.P.); (M.G.); (M.K.)
| | - Marija Kos
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; (N.P.); (M.G.); (M.K.)
| | - Leentje Persoons
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - Ivana Fabijanić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (I.F.); (M.R.S.)
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (I.F.); (M.R.S.)
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000 Zagreb, Croatia; (N.P.); (M.G.); (M.K.)
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5
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Boukar O, Fifen JJ, Conradie J, Conradie MM. Solvation energies of the ferrous ion in water and in ammonia at various temperatures. J Mol Model 2024; 30:52. [PMID: 38285315 DOI: 10.1007/s00894-024-05839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
CONTEXT The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion. METHOD All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.
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Affiliation(s)
- Ousman Boukar
- Department of Physics, Faculty of Science, University of Maroua, P.O. Box 46, Maroua, Cameroon.
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit, Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
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Racané L, Zlatić K, Cindrić M, Mehić E, Karminski-Zamola G, Taylor MC, Kelly JM, Malić SR, Stojković MR, Kralj M, Hranjec M. Synthesis and Biological Activity of 2-Benzo[b]thienyl and 2-Bithienyl Amidino-Substituted Benzothiazole and Benzimidazole Derivatives. ChemMedChem 2023; 18:e202300261. [PMID: 37376962 DOI: 10.1002/cmdc.202300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 06/29/2023]
Abstract
Novel benzo[b]thienyl- and 2,2'-bithienyl-derived benzothiazoles and benzimidazoles were synthesized to study their antiproliferative and antitrypanosomal activities in vitro. Specifically, we assessed the impact that amidine group substitutions and the type of thiophene backbone have on biological activity. In general, the benzothiazole derivatives were more active than their benzimidazole analogs as both antiproliferative and antitrypanosomal agents. The 2,2'-bithienyl-substituted benzothiazoles with unsubstituted and 2-imidazolinyl amidine showed the most potent antitrypanosomal activity, and the greatest selectivity was observed for the benzimidazole derivatives bearing isopropyl, unsubstituted and 2-imidazolinyl amidine. The 2,2'-bithiophene derivatives showed most selective antiproliferative activity. Whereas the all 2,2'-bithienyl-substituted benzothiazoles were selectively active against lung carcinoma, the benzimidazoles were selective against cervical carcinoma cells. The compounds with an unsubstituted amidine group also produced strong antiproliferative effects. The more pronounced antiproliferative activity of the benzothiazole derivatives was attributed to different cytotoxicity mechanisms. Cell cycle analysis, and DNA binding experiments provide evidence that the benzimidazoles target DNA, whereas the benzothiazoles have a different cellular target because they are localized in the cytoplasm and do not interact with DNA.
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Affiliation(s)
- Livio Racané
- Department of Applied Chemistry, Faculty of Textile Technology, University of Zagreb, Prilaz baruna Filipovića, 10000, Zagreb, Croatia
| | - Katarina Zlatić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Maja Cindrić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
| | - Emina Mehić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
| | - Grace Karminski-Zamola
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
| | - Martin C Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - John M Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Silvana Raić Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Marijeta Kralj
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000, Zagreb, Croatia
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7
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Dabin A, Stirnemann G. Toward a Molecular Mechanism of Complementary RNA Duplexes Denaturation. J Phys Chem B 2023. [PMID: 37389985 DOI: 10.1021/acs.jpcb.3c00908] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
RNA duplexes are relatively rare but play very important biological roles. As an end-product of template-based RNA replication, they also have key implications for hypothetical primitive forms of life. Unless they are specifically separated by enzymes, these duplexes denature upon a temperature increase. However, mechanistic and kinetic aspects of RNA (and DNA) duplex thermal denaturation remain unclear at the microscopic level. We propose an in silico strategy that probes the thermal denaturation of RNA duplexes and allows for an extensive conformational space exploration along a wide temperature range with atomistic precision. We show that this approach first accounts for the strong sequence and length dependence of the duplexes melting temperature, reproducing the trends seen in the experiments and predicted by nearest-neighbor models. The simulations are then instrumental at providing a molecular picture of the temperature-induced strand separation. The textbook canonical "all-or-nothing" two-state model, very much inspired by the protein folding mechanism, can be nuanced. We demonstrate that a temperature increase leads to significantly distorted but stable structures with extensive base-fraying at the extremities, and that the fully formed duplexes typically do not form around melting. The duplex separation therefore appears as much more gradual than commonly thought.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
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8
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Tumir LM, Pavlović Saftić D, Crnolatac I, Ban Ž, Maslać M, Griesbeck S, Marder TB, Piantanida I. The Nature of the (Oligo/Hetero)Arene Linker Connecting Two Triarylborane Cations Controls Fluorimetric and Circular Dichroism Sensing of Various ds-DNAs and ds-RNAs. Molecules 2023; 28:4348. [PMID: 37298825 PMCID: PMC10254923 DOI: 10.3390/molecules28114348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
A series of tetracationic bis-triarylborane dyes, differing in the aromatic linker connecting two dicationic triarylborane moieties, showed very high submicromolar affinities toward ds-DNA and ds-RNA. The linker strongly influenced the emissive properties of triarylborane cations and controlled the fluorimetric response of dyes. The fluorene-analog shows the most selective fluorescence response between AT-DNA, GC-DNA, and AU-RNA, the pyrene-analog's emission is non-selectively enhanced by all DNA/RNA, and the dithienyl-diketopyrrolopyrrole analog's emission is strongly quenched upon DNA/RNA binding. The emission properties of the biphenyl-analog were not applicable, but the compound showed specific induced circular dichroism (ICD) signals only for AT-sequence-containing ds-DNAs, whereas the pyrene-analog ICD signals were specific for AT-DNA with respect to GC-DNA, and also recognized AU-RNA by giving a different ICD pattern from that observed upon interaction with AT-DNA. The fluorene- and dithienyl-diketopyrrolopyrrole analogs were ICD-signal silent. Thus, fine-tuning of the aromatic linker properties connecting two triarylborane dications can be used for the dual sensing (fluorimetric and CD) of various ds-DNA/RNA secondary structures, depending on the steric properties of the DNA/RNA grooves.
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Affiliation(s)
- Lidija-Marija Tumir
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
| | - Dijana Pavlović Saftić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
| | - Željka Ban
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
| | - Matea Maslać
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
| | - Stefanie Griesbeck
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany;
| | - Todd B. Marder
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany;
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (L.-M.T.); (D.P.S.); (I.C.); (Ž.B.); (M.M.)
