1
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Tanabe K, Miyazaki K, Umeno H, Takemoto M, Nakano S. Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes. Biochimie 2024; 219:110-117. [PMID: 37972915 DOI: 10.1016/j.biochi.2023.11.005] [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: 07/31/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Affiliation(s)
- Kazuya Tanabe
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouichi Miyazaki
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hikari Umeno
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Marina Takemoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - S Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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2
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Bethur E, Guha R, Zhao Z, Katz BB, Ashby PD, Zeng H, Copp SM. Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution. ACS NANO 2024; 18:3002-3010. [PMID: 38227309 PMCID: PMC10832345 DOI: 10.1021/acsnano.3c08008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Silver cations can mediate base pairing of guanine (G) DNA oligomers, yielding linear parallel G-Ag+-G duplexes with enhanced stabilities compared to those of canonical DNA duplexes. To enable their use in programmable DNA nanotechnologies, it is critical to understand solution-state formation and the nanomechanical stiffness of G-Ag+-G duplexes. Using temperature-controlled circular dichroism (CD) spectroscopy, we find that heating mixtures of G oligomers and silver salt above 50 °C fully destabilizes G-quadruplex structures and converts oligomers to G-Ag+-G duplexes. Electrospray ionization mass spectrometry supports that G-Ag+-G duplexes form at stoichiometries of 1 Ag+ per base pair, and CD spectroscopy suggests that as the Ag+/base stoichiometry increases further, G-Ag+-G duplexes undergo additional morphological changes. Using liquid-phase atomic force microscopy, we find that this excess Ag+ enables assembly of long fiberlike structures with ∼2.5 nm heights equivalent to a single DNA duplex but with lengths that far exceed a single duplex. Finally, using the conditions established to form single G-Ag+-G duplexes, we use a surface forces apparatus (SFA) to compare the solution-phase stiffness of single G-Ag+-G duplexes with dG-dC Watson-Crick-Franklin duplexes. SFA shows that G-Ag+-G duplexes are 1.3 times stiffer than dG-dC duplexes, confirming gas-phase ion mobility spectrometry measurements and computational predictions. These findings may guide the development of structural DNA nanotechnologies that rely on silver-mediated base pairing.
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Affiliation(s)
- Eshana Bethur
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Rweetuparna Guha
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Ziqian Zhao
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Paul D. Ashby
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongbo Zeng
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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3
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Zalar M, Wang B, Plavec J, Šket P. Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure. Int J Mol Sci 2023; 24:13437. [PMID: 37686239 PMCID: PMC10487854 DOI: 10.3390/ijms241713437] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The G4C2 hexanucleotide repeat expansion in the c9orf72 gene is a major genetic cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), with the formation of G-quadruplexes directly linked to the development of these diseases. Cations play a crucial role in the formation and structure of G-quadruplexes. In this study, we investigated the impact of biologically relevant potassium ions on G-quadruplex structures and utilized 15N-labeled ammonium cations as a substitute for K+ ions to gain further insights into cation binding and exchange dynamics. Through nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we demonstrate that the single d(G4C2) repeat, in the presence of 15NH4+ ions, adopts a tetramolecular G-quadruplex with an all-syn quartet at the 5'-end. The movement of 15NH4+ ions through the central channel of the G-quadruplex, as well as to the bulk solution, is governed by the vacant cation binding site, in addition to the all-syn quartet at the 5'-end. Furthermore, the addition of K+ ions to G-quadruplexes folded in the presence of 15NH4+ ions induces stacking of G-quadruplexes via their 5'-end G-quartets, leading to the formation of stable higher-ordered species.
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Affiliation(s)
- Matja Zalar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Baifan Wang
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
- EN-FIST Center of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Primož Šket
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.Z.); (B.W.); (J.P.)
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4
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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5
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Winnerdy FR, Bakalar B, Das P, Heddi B, Marchand A, Rosu F, Gabelica V, Phan AT. Unprecedented hour-long residence time of a cation in a left-handed G-quadruplex. Chem Sci 2021; 12:7151-7157. [PMID: 34123342 PMCID: PMC8153214 DOI: 10.1039/d1sc00515d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
Abstract
Cations are critical for the folding and assembly of nucleic acids. In G-quadruplex structures, cations can bind between stacked G-tetrads and coordinate with negatively charged guanine carbonyl oxygens. They usually exchange between binding sites and with the bulk in solution with time constants ranging from sub-millisecond to seconds. Here we report the first observation of extremely long-lived K+ and NH4 + ions, with an exchange time constant on the order of an hour, when coordinated at the center of a left-handed G-quadruplex DNA. A single-base mutation, that switched one half of the structure from left- to right-handed conformation resulting in a right-left hybrid G-quadruplex, was shown to remove this long-lived behaviour of the central cation.
