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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs. Biophys J 2023; 122:3323-3339. [PMID: 37469144 PMCID: PMC10465710 DOI: 10.1016/j.bpj.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023] Open
Abstract
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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2
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Kaußler C, Wragg D, Schmidt C, Moreno-Alcántar G, Jandl C, Stephan J, Fischer RA, Leoni S, Casini A, Bonsignore R. "Dynamical Docking" of Cyclic Dinuclear Au(I) Bis-N-heterocyclic Complexes Facilitates Their Binding to G-Quadruplexes. Inorg Chem 2022; 61:20405-20423. [PMID: 36484812 PMCID: PMC9953335 DOI: 10.1021/acs.inorgchem.2c03041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the aim to improve the design of metal complexes as stabilizers of noncanonical DNA secondary structures, namely, G-quadruplexes (G4s), a series of cyclic dinuclear Au(I) N-heterocyclic carbene complexes based on xanthine and benzimidazole ligands has been synthesized and characterized by various methods, including X-ray diffraction. Fluorescence resonance energy transfer (FRET) and CD DNA melting assays unraveled the compounds' stabilization properties toward G4s of different topologies of physiological relevance. Initial structure-activity relationships have been identified and recognize the family of xanthine derivatives as those more selective toward G4s versus duplex DNA. The binding modes and free-energy landscape of the most active xanthine derivative (featuring a propyl linker) with the promoter sequence cKIT1 have been studied by metadynamics. The atomistic simulations evidenced that the Au(I) compound interacts noncovalently with the top G4 tetrad. The theoretical results on the Au(I) complex/DNA Gibbs free energy of binding were experimentally validated by FRET DNA melting assays. The compounds have also been tested for their antiproliferative properties in human cancer cells in vitro, showing generally moderate activity. This study provides further insights into the biological activity of Au(I) organometallics acting via noncovalent interactions and underlines their promise for tunable targeted applications by appropriate chemical modifications.
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Affiliation(s)
- Clemens Kaußler
- Chair
of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching b. MünchenD-85748, Germany
| | - Darren Wragg
- Chair
of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching b. MünchenD-85748, Germany
| | - Claudia Schmidt
- Chair
of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching b. MünchenD-85748, Germany
| | - Guillermo Moreno-Alcántar
- Chair
of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching b. MünchenD-85748, Germany
| | - Christian Jandl
- Catalysis
Research Center & Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 1, Garching b. MünchenD-85748, Germany
| | - Johannes Stephan
- Catalysis
Research Center & Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 1, Garching b. MünchenD-85748, Germany
| | - Roland A. Fischer
- Catalysis
Research Center & Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 1, Garching b. MünchenD-85748, Germany,Chair
of Inorganic and Metal-Organic Chemistry, Department of Chemistry, Technische Universität München, Ernst-Otto-Fischer Str. 1, Garching b. MünchenD-85748, Germany
| | - Stefano Leoni
- School
of Chemistry, Cardiff University, Park Place, CardiffCF10 3AT, U.K.
| | - Angela Casini
- Chair
of Medicinal and Bioinorganic Chemistry, Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching b. MünchenD-85748, Germany,
| | - Riccardo Bonsignore
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Edificio 17, Palermo90128, Italy,
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [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
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Wragg D, de Almeida A, Bonsignore R, Kühn FE, Leoni S, Casini A. On the Mechanism of Gold/NHC Compounds Binding to DNA G-Quadruplexes: Combined Metadynamics and Biophysical Methods. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Darren Wragg
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | | | | | - Fritz E. Kühn
- Molecular Catalysis; Department of Chemistry; Catalysis Research Center; Technische Universität München; Lichtenbergstr. 4 85747 Garching bei München Germany
| | - Stefano Leoni
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | - Angela Casini
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
- Institute for Advanced Study; Technische Universität München; Lichtenbergstr. 2a 85747 Garching bei München Germany
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5
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Wragg D, de Almeida A, Bonsignore R, Kühn FE, Leoni S, Casini A. On the Mechanism of Gold/NHC Compounds Binding to DNA G-Quadruplexes: Combined Metadynamics and Biophysical Methods. Angew Chem Int Ed Engl 2018; 57:14524-14528. [DOI: 10.1002/anie.201805727] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Darren Wragg
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | | | | | - Fritz E. Kühn
- Molecular Catalysis; Department of Chemistry; Catalysis Research Center; Technische Universität München; Lichtenbergstr. 4 85747 Garching bei München Germany
| | - Stefano Leoni
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
| | - Angela Casini
- School of Chemistry; Cardiff University; Park Place CF10 3AT Cardiff UK
- Institute for Advanced Study; Technische Universität München; Lichtenbergstr. 2a 85747 Garching bei München Germany
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de Bruin D, Bossert N, Aartsma-Rus A, Bouwmeester D. Measuring DNA hybridization using fluorescent DNA-stabilized silver clusters to investigate mismatch effects on therapeutic oligonucleotides. J Nanobiotechnology 2018; 16:37. [PMID: 29622040 PMCID: PMC5887185 DOI: 10.1186/s12951-018-0361-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/21/2018] [Indexed: 01/07/2023] Open
Abstract
Background Short nucleic acid oligomers have found a wide range of applications in experimental physics, biology and medicine, and show potential for the treatment of acquired and genetic diseases. These applications rely heavily on the predictability of hybridization through Watson–Crick base pairing to allow positioning on a nanometer scale, as well as binding to the target transcripts, but also off-target binding to transcripts with partial homology. These effects are of particular importance in the development of therapeutic oligonucleotides, where off-target effects caused by the binding of mismatched sequences need to be avoided. Results We employ a novel method of probing DNA hybridization using optically active DNA-stabilized silver clusters (Ag-DNA) to measure binding efficiencies through a change in fluorescence intensity. In this way we can determine their location-specific sensitivity to individual mismatches in the sequence. The results reveal a strong dependence of the hybridization on the location of the mismatch, whereby mismatches close to the edges and center show a relatively minor impact. In parallel, we propose a simple model for calculating the annealing ratios of mismatched DNA sequences, which supports our experimental results. Conclusion The primary result shown in this work is a demonstration of a novel technique to measure DNA hybridization using fluorescent Ag-DNA. With this technique, we investigated the effect of mismatches on the hybridization efficiency, and found a significant dependence on the location of individual mismatches. These effects are strongly influenced by the length of the used oligonucleotides. The novel probe method based on fluorescent Ag-DNA functions as a reliable tool in measuring this behavior. As a secondary result, we formulated a simple model that is consistent with the experimental data. Electronic supplementary material The online version of this article (10.1186/s12951-018-0361-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donny de Bruin
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.
| | - Nelli Bossert
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands
| | | | - Dirk Bouwmeester
- Leiden Institute of Physics, Leiden University, Leiden, 2333 CA, The Netherlands.,Department of Physics, University of California, Santa Barbara, CA, 93106, USA
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