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9
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Fabijanić I, Kurutos A, Tomašić Paić A, Tadić V, Kamounah FS, Horvat L, Brozovic A, Crnolatac I, Radić Stojković M. Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential. Biomolecules 2023; 13:biom13010128. [PMID: 36671513 PMCID: PMC9856044 DOI: 10.3390/biom13010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect.
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Affiliation(s)
- Ivana Fabijanić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 9, 1113 Sofia, Bulgaria
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Vanja Tadić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Fadhil S. Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Lucija Horvat
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-14571220; Fax: +385-14680195
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10
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Matić J, Tandarić T, Radić Stojković M, Šupljika F, Karačić Z, Tomašić Paić A, Horvat L, Vianello R, Tumir LM. Phenanthridine-pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme. Beilstein J Org Chem 2023; 19:550-565. [PMID: 37153642 PMCID: PMC10155618 DOI: 10.3762/bjoc.19.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular modelling combined with spectrophotometric experiments revealed that in neutral and acidic buffered water solutions conjugates predominantly exist in intramolecularly stacked conformations because of the π-π stacking interaction between pyrene and phenanthridine moieties. The investigated systems exhibited a pH-dependent excimer formation that is significantly red-shifted relative to the pyrene and phenanthridine fluorescence. While the conjugate with a short linker showed negligible spectrophotometric changes due to the polynucleotide addition, the conjugate with a longer and more flexible linker exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated in the cell membrane.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tana Tandarić
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Filip Šupljika
- Laboratory for Physical Chemistry and Corrosion, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia
| | - Zrinka Karačić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ana Tomašić Paić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lucija Horvat
- Laboratory for Molecular Plant Biology and Biotechnology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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11
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Jiang Y, Cai Z, Yuan Q, Cao W, Hu Z, Sun H, Wang XB, Sun Z. Highly Structured Water Networks in Microhydrated Dodecaborate Clusters. J Phys Chem Lett 2022; 13:11787-11794. [PMID: 36516831 DOI: 10.1021/acs.jpclett.2c03537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B12X122-·nH2O (X = H, F, or I; n = 1-6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B12X122- bases, illustrating the evident solute specificity. Because B-H···H-O dihydrogen bonds are stronger than O···H-O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B12H122-. As a comparison, the hydrated B12F122- clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B12I122- share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.
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Affiliation(s)
- Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China
| | - Zhaojie Cai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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12
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Makhatadze GI, Chen CR, Khutsishvili I, Marky LA. The volume changes of unfolding of dsDNA. Biophys J 2022; 121:4892-4899. [PMID: 35962547 PMCID: PMC9811605 DOI: 10.1016/j.bpj.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/07/2023] Open
Abstract
High hydrostatic pressure can have profound effects on the stability of biomacromolecules. The magnitude and direction (stabilizing or destabilizing) of this effect is defined by the volume changes in the system, ΔV. Positive volume changes will stabilize the starting native state, whereas negative volume changes will lead to the stabilization of the final unfolded state. For the DNA double helix, experimental data suggested that when the thermostability of dsDNA is below 50°C, increase in hydrostatic pressure will lead to destabilization; i.e., helix-to-coil transition has negative ΔV. In contrast, the dsDNA sequences with the thermostability above 50°C showed positive ΔV values and were stabilized by hydrostatic pressure. In order to get insight into this switch in the response of dsDNA to hydrostatic pressure as a function of temperature, first we further validated this trend using experimental measurements of ΔV for 10 different dsDNA sequences using pressure perturbation calorimetry. We also developed a computational protocol to calculate the expected volume changes of dsDNA unfolding, which was benchmarked against the experimental set of 50 ΔV values that included, in addition to our data, the values from the literature. Computation predicts well the experimental values of ΔV. Such agreement between computation and experiment lends credibility to the computation protocol and provides molecular level rational for the observed temperature dependence of ΔV that can be traced to the hydration. Difference in the ΔV value for A/T versus G/C basepairs is also discussed.
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Affiliation(s)
- George I Makhatadze
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.
| | - Calvin R Chen
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
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13
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Rep V, Štulić R, Koštrun S, Kuridža B, Crnolatac I, Radić Stojković M, Paljetak HČ, Perić M, Matijašić M, Raić-Malić S. Novel tetrahydropyrimidinyl-substituted benzimidazoles and benzothiazoles: synthesis, antibacterial activity, DNA interactions and ADME profiling. RSC Med Chem 2022; 13:1504-1525. [PMID: 36561067 PMCID: PMC9749923 DOI: 10.1039/d2md00143h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/12/2022] [Indexed: 12/25/2022] Open
Abstract
A series of tetrahydropyrimidinyl-substituted benzimidazoles attached to various aliphatic or aromatic residues via phenoxymethylene were synthesised to investigate their antibacterial activities against selected Gram-positive and Gram-negative bacteria. The influence of the type of substituent at the C-3 and C-4 positions of the phenoxymethylene linker on the antibacterial activity was observed, showing that the aromatic moiety improved the antibacterial potency. Of all the evaluated compounds, benzoyl-substituted benzimidazole derivative 15a was the most active compound, particularly against the Gram-negative pathogens E. coli (MIC = 1 μg mL-1) and M. catarrhalis (MIC = 2 μg mL-1). Compound 15a also exhibited the most promising antibacterial activity against sensitive and resistant strains of S. pyogenes (MIC = 2 μg mL-1). Significant stabilization effects and positive induced CD bands strongly support the binding of the most biologically active benzimidazoles inside the minor grooves of AT-rich DNA, in line with docking studies. The predicted physico-chemical and ADME properties lie within drug-like space except for low membrane permeability, which needs further optimization. Our findings encourage further development of novel structurally related 5(6)-tetrahydropyrimidinyl substituted benzimidazoles in order to optimize their antibacterial effect against common respiratory pathogens.