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Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
- Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay Gif-sur-Yvette 91190 France
| | - Adrien Marchand
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie, Université de Bordeaux, CNRS & Inserm (IECB, UMS3033, US001) Pessac 33607 France
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB Pessac 33600 France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371 Singapore
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6
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Yu B, Iwahara J. Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 2021; 19:2279-2285. [PMID: 33995919 PMCID: PMC8102144 DOI: 10.1016/j.csbj.2021.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/26/2023] Open
Abstract
Ionic interactions are crucial to biological functions of DNA, RNA, and proteins. Experimental research on how ions behave around biological macromolecules has lagged behind corresponding theoretical and computational research. In the 21st century, quantitative experimental approaches for investigating ionic interactions of biomolecules have become available and greatly facilitated examinations of theoretical electrostatic models. These approaches utilize anomalous small-angle X-ray scattering, atomic emission spectroscopy, mass spectrometry, or nuclear magnetic resonance (NMR) spectroscopy. We provide an overview on the experimental methodologies that can quantify and characterize ions within the ion atmospheres around nucleic acids, proteins, and their complexes.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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7
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Alenaizan A, Borca CH, Karunakaran SC, Kendall AK, Stubbs G, Schuster GB, Sherrill CD, Hud NV. X-ray Fiber Diffraction and Computational Analyses of Stacked Hexads in Supramolecular Polymers: Insight into Self-Assembly in Water by Prospective Prebiotic Nucleobases. J Am Chem Soc 2021; 143:6079-6094. [DOI: 10.1021/jacs.0c12010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Carlos H. Borca
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
| | - Amy K. Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0765, United States
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
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8
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Das P, Winnerdy FR, Maity A, Mechulam Y, Phan AT. A novel minimal motif for left-handed G-quadruplex formation. Chem Commun (Camb) 2021; 57:2527-2530. [PMID: 33690751 DOI: 10.1039/d0cc08146a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A recent study on the left-handed G-quadruplex (LHG4) DNA revealed a 12-nt minimal motif GTGGTGGTGGTG with the ability to independently form an LHG4 and to drive an adjacent sequence to LHG4 formation. Here we have identified a second LHG4-forming motif, GGTGGTGGTGTG, and determined the X-ray crystal structure of an LHG4 involving this motif. Our structural analysis indicated the role of split guanines and single thymine loops in promoting LHG4 formation.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore. and NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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9
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Balasubramanian S, Senapati S. Dynamics and Barrier of Movements of Sodium and Potassium Ions Across the Oxytricha nova G-Quadruplex Core. J Phys Chem B 2020; 124:11055-11066. [PMID: 33238706 DOI: 10.1021/acs.jpcb.0c04826] [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
G-quadruplexes (GQs) are highly stable noncanonical forms of nucleic acids that are present in important genomic regions. The central core of the GQ is lined up by four closely spaced carbonyl groups from the G-quartets, and the resulting electrostatic repulsion is neutralized by the coordinating cations. In spite of several reports on GQ structure and cation-GQ interactions, the atomic- to molecular-level understanding of the ion dynamics and ion exchange in the GQ core is quite poor. Here, we attempt to elucidate the mechanism of Na+ and K+ binding to the GQ core and trace the exchange of these ions with the ions in bulk by means of all-atomic molecular dynamics (MD) simulations. One of the most studied GQs, Oxytricha nova telomeric G-quadruplex (OxyGQ), is taken as the representative GQ. Subsequently, umbrella sampling MD simulations were performed to elucidate the energetics of ion translocation from one end to the other end of the GQ central core. Our study highlights the importance of ion hydration for the uptake and correct positioning of the cations in the core. The free-energy landscape of ion transport has shown favorable in-plane binding of Na+ ions with GQ quartets, which matches very well with the crystal structure. The binding of K+ ions, on the other hand, was out-of-plane and its translocation required a larger barrier to cross.
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Affiliation(s)
- Sangeetha Balasubramanian
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Sanjib Senapati
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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10
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Abstract
![]()
Molecular association of proteins with nucleic
acids is required
for many biological processes essential to life. Electrostatic interactions
via ion pairs (salt bridges) of nucleic acid phosphates and protein
side chains are crucial for proteins to bind to DNA or RNA. Counterions
around the macromolecules are also key constituents for the thermodynamics
of protein–nucleic acid association. Until recently, there
had been only a limited amount of experiment-based information about
how ions and ionic moieties behave in biological macromolecular processes.