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Affiliation(s)
- Valentina Rep
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Rebeka Štulić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Sanja Koštrun
- Selvita d.o.oPrilaz baruna Filipovića 2910000 ZagrebCroatia
| | - Bojan Kuridža
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Hana Čipčić Paljetak
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mihaela Perić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mario Matijašić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
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14
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Minetti CA, Remeta DP. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:1438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [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: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying "magic bullets" amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand-target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural-energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Affiliation(s)
- Conceição A. Minetti
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David P. Remeta
- Department of Chemistry and Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, NJ 08854, USA
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15
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Dasgupta S, Shahi C, Bhetwal P, Perdew JP, Paesani F. How Good Is the Density-Corrected SCAN Functional for Neutral and Ionic Aqueous Systems, and What Is So Right about the Hartree-Fock Density? J Chem Theory Comput 2022; 18:4745-4761. [PMID: 35785808 DOI: 10.1021/acs.jctc.2c00313] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT) is the most widely used electronic structure method, due to its simplicity and cost effectiveness. The accuracy of a DFT calculation depends not only on the choice of the density functional approximation (DFA) adopted but also on the electron density produced by the DFA. SCAN is a modern functional that satisfies all known constraints for meta-GGA functionals. The density-driven errors, defined as energy errors arising from errors of the self-consistent DFA electron density, can hinder SCAN from achieving chemical accuracy in some systems, including water. Density-corrected DFT (DC-DFT) can alleviate this shortcoming by adopting a more accurate electron density which, in most applications, is the electron density obtained at the Hartree-Fock level of theory due to its relatively low computational cost. In this work, we present extensive calculations aimed at determining the accuracy of the DC-SCAN functional for various aqueous systems. DC-SCAN (SCAN@HF) shows remarkable consistency in reproducing reference data obtained at the coupled cluster level of theory, with minimal loss of accuracy. Density-driven errors in the description of ionic aqueous clusters are thoroughly investigated. By comparison with the orbital-optimized CCD density in the water dimer, we find that the self-consistent SCAN density transfers a spurious fraction of an electron across the hydrogen bond to the hydrogen atom (H*, covalently bound to the donor oxygen atom) from the acceptor (OA) and donor (OD) oxygen atoms, while HF makes a much smaller spurious transfer in the opposite direction, consistent with DC-SCAN (SCAN@HF) reduction of SCAN overbinding due to delocalization error. While LDA seems to be the conventional extreme of density delocalization error, and HF the conventional extreme of (usually much smaller) density localization error, these two densities do not quite yield the conventional range of density-driven error in energy differences. Finally, comparisons of the DC-SCAN results with those obtained with the Fermi-Löwdin orbital self-interaction correction (FLOSIC) method show that DC-SCAN represents a more accurate approach to reducing density-driven errors in SCAN calculations of ionic aqueous clusters. While the HF density is superior to that of SCAN for noncompact water clusters, the opposite is true for the compact water molecule with exactly 10 electrons.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Chandra Shahi
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Pradeep Bhetwal
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John P Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States.,Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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16
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Developing Community Resources for Nucleic Acid Structures. Life (Basel) 2022; 12:life12040540. [PMID: 35455031 PMCID: PMC9031032 DOI: 10.3390/life12040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.
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17
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Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands. Biomolecules 2022; 12:biom12030374. [PMID: 35327566 PMCID: PMC8945811 DOI: 10.3390/biom12030374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences.
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18
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Maračić S, Grbčić P, Shammugam S, Radić Stojković M, Pavelić K, Sedić M, Kraljević Pavelić S, Raić-Malić S. Amidine- and Amidoxime-Substituted Heterocycles: Synthesis, Antiproliferative Evaluations and DNA Binding. Molecules 2021; 26:molecules26227060. [PMID: 34834151 PMCID: PMC8625065 DOI: 10.3390/molecules26227060] [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: 10/27/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
The novel 1,2,3-triazolyl-appended N- and O-heterocycles containing amidine 4–11 and amidoxime 12–22 moiety were prepared and evaluated for their antiproliferative activities in vitro. Among the series of amidine-substituted heterocycles, aromatic diamidine 5 and coumarine amidine 11 had the most potent growth-inhibitory effect on cervical carcinoma (HeLa), hepatocellular carcinoma (HepG2) and colorectal adenocarcinoma (SW620), with IC50 values in the nM range. Although compound 5 was toxic to non-tumor HFF cells, compound 11 showed certain selectivity. From the amidoxime series, quinoline amidoximes 18 and 20 showed antiproliferative effects on lung adenocarcinoma (A549), HeLa and SW620 cells emphasizing compound 20 that exhibited no cytostatic effect on normal HFF fibroblasts. Results of CD titrations and thermal melting experiments indicated that compounds 5 and 10 most likely bind inside the minor groove of AT-DNA and intercalate into AU-RNA. Compounds 6, 9 and 11 bind to AT-DNA with mixed binding mode, most probably minor groove binding accompanied with aggregate binding along the DNA backbone.
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Affiliation(s)
- Silvija Maračić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
| | - Petra Grbčić
- Department of Biotechnology, University of Rijeka, Ulica Radmile Matejčić 2, HR-51000 Rijeka, Croatia;
| | - Suresh Shammugam
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia;
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia;
- Correspondence: (M.R.S.); (S.R.-M.); Tel.: +385-1-4571220 (M.R.S.); +385-1-4597213 (S.R.-M.)
| | - Krešimir Pavelić
- Faculty of Medicine, Juraj Dobrila University of Pula, HR-52100 Pula, Croatia;
| | - Mirela Sedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, HR-10000 Zagreb, Croatia;
| | - Sandra Kraljević Pavelić
- Faculty of Health Studies, University of Rijeka, Ulica Viktora Cara Emina 5, HR-51000 Rijeka, Croatia;
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
- Correspondence: (M.R.S.); (S.R.-M.); Tel.: +385-1-4571220 (M.R.S.); +385-1-4597213 (S.R.-M.)
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19
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Nicholson DA, Jia B, Nesbitt DJ. Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level. J Phys Chem B 2021; 125:9719-9726. [PMID: 34415161 DOI: 10.1021/acs.jpcb.1c05555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Measurements of the thermodynamic properties of biomolecular folding (ΔG°, ΔH°, ΔS°, etc.) provide a wealth of information on the folding process and have long played a central role in biophysical investigation. In particular, the excess heat capacity of folding (ΔCP) is crucial, as typically measured in bulk ensemble studies by differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). Here, we report the first measurements of ΔCP at the single-molecule level using the single-molecule fluorescence resonance energy transfer (smFRET) as well as the very first measurements of the heat capacity change associated with achieving the transition state (ΔC‡P) for nucleic acid folding. The deoxyribonucleic acid (DNA) hairpin used in these studies exhibits an excess heat capacity for hybridization (ΔCP = -340 ± 60 J/mol/K per base pair) consistent with the range of literature expectations (ΔCP = -100 to -420 J/mol/K per base pair). Furthermore, the measured activation heat capacities (ΔC‡P) for such hairpin unfolding are consistent with a folding transition state containing few fully formed base pairs, in agreement with prevailing models of DNA hybridization.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Bin Jia
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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20
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Racané L, Rep V, Kraljević Pavelić S, Grbčić P, Zonjić I, Radić Stojković M, Taylor MC, Kelly JM, Raić-Malić S. Synthesis, antiproliferative and antitrypanosomal activities, and DNA binding of novel 6-amidino-2-arylbenzothiazoles. J Enzyme Inhib Med Chem 2021; 36:1952-1967. [PMID: 34455887 PMCID: PMC8409973 DOI: 10.1080/14756366.2021.1959572] [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] [Indexed: 10/27/2022] Open
Abstract
A series of 6-amidinobenzothiazoles, linked via phenoxymethylene or directly to the 1,2,3-triazole ring with a p-substituted phenyl or benzyl moiety, were synthesised and evaluated in vitro against four human tumour cell lines and the protozoan parasite Trypanosoma brucei. The influence of the type of amidino substituent and phenoxymethylene linker on antiproliferative and antitrypanosomal activities was observed, showing that the imidazoline moiety had a major impact on both activities. Benzothiazole imidazoline 14a, which was directly connected to N-1-phenyl-1,2,3-triazole, had the most potent growth-inhibitory effect (IC50 = 0.25 µM) on colorectal adenocarcinoma (SW620), while benzothiazole imidazoline 11b, containing a phenoxymethylene linker, exhibited the best antitrypanosomal potency (IC90 = 0.12 µM). DNA binding assays showed a non-covalent interaction of 6-amidinobenzothiazole ligands, indicating both minor groove binding and intercalation modes of DNA interaction. Our findings encourage further development of novel structurally related 6-amidino-2-arylbenzothiazoles to obtain more selective anticancer and anti-HAT agents.
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Affiliation(s)
- Livio Racané
- Faculty of Textile Technology, Department of Applied Chemistry, University of Zagreb, Zagreb, Croatia
| | - Valentina Rep
- Faculty of Chemical Engineering and Technology, Department of Organic Chemistry, University of Zagreb, Zagreb, Croatia
| | | | - Petra Grbčić
- Faculty of Health Studies, University of Rijeka, Rijeka, Croatia
| | - Iva Zonjić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Martin C Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - John M Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Silvana Raić-Malić
- Faculty of Chemical Engineering and Technology, Department of Organic Chemistry, University of Zagreb, Zagreb, Croatia
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21
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Racané L, Zlatar I, Perin N, Cindrić M, Radovanović V, Banjanac M, Shanmugam S, Stojković MR, Brajša K, Hranjec M. Biological Activity of Newly Synthesized Benzimidazole and Benzothizole 2,5-Disubstituted Furane Derivatives. Molecules 2021; 26:molecules26164935. [PMID: 34443523 PMCID: PMC8401404 DOI: 10.3390/molecules26164935] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Newly designed and synthesized cyano, amidino and acrylonitrile 2,5-disubstituted furane derivatives with either benzimidazole/benzothiazole nuclei have been evaluated for antitumor and antimicrobial activity. For potential antitumor activity, the compounds were tested in 2D and 3D cell culture methods on three human lung cancer cell lines, A549, HCC827 and NCI-H358, with MTS cytotoxicity and BrdU proliferation assays in vitro. Compounds 5, 6, 8, 9 and 15 have been proven to be compounds with potential antitumor activity with high potential to stop the proliferation of cells. In general, benzothiazole derivatives were more active in comparison to benzimidazole derivatives. Antimicrobial activity was evaluated with Broth microdilution testing (according to CLSI (Clinical Laboratory Standards Institute) guidelines) on Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Additionally, Saccharomyces cerevisiae was included in testing as a eukaryotic model organism. Compounds 5, 6, 8, 9 and 15 showed the most promising antibacterial activity. In general, the compounds showed antitumor activity, higher in 2D assays in comparison with 3D assays, on all three cell lines in both assays. In natural conditions, compounds with such an activity profile (less toxic but still effective against tumor growth) could be promising new antitumor drugs. Some of the tested compounds showed antimicrobial activity. In contrast to ctDNA, the presence of nitro group or chlorine in selected furane-benzothiazole structures did not influence the binding mode with AT-DNA. All compounds dominantly bound inside the minor groove of AT-DNA either in form of monomers or dimer and higher-order aggregates.
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Affiliation(s)
- Livio Racané
- Department of Applied Chemistry, Faculty of Textile Technology, University of Zagreb, Prilaz baruna Filipovića 28a, 10000 Zagreb, Croatia;
| | - Ivo Zlatar
- Pharmacology In Vitro, Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (I.Z.); (V.R.); (M.B.)
| | - Nataša Perin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia; (N.P.); (M.C.)
| | - Maja Cindrić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia; (N.P.); (M.C.)
| | - Vedrana Radovanović
- Pharmacology In Vitro, Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (I.Z.); (V.R.); (M.B.)
| | - Mihailo Banjanac
- Pharmacology In Vitro, Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (I.Z.); (V.R.); (M.B.)
| | - Suresh Shanmugam
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (S.S.); (M.R.S.)
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (S.S.); (M.R.S.)
| | - Karmen Brajša
- Pharmacology In Vitro, Fidelta Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia; (I.Z.); (V.R.); (M.B.)
- Correspondence: (K.B.); (M.H.); Tel.: +385-1-4597245 (M.H.)
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia; (N.P.); (M.C.)
- Correspondence: (K.B.); (M.H.); Tel.: +385-1-4597245 (M.H.)
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22
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Mikulin I, Ljubić I, Piantanida I, Vasilev A, Mondeshki M, Kandinska M, Uzelac L, Martin-Kleiner I, Kralj M, Tumir LM. Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality-Strong Affinity Nucleic Acids Binders. Biomolecules 2021; 11:biom11081075. [PMID: 34439741 PMCID: PMC8391988 DOI: 10.3390/biom11081075] [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: 06/14/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.
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Affiliation(s)
- Ivana Mikulin
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivana Ljubić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
| | - Aleksey Vasilev
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
| | - Mihail Mondeshki
- Department of Chemistry, Johannes Gutenberg Universität Mainz, Duesbergweg 10–14, 55128 Mainz, Germany;
| | - Meglena Kandinska
- Faculty of Chemistry and Pharmacy, Department of Pharmaceutical and Applied Organic Chemistry, Sofia University “St. Kliment Ohridski”, 1000 Sofia, Bulgaria;
| | - Lidija Uzelac
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Irena Martin-Kleiner
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Marijeta Kralj
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (L.U.); (I.M.-K.); (M.K.)
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P.O. Box 180, 10002 Zagreb, Croatia; (I.M.); (I.L.); (I.P.)
- Correspondence: (A.V.); (L.-M.T.); Tel.: +359-98-836-6528 (A.V.); +385-1-457-1220 (L.-M.T.)