In the past decade, there has been significant progress in quantitative
experimental research on ionic interactions with nucleic acids and
their complexes with proteins. The highly negatively charged surfaces
of DNA and RNA electrostatically attract and condense cations, creating
a zone called the ion atmosphere. Recent experimental studies were
able to examine and validate theoretical models on ions and their
mobility and interactions with macromolecules. The ionic interactions
are highly dynamic. The counterions rapidly diffuse within the ion
atmosphere. Some of the ions are released from the ion atmosphere
when proteins bind to nucleic acids, balancing the charge via intermolecular
ion pairs of positively charged side chains and negatively charged
backbone phosphates. Previously, the release of counterions had been
implicated indirectly by the salt-concentration dependence of the
association constant. Recently, direct detection of counterion
release by NMR spectroscopy
has become possible and enabled more accurate and quantitative analysis
of the counterion release and its entropic impact on the thermodynamics
of protein–nucleic acid association. Recent studies also revealed
the dynamic nature of ion pairs of protein side chains and nucleic
acid phosphates. These ion pairs undergo transitions between two major
states. In one of the major states, the cation and the anion are in
direct contact and form hydrogen bonds. In the other major state,
the cation and the anion are separated by water. Transitions between
these states rapidly occur on a picosecond to nanosecond time scale.
When proteins interact with nucleic acids, interfacial arginine (Arg)
and lysine (Lys) side chains exhibit considerably different behaviors.
Arg side chains show a higher propensity to form rigid contacts with
nucleotide bases, whereas Lys side chains tend to be more mobile at
the molecular interfaces. The dynamic ionic interactions may facilitate
adaptive molecular recognition and play both thermodynamic and kinetic
roles in protein–nucleic acid interactions.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - B. Montgomery Pettitt
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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11
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Xi M, Li Y, Zhou J. Exploration of the formation and structure characteristics of a miR-92a promoter G-quadruplex by ESI-MS and CD. Talanta 2020; 211:120708. [PMID: 32070614 DOI: 10.1016/j.talanta.2019.120708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/24/2019] [Accepted: 12/30/2019] [Indexed: 10/25/2022]
Abstract
Combining electrospray ionization mass spectrometry (ESI-MS) with circular dichroism (CD) spectroscopy, a G-rich sequence from miR-92a promoter region was discovered to form a parallel G-quadruplex structures in KCl or NH4OAc solution. In case of high concentration of NH4OAc, the ESI mass spectra showed peaks of a dimeric G-quadruplex structure with 4 ammonium ions. Meanwhile, palmatine, a natural alkaloid, was screened by ESI-MS to bind with the miR-92a G-quadruplex affinitively. The variable temperature experiment of CD also proved that high concentration of NH4OAc or palmatine could promote the stability of the dimeric G-quadruplex structure. To get the specific characteristics of the miR-92a G-quadruplex structure, systematic mutations of guanine were tested. Based on the number of NH4+ or ligands, the important guanines involved in the G-quadruplex could be determined. Considering the importance of involved guanines and the number of G-quartets, we speculated an interlocked dimeric parallel G-quadruplex as a possible conformation of the miR-92a promoter G-quadruplex. All results obtained from ESI-MS and CD illustrate structure characteristics of the miR-92a G-quadruplex, which is a promising method for preliminary structural analysis of G-quadruplexes. Besides, this study also provides a strategy for regulating the functions of microRNA by exploring and targeting higher-order structures of miRNAs.
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Affiliation(s)
- Min Xi
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China; Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China.
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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12
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Pletka CC, Nepravishta R, Iwahara J. Detecting Counterion Dynamics in DNA–Protein Association. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201910960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Channing C. Pletka
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
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13
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Pletka CC, Nepravishta R, Iwahara J. Detecting Counterion Dynamics in DNA-Protein Association. Angew Chem Int Ed Engl 2020; 59:1465-1468. [PMID: 31743557 PMCID: PMC6980997 DOI: 10.1002/anie.201910960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/14/2019] [Indexed: 01/10/2023]
Abstract
Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called "ion atmosphere". Although the release of counterions upon DNA-protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA-protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA-protein association.
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Affiliation(s)
- Channing C Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
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14
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Nakano SI, Ayusawa T, Tanino Y, Sugimoto N. Stabilization of DNA Loop Structures by Large Cations. J Phys Chem B 2019; 123:7687-7694. [PMID: 31465227 DOI: 10.1021/acs.jpcb.9b06074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DNA-binding properties of large cations differ from those of metal ions due to steric exclusion from base-paired regions. In this study, the thermal stability of DNA secondary structures, including duplexes, internal loops, bulge loops, hairpin loops, dangling ends, and G-quadruplexes, was investigated in the presence of cations of different sizes. Large cations, such as tetrabutylammonium and tetrapentylammonium ions, reduced the stability of fully matched duplexes but increased the stability of duplexes with a long loop. The cations also increased the stability of G-quadruplexes with a long loop, and the degree of stabilization was greater for low-stability G-quadruplexes. Analysis of the salt concentration dependence indicates that large cations bind to the loop nucleotides, leading to counteracting the destabilization effect on base pairing. It is likely that binding occurs when loop nucleotides are sufficiently flexible to allow for greater accessibility for large cations. These results provide insight into nucleic acid interactions with large cationic molecules and suggest a potential method for stabilizing noncanonical DNA structures under intracellular conditions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Toshiya Ayusawa
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Yuichi Tanino
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
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15
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Eichmann C, Frey L, Maslennikov I, Riek R. Probing Ion Binding in the Selectivity Filter of the KcsA Potassium Channel. J Am Chem Soc 2019; 141:7391-7398. [DOI: 10.1021/jacs.9b01092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Lukas Frey
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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16
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Giambasu GM, Case DA, York DM. Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory. J Am Chem Soc 2019; 141:2435-2445. [PMID: 30632365 PMCID: PMC6574206 DOI: 10.1021/jacs.8b11474] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Site binding of ions and water shapes nucleic acids folding, dynamics, and biological function, complementing the more diffuse, nonspecific "territorial" ion binding. Unlike territorial binding, prediction of site-specific binding to nucleic acids remains an unsolved challenge in computational biophysics. This work presents a new toolset based on the 3D-RISM molecular solvation theory and topological analysis that predicts cation and water site binding to nucleic acids. 3D-RISM is shown to accurately capture alkali cations and water binding to the central channel, transversal loops, and grooves of the Oxytricha nova's telomeres' G-quadruplex ( Oxy-GQ), in agreement with high-resolution crystallographic data. To improve the computed cation occupancy along the Oxy-GQ central channel, it was necessary to refine and validate new cation-oxygen parameters using structural and thermodynamic data available for crown ethers and ion channels. This single set of parameters that describes both localized and delocalized binding to various biological systems is used to gain insight into cation occupancy along the Oxy-GQ channel under various salt conditions. The paper concludes with prospects for extending the method to predict divalent cation binding to nucleic acids. This work advances the forefront of theoretical methods able to provide predictive insight into ion atmosphere effects on nucleic acids function.
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Affiliation(s)
- George M. Giambasu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Darrin M. York
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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17
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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18
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Akhshi P, Wu G. Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels. Phys Chem Chem Phys 2018; 19:11017-11025. [PMID: 28327752 DOI: 10.1039/c7cp01028a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system. We anticipate that these modern free-energy methods will be useful tools in evaluating ion transport properties of other G-quadruplex DNA channels.
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Affiliation(s)
- Parisa Akhshi
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.
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19
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Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Sci Rep 2018; 8:6989. [PMID: 29725066 PMCID: PMC5934368 DOI: 10.1038/s41598-018-25270-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
| | - Jerzy Wieslaw Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom
| | - Jing-Ying Gu
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ulrich Stimming
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
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20
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Tan W, Yi L, Zhu Z, Zhang L, Zhou J, Yuan G. Hsa-miR-1587 G-quadruplex formation and dimerization induced by NH 4+, molecular crowding environment and jatrorrhizine derivatives. Talanta 2017; 179:337-343. [PMID: 29310241 DOI: 10.1016/j.talanta.2017.11.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 10/23/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022]
Abstract
A guanine-rich human mature microRNA, miR-1587, was discovered to form stable intramolecular G-quadruplexes in the presence of K+, Na+ and low concentration of NH4+ (25mM) by electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism (CD) spectroscopy. Furthermore, under high concentration of NH4+ (100mM) or molecular crowding environments, miR-1587 formed a dimeric G-quadruplex through 3'-to-3' stacking of two monomeric G-quadruplex subunits with one ammonium ion sandwiched between the interfaces. Specifically, two synthesized jatrorrhizine derivatives with terminal amine groups could also induce the dimerization of miR-1587 G-quadruplex and formed 1:1 and 2:1 complexes with the dimeric G-quadruplex. In contrast, jatrorrhizine could bind with the dimeric miR-1587 G-quadruplex, but could not induce dimerization of miR-1587 G-quadruplex. These results provide a new strategy to regulate the functions of miR-1587 through induction of G-quadruplex formation and dimerization.