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23
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Liu L, Scott L, Tariq N, Kume T, Dubins DN, Macgregor RB, Chalikian TV. Volumetric Interplay between the Conformational States Adopted by Guanine-Rich DNA from the c-MYC Promoter. J Phys Chem B 2021; 125:7406-7416. [PMID: 34185535 DOI: 10.1021/acs.jpcb.1c04075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The kinetic and thermodynamic stabilities of G-quadruplex structures have been extensively studied. In contrast, systematic investigations of the volumetric properties of G-quadruplexes determining their pressure stability are still relatively scarce. The G-rich strand from the promoter region of the c-MYC oncogene (G-strand) is known to adopt a range of conformational states including the duplex, G-quadruplex, and coil states depending on the presence of the complementary C-rich strand (C-strand) and solution conditions. In this work, we report changes in volume, ΔV, and adiabatic compressibility, ΔKS, accompanying interconversions of G-strand between the G-quadruplex, duplex, and coil conformations in the presence and absence of C-strand. We rationalize these volumetric characteristics in terms of the hydration and intrinsic properties of the DNA in each of the sampled conformational states. We further use our volumetric results in conjunction with the reported data on changes in expansibility, ΔE, and heat capacity, ΔCP, associated with G-quadruplex-to-coil transitions to construct the pressure-temperature phase diagram describing the stability of the G-quadruplex. The phase diagram is elliptic in shape, resembling the classical elliptic phase diagram of a globular protein, and is distinct from the phase diagram for duplex DNA. The observed similarity of the pressure-temperature phase diagrams of G-quadruplexes and globular proteins stems from their shared structural and hydration features that, in turn, result in the similarity of their volumetric properties. To the best of our knowledge, this is the first pressure-temperature stability diagram reported for a G-quadruplex.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Lily Scott
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Nabeel Tariq
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Takuma Kume
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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24
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Breslauer KJ. The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J Biol Chem 2021; 296:100522. [PMID: 34237886 PMCID: PMC8058554 DOI: 10.1016/j.jbc.2021.100522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023] Open
Abstract
My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial “late bloomer.” Ultimately, I earned my PhD in biophysical chemistry at Yale, followed by a postdoc fellowship at Berkeley. These two meccas of thermodynamics, coupled with my deep fascination with biology, instilled in me a passion to pursue an academic career focused on mapping the energy landscapes of biological systems. I viewed differential energetics as the language of molecular communication that would dictate and control biological structures, as well as modulate the modes of action associated with biological functions. I wanted to be a “molecular linguist.” For the next 50 years, my group and I used a combination of spectroscopic and calorimetric techniques to characterize the energy profiles of the polymorphic conformational space of DNA molecules, their differential ligand-binding properties, and the energy landscapes associated with mutagenic DNA damage recognition, repair, and replication. As elaborated below, the resultant energy databases have enabled the development of quantitative molecular biology through the rational design of primers, probes, and arrays for diagnostic, therapeutic, and molecular-profiling protocols, which collectively have contributed to a myriad of biomedical assays. Such profiling is further justified by yielding unique energy-based insights that complement and expand elegant, structure-based understandings of biological processes.
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Affiliation(s)
- Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.
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25
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Lončar B, Perin N, Mioč M, Boček I, Grgić L, Kralj M, Tomić S, Stojković MR, Hranjec M. Novel amino substituted tetracyclic imidazo[4,5-b]pyridine derivatives: Design, synthesis, antiproliferative activity and DNA/RNA binding study. Eur J Med Chem 2021; 217:113342. [PMID: 33751978 DOI: 10.1016/j.ejmech.2021.113342] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
A novel series of tetracyclic imidazo[4,5-b]pyridine derivatives was designed and synthesized as potential antiproliferative agents. Their antiproliferative activity against human cancer cells was influenced by the introduction of chosen amino side chains on the different positions on the tetracyclic skeleton and particularly, by the position of N atom in the pyridine nuclei. Thus, the majority of compounds showed improved activity in comparison to standard drug etoposide. Several compounds showed pronounced cytostatic effect in the submicromolar range, especially on HCT116 and MCF-7 cancer cells. The obtained results have confirmed the significant impact of the position of N nitrogen in the pyridine ring on the enhancement of antiproliferative activity, especially for derivatives bearing amino side chains on position 2. Thus, regioisomers 6, 7 and 9 showed noticeable enhancement of activity in comparison to their counterparts 10, 11 and 13 with IC50 values in a nanomolar range of concentration (0.3-0.9 μM). Interactions with DNA (including G-quadruplex structure) and RNA were influenced by the position of amino side chains on the tetracyclic core of imidazo[4,5-b]pyridine derivatives and the ligand charge. Moderate to high binding affinities (logKs = 5-7) obtained for selected imidazo[4,5-b]pyridine derivatives suggest that DNA/RNA are potential cell targets.
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Affiliation(s)
- Borka Lončar
- Pliva d.o.o., odjel TAPI I&R, Unapređenje tehnoloških procesa i Podrška proizvodnji, Croatia
| | - Nataša Perin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia
| | - Marija Mioč
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Ida Boček
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia
| | - Lea Grgić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Marijeta Kralj
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Sanja Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia.
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia.
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26
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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27
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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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28
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Tumir LM, Zonjić I, Žuna K, Brkanac SR, Jukić M, Huđek A, Durgo K, Crnolatac I, Glavaš-Obrovac L, Cardullo N, Pulvirenti L, Muccilli V, Tringali C, Stojković MR. Synthesis, DNA/RNA-interaction and biological activity of benzo[k,l]xanthene lignans. Bioorg Chem 2020; 104:104190. [PMID: 32919130 DOI: 10.1016/j.bioorg.2020.104190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Interactions of two newly synthesized and six previously reported benzoxanthene lignans (BXLs), analogues of rare natural products, with DNA/RNA, G-quadruplex and HSA were evaluated by a set of spectrophotometric methods. Presence/absence of methoxy and hydroxy groups on the benzoxanthene core and minor modifications at C-1/C-2 side pendants - presence/absence of phenyl ring and presence/absence of methoxy and hydroxy groups on phenyl ring - influenced the fluorescence changes and the binding strength to double-stranded (ds-) and G-quadruplex structures. In general, compounds without phenyl ring showed stronger fluorescence changes upon binding than phenyl-substituted BXLs. On the other hand, BXLs with an unsubstituted phenyl ring showed the best stabilization effects of G-quadruplex. Circular dichroism spectroscopy results suggest mixed binding mode, groove binding and partial intercalation, to ds-DNA/RNA and end-stacking to top or bottom G-tetrads as the main binding modes of BXLs to those targets. All compounds exhibited micromolar binding affinities toward HSA and an increased protein thermal stability. Moderate to strong antiradical scavenging activity was observed for all BXLs with hydroxy groups at C-6, C-9 and C-10 positions of the benzoxanthene core, except for derivative bearing methoxy groups at these positions. BXLs with unsubstituted or low-substituted phenyl ring and one derivative without phenyl ring showed strong growth inhibition of Gram-positive Staphylococcus aureus. All compounds showed moderate to strong tumor cell growth-inhibitory activity and cytotoxicity.
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Affiliation(s)
- Lidija-Marija Tumir
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Iva Zonjić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Kristina Žuna
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Sandra Radić Brkanac
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6/III, HR-10 000 Zagreb, Croatia
| | - Marijana Jukić
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Ana Huđek
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ksenija Durgo
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ljubica Glavaš-Obrovac
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Luana Pulvirenti
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Corrado Tringali
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
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29
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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30
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Design, synthesis, antitrypanosomal activity, DNA/RNA binding and in vitro ADME profiling of novel imidazoline-substituted 2-arylbenzimidazoles. Eur J Med Chem 2020; 207:112802. [PMID: 32927230 DOI: 10.1016/j.ejmech.2020.112802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 01/10/2023]
Abstract
Novel imidazoline benzimidazole derivatives containing diversely substituted phenoxy moieties were synthesized with the aim of evaluating their antitrypanosomal activity, DNA/RNA binding affinity and in vitro ADME properties. The presence of the diethylaminoethyl subunit in 18a-18c led to enhanced antitrypanosomal potency, particularly for 18a and 18c, which contain unsubstituted and methoxy-substituted phenoxy moieties. They were found to be > 2-fold more potent against African trypanosomes than nifurtimox. Fluorescence and CD spectroscopy, thermal denaturation assays and computational analysis indicated a preference of 18a-18c toward AT-rich DNA and their minor groove binding mode. Replacement of the amidine group with less basic and ionisable nitrogen-containing moieties failed to improve membrane permeability of the investigated compounds. Due to structural diversification, the compounds displayed a range of physico-chemical features resulting in variable in vitro ADME properties, leaving space for further optimization of the biological profiles.
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31
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Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (Δ Cp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. J Phys Chem B 2020; 124:5614-5625. [PMID: 32531155 DOI: 10.1021/acs.jpcb.0c04065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Knowledge of differences in heat capacity changes (ΔCp) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔCp of 61 ± 7 cal molbp -1 K -1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - G Eric Plum
- UNICON International, Inc. 241 Outerbelt Street, Columbus, Ohio 43213, United States
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.,The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08901, United States
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32
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Forces maintaining the DNA double helix. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:315-321. [PMID: 32462263 PMCID: PMC7351851 DOI: 10.1007/s00249-020-01437-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/22/2020] [Accepted: 05/10/2020] [Indexed: 10/28/2022]
Abstract
Despite the common acceptance that the enthalpy of DNA duplex unfolding does not depend on temperature and is greater for the CG base pair held by three hydrogen bonds than for the AT base pair held by only two, direct calorimetric measurements have shown that the enthalpic and entropic contributions of both base pairs are temperature dependent and at all temperatures are greater for the AT than the CG pair. The temperature dependence results from hydration of the apolar surfaces of bases that become exposed upon duplex dissociation. The larger enthalpic and entropic contributions of the AT pair are caused by water fixed by this pair in the minor groove of DNA and released on duplex dissociation. Analysis of the experimental thermodynamic characteristics of unfolding/refolding DNA duplexes of various compositions shows that the enthalpy of base pairing is negligibly small, while the entropic contribution is considerable. Thus, DNA base pairing is entropy driven and is coupled to the enthalpy driven van der Waals base pair stacking. Each of these two processes is responsible for about half the Gibbs energy of duplex stabilization, but all the enthalpy, i.e., the total heat of melting, results from dissociation of the stacked base pairs. Both these processes tightly cooperate: while the pairing of conjugate bases is critical for recognition of complementary strands, stacking of the flat apolar surfaces of the base pairs reinforces the DNA duplex formed.
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Hussain S, Haji-Akbari A. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J Chem Phys 2020; 152:060901. [DOI: 10.1063/1.5127780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sarwar Hussain
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
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Liu L, Ma C, Wells JW, Chalikian TV. Conformational Preferences of DNA Strands from the Promoter Region of the c-MYC Oncogene. J Phys Chem B 2020; 124:751-762. [PMID: 31923361 DOI: 10.1021/acs.jpcb.9b10518] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized the conformational preferences of DNA in an equimolar mixture of complementary G-rich and C-rich strands from the promoter region of the c-MYC oncogene. Our CD-based approach presupposes that the CD spectrum of such a mixture is the spectral sum of the constituent duplex, G-quadruplex, i-motif, and coiled conformations. Spectra were acquired over a range of temperatures at different pHs and concentrations of KCl. Each spectrum was unmixed in terms of the predetermined spectra of the constituent conformational states to obtain the corresponding weighting factors for their fractional contributions to the total population of DNA. The temperature dependences of those contributions then were analyzed in concert according to a model based on a thermodynamic representation of the underlying equilibria. Fitted estimates of the melting enthalpy and temperature obtained for the duplex, G-quadruplex, and i-motif imply that the driving force behind dissociation of the duplex and the concomitant formation of tetrahelical structures is the folding of the G-strand into the G-quadruplex. The liberated C-strand adopts the i-motif conformation at acidic pH and exists in the coiled state at neutral pH. The i-motif alone cannot induce dissociation of the duplex even at pH 5.0, at which it is most stable. Under the physiological conditions of neutral pH, elevated potassium, and room temperature, the duplex and G-quadruplex conformations coexist with the C-strand in the coiled state. Taken together, our results suggest a novel, thermodynamically controlled mechanism for the regulation of gene expression.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Congshan Ma
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
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35
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Thermodynamics of DNA: heat capacity changes on duplex unfolding. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:773-779. [PMID: 31690971 PMCID: PMC6853854 DOI: 10.1007/s00249-019-01403-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 11/11/2022]
Abstract
The heat capacity change, ΔCp, accompanying the folding/unfolding of macromolecules reflects their changing state of hydration. Thermal denaturation of the DNA duplex is characterized by an increase in ΔCp but of much lower magnitude than observed for proteins. To understand this difference, the changes in solvent accessible surface area (ΔASA) have been determined for unfolding the B-form DNA duplex into disordered single strands. These showed that the polar component represents ~ 55% of the total increase in ASA, in contrast to globular proteins of similar molecular weight for which the polar component is only about 1/3rd of the total. As the exposure of polar surface results in a decrease of ΔCp, this explains the much reduced heat capacity increase observed for DNA and emphasizes the enhanced role of polar interactions in maintaining duplex structure. Appreciation of a non-zero ΔCp for DNA has important consequences for the calculation of duplex melting temperatures (Tm). A modified approach to Tm prediction is required and comparison is made of current methods with an alternative protocol.
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36
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Privalov PL, Crane-Robinson C. Translational Entropy and DNA Duplex Stability. Biophys J 2019; 114:15-20. [PMID: 29320682 DOI: 10.1016/j.bpj.2017.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/26/2017] [Accepted: 11/03/2017] [Indexed: 10/18/2022] Open
Abstract
Investigation of folding/unfolding DNA duplexes of various size and composition by superprecise calorimetry has revised several long-held beliefs concerning the forces responsible for the formation of the double helix. It was established that: 1) the enthalpy and the entropy of duplex unfolding are temperature dependent, increasing with temperature rise and having the same heat capacity increment for CG and AT pairs; 2) the enthalpy of AT melting is greater than that of the CG pair, so the stabilizing effect of the CG pair in comparison with AT results not from its larger enthalpic contribution (as expected from its extra hydrogen bond), but from the larger entropic contribution of the AT pair that results from its ability to fix ordered water in the minor groove and release it upon duplex unfolding; 3) the translation entropy, resulting from the appearance of a new kinetic unit on duplex dissociation, determines the dependence of duplex stability on its length and its concentration (it is an order-of-magnitude smaller than predicted from the statistical mechanics of gases and is fully expressed by the stoichiometric correction term); 4) changes in duplex stability on reshuffling the sequence (the "nearest-neighbor effect") result from the immobilized water molecules fixed by AT pairs in the minor groove; and 5) the evaluated thermodynamic components permit a quantitative expression of DNA duplex stability.
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Affiliation(s)
- Peter L Privalov
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, United Kingdom.
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Kahn PC. The measurement of volume change by capillary dilatometry. Protein Sci 2019; 28:1135-1142. [PMID: 30993790 PMCID: PMC6511832 DOI: 10.1002/pro.3626] [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: 03/12/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/03/2022]
Abstract
Capillary dilatometry enables direct measurement of changes in volume, an extensive thermodynamic property. The results provide insight into the changes in hydration that occur upon protein folding, ligand binding, and the interactions of proteins with nucleic acids and other cellular components. Often the entropy change arising from release of hydrating solvent provides the main driving force of a binding reaction. For technical reasons, though, capillary dilatometry has not been as widely used in protein biochemistry and biophysics as other methods such as calorimetry. Described here are simple apparatus and simple methods, which bring the technique within the capacity of any laboratory. Even very simple results are shown to have implications for macromolecular‐based phenomena. Protein examples are described.
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Affiliation(s)
- Peter C Kahn
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901
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38
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Carr CE, Khutsishvili I, Marky LA. Energetics, Ion, and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA. J Phys Chem B 2018; 122:7057-7065. [PMID: 29932334 DOI: 10.1021/acs.jpcb.8b05575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Triplex formation occurs via interaction of a third strand with the major groove of double-stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of polyadenylic acid (poly(rA))·polyuridylic acid (poly(rU)) (duplex) and poly(rA)·2poly(rU) (triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, Δ nNa+ = 0.15 mol Na+/mol base pair (duplex) and 0.30 mol Na+/mole base triplet (triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, Δ nW = 2 mol H2O/mol base pair (duplex unfolding into single strands) and an uptake of structural water, Δ nW = 2 mol H2O/mole base pair (triplex unfolding into duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the Δ V values obtained for the unfolding of triplex into duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The Δ V values obtained for the unfolding of duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , 986025 Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , 986025 Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
| | - Luis A Marky
- Department of Pharmaceutical Sciences , University of Nebraska Medical Center , 986025 Nebraska Medical Center , Omaha , Nebraska 68198-6025 , United States
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39
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Privalov PL, Crane-Robinson C. Forces maintaining the DNA double helix and its complexes with transcription factors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 135:30-48. [DOI: 10.1016/j.pbiomolbio.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/22/2018] [Indexed: 10/18/2022]
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40
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Carr CE, Marky LA. Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges. Biophys J 2018; 114:2764-2774. [PMID: 29925014 PMCID: PMC6026347 DOI: 10.1016/j.bpj.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Intramolecular junctions are a ubiquitous structure within DNA and RNA; three-way junctions in particular have high strain around the junction because of the lack of flexibility, preventing the junctions from adopting conformations that would allow for optimal folding. In this work, we used a combination of calorimetric and spectroscopic techniques to study the unfolding of four intramolecular three-way junctions. The control three-way junction, 3H, has the sequence d(GAAATTGCGCT5GCGCGTGCT5GCACAATTTC), which has three arms of different sequences. We studied three other three-way junctions in which one (2HS1H), two (HS12HS1), and three (HS1HS1HS1) cytosine bulges were placed at the junction to allow the arms to adopt a wider range of conformations that may potentially relieve strain. Through calorimetric studies, it was concluded that bulges produce only minor effects on the enthalpic and thermal stability at physiological salt concentrations for 2HS1H and HS1HS1HS1. HS12HS1 displays the strongest effect, with the GTGC stem lacking a defined transition. In addition to unfolding thermodynamics, the differential binding of counterions, water, and protons was determined. It was found that with each bulge, there was a large increase in the binding of counterions; this correlated with a decrease in the immobilization of structural water molecules. The increase in counterion uptake upon folding likely displaces binding of structural water, which is measured by the osmotic stress method, in favor of electrostricted waters. The cytosine bulges do not affect the binding of protons; this finding indicates that the bulges are not forming base-triplet stacks. These results indicate that bulges in junctions do not affect the unfolding profile or the enthalpy of oligonucleotides but do affect the number and amount of molecules immobilized by the junction.
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Affiliation(s)
- Carolyn E Carr
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska.
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41
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Minetti CA, Sun JY, Jacobs DP, Kang I, Remeta DP, Breslauer KJ. Impact of bistrand abasic sites and proximate orientation on DNA global structure and duplex energetics. Biopolymers 2018; 109:e23098. [PMID: 29322505 PMCID: PMC6175389 DOI: 10.1002/bip.23098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/05/2017] [Accepted: 11/10/2017] [Indexed: 11/11/2022]
Abstract
Bistrand lesions embedded within a single helical turn of tridecameric deoxyoligonucleotide duplexes represent a model system for exploring the impact of clustered lesions that occur in vivo and pose a significant challenge to cellular repair machineries. Such investigations are essential for understanding the forces that dictate lesion‐induced mutagenesis, carcinogenesis, and cytotoxicity within a context that mimics local helical perturbations caused by an ionizing radiation event. This study characterizes the structural and energy profiles of DNA duplexes harboring synthetic abasic sites (tetrahydrofuran, F) as models of clustered bistrand abasic (AP) lesions. The standard tridecameric dGCGTACCCATGCG·dCGCATGGGTACGC duplex is employed to investigate the energetic impact of single and bistrand AP sites by strategically replacing one or two bases within the central CCC/GGG triplet. Our combined analysis of temperature‐dependent UV and circular dichroism (CD) profiles reveals that the proximity and relative orientation of AP sites within bistrand‐damaged duplexes imparts a significant thermodynamic impact. Specifically, 3′‐staggered lesions (CCF/GFG) exert a greater destabilizing effect when compared with their 5′‐counterpart (FCC/GFG). Moreover, a duplex harboring the central bistrand AP lesion (CFC/GFG) is moderately destabilized yet exhibits distinct properties relative to both the 3′ and 5′‐orientations. Collectively, our energetic data are consistent with structural studies on bistrand AP‐duplexes of similar sequence in which a 3′‐staggered lesion exerts the greatest perturbation, a finding that provides significant insight regarding the impact of orientation on lesion repair processing efficiency.
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Affiliation(s)
- Conceição A Minetti
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
| | - Jeffrey Y Sun
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
| | - Daniel P Jacobs
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
| | - Inkoo Kang
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey
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42
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Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure. Biophys Chem 2017; 231:146-154. [DOI: 10.1016/j.bpc.2017.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 11/21/2022]
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43
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Yamazaki H, Hu R, Henley RY, Halman J, Afonin KA, Yu D, Zhao Q, Wanunu M. Label-Free Single-Molecule Thermoscopy Using a Laser-Heated Nanopore. NANO LETTERS 2017; 17:7067-7074. [PMID: 28975798 DOI: 10.1021/acs.nanolett.7b03752] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
When light is used to excite electronic transitions in a material, nonradiative energy during relaxation is often released in the form of heat. In this work, we show that photoexcitation of a silicon nitride nanopore using a focused visible laser results in efficient localized photothermal heating, which reduces the nearby electrolyte viscosity and increases the ionic conductance. In addition, a strong localized thermal gradient in the pore vicinity is produced, evidenced by finite-element simulations and experimental observation of both ion and DNA thermophoresis. After correcting for thermophoresis, the nanopore current can be used as a nanoscale thermometer, enabling rapid force thermoscopy. We utilize this to probe thermal melting transitions in synthetic and native biomolecules that are heated at the nanopore. Our results on single molecules are validated by correspondence to bulk measurements, which paves the way to various biophysical experiments that require rapid temperature and force control on individual molecules.
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Affiliation(s)
- Hirohito Yamazaki
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Rui Hu
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | - Robert Y Henley
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | - Meni Wanunu
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
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44
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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45
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Amnuanpol S. Ionic effects on the temperature-force phase diagram of DNA. J Biol Phys 2017; 43:535-550. [PMID: 28913768 DOI: 10.1007/s10867-017-9468-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/16/2017] [Indexed: 11/24/2022] Open
Abstract
Double-stranded DNA (dsDNA) undergoes a structural transition to single-stranded DNA (ssDNA) in many biologically important processes such as replication and transcription. This strand separation arises in response either to thermal fluctuations or to external forces. The roles of ions are twofold, shortening the range of the interstrand potential and renormalizing the DNA elastic modulus. The dsDNA-to-ssDNA transition is studied on the basis that dsDNA is regarded as a bound state while ssDNA is regarded as an unbound state. The ground state energy of DNA is obtained by mapping the statistical mechanics problem to the imaginary time quantum mechanics problem. In the temperature-force phase diagram the critical force F c (T) increases logarithmically with the Na+ concentration in the range from 32 to 110 mM. Discussing this logarithmic dependence of F c (T) within the framework of polyelectrolyte theory, it inevitably suggests a constraint on the difference between the interstrand separation and the length per unit charge during the dsDNA-to-ssDNA transition.
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Affiliation(s)
- Sitichoke Amnuanpol
- Physics Department, Thammasat University, Klong Luang, Pathumthani, 12120, Thailand.
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46
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Chang CL, Fridman AS, Wartell RM, Hu CK, Lando DY. Relationship between calorimetric profiles and differential melting curves for natural DNAs. Int J Biol Macromol 2017; 102:591-598. [DOI: 10.1016/j.ijbiomac.2017.04.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 10/19/2022]
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47
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Aslanyan L, Ko J, Kim BG, Vardanyan I, Dalyan YB, Chalikian TV. Effect of Urea on G-Quadruplex Stability. J Phys Chem B 2017; 121:6511-6519. [DOI: 10.1021/acs.jpcb.7b03479] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lusine Aslanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Jordan Ko
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ishkhan Vardanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Yeva B. Dalyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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48
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Gardner CM, Gunsch CK. Adsorption capacity of multiple DNA sources to clay minerals and environmental soil matrices less than previously estimated. CHEMOSPHERE 2017; 175:45-51. [PMID: 28211334 DOI: 10.1016/j.chemosphere.2017.02.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/15/2016] [Accepted: 02/04/2017] [Indexed: 05/25/2023]
Abstract
The cultivation and consumption of transgenic crops continues to be a widely debated topic, as the potential ecological impacts are not fully understood. In particular, because antibiotic resistance genes (ARGs) have historically been used as selectable markers in the genetic engineering of transgenic crops, it is important to determine if the genetic constructs found in decomposing transgenic crops persist long enough in the environment and if they can be transferred horizontally to indigenous microorganisms. In the present study, we address the question of persistence. Others have also estimated the DNA adsorption capacity of various clays, but have done so by manipulating the surface charge and size of particles tested which may overestimate sorption and underestimate the DNA available for horizontal transfer. In the present study, isotherms were generated using model Calf Thymus DNA and transgenic maize DNA without surface modification. Montmorillonite, kaolinite, and 3 soil mixtures with varying clay content were used in this study. The adsorption capacity of pure montmorillonite and kaolinite minerals was found to be one to two orders of magnitude less than previously estimated likely due to the distribution of clay particle sizes and heteroionic particle surface charge. However, it appears that a substantial amount of DNA is still able to adsorb onto these matrices (up to 200 mg DNA per gram of clay) suggesting the potential availability of free transgenic DNA in the environment may still be significant. Future studies should be conducted to determine the fate of these genes in agricultural soils.
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Affiliation(s)
- Courtney M Gardner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA.
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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50
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017; 56:5045-5049. [DOI: 10.1002/anie.201701420] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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