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Affiliation(s)
- Wei Tan
- College of Chemistry and Molecular Engineering, Peking University, 202 Chengfu Road, Haidian District, Beijing 100871, China
| | - Long Yi
- Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Engineering, Beijing 100029, China
| | - Zhentao Zhu
- Beijing Key Laboratory of Bioprocess, Beijing University of Chemical Engineering, Beijing 100029, China
| | - Lulu Zhang
- College of Chemistry and Molecular Engineering, Peking University, 202 Chengfu Road, Haidian District, Beijing 100871, China
| | - Jiang Zhou
- College of Chemistry and Molecular Engineering, Peking University, 202 Chengfu Road, Haidian District, Beijing 100871, China.
| | - Gu Yuan
- College of Chemistry and Molecular Engineering, Peking University, 202 Chengfu Road, Haidian District, Beijing 100871, China.
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21
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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22
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Hansen DF. Measurement of 15N longitudinal relaxation rates in 15NH 4+ spin systems to characterise rotational correlation times and chemical exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 279:91-98. [PMID: 28511856 PMCID: PMC5441844 DOI: 10.1016/j.jmr.2017.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 06/07/2023]
Abstract
Many chemical and biological processes rely on the movement of monovalent cations and an understanding of such processes can therefore only be achieved by characterising the dynamics of the involved ions. It has recently been shown that 15N-ammonium can be used as a proxy for potassium to probe potassium binding in bio-molecules such as DNA quadruplexes and enzymes. Moreover, equations have been derived to describe the time-evolution of 15N-based spin density operator elements of 15NH4+ spin systems. Herein NMR pulse sequences are derived to select specific spin density matrix elements of the 15NH4+ spin system and to measure their longitudinal relaxation in order to characterise the rotational correlation time of the 15NH4+ ion as well as report on chemical exchange events of the 15NH4+ ion. Applications to 15NH4+ in acidic aqueous solutions are used to cross-validate the developed pulse sequence while measurements of spin-relaxation rates of 15NH4+ bound to a 41kDa domain of the bacterial Hsp70 homologue DnaK are presented to show the general applicability of the derived pulse sequence. The rotational correlation time obtained for 15N-ammonium bound to DnaK is similar to the correlation time that describes the rotation about the threefold axis of a methyl group. The methodology presented here provides, together with the previous theoretical framework, an important step towards characterising the motional properties of cations in macromolecular systems.
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Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
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23
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Li YY, Dubins DN, Le DMNT, Leung K, Macgregor RB. The role of loops and cation on the volume of unfolding of G-quadruplexes related to HTel. Biophys Chem 2017; 231:55-63. [PMID: 28162829 DOI: 10.1016/j.bpc.2016.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/28/2022]
Abstract
In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)3GGG]), which contains four repeats of the human telomeric sequence. The experiments are conducted in aqueous buffers containing either 100mM NaCl or KCl at pH7.4. The G4s stabilized by Na+ are less sensitive to pressure perturbation than those stabilized by K+. The overall molar volume changes (ΔVtot) of the unfolding transition for all of the G4s are large and negative. A large fraction of the measured ΔVtot value arises from the re-hydration of the cations released from the interior of the folded structure. However, the differences in the measured ΔVtot values demonstrate that variations in the structure of G4s formed by each ODN, arising from differences in the sequence of the loops, contribute significantly to ΔVtot and presumably the hydration of the folded structures. Depending on the sequence of the loops, the magnitude of the measured ΔVtot can be larger or smaller than that of HTel in solutions containing sodium. However, the magnitude of ΔVtot is smaller than HTel for the unfolding of all G4s that are stabilized by potassium ions.
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Affiliation(s)
- Yang Yun Li
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - David N Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Dianna My Nhi Thi Le
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Karen Leung
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
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24
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Nasiri AH, Wurm JP, Immer C, Weickhmann AK, Wöhnert J. An intermolecular G-quadruplex as the basis for GTP recognition in the class V-GTP aptamer. RNA (NEW YORK, N.Y.) 2016; 22:1750-1759. [PMID: 27659052 PMCID: PMC5066627 DOI: 10.1261/rna.058909.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
Many naturally occurring or artificially created RNAs are capable of binding to guanine or guanine derivatives with high affinity and selectivity. They bind their ligands using very different recognition modes involving a diverse set of hydrogen bonding and stacking interactions. Apparently, the potential structural diversity for guanine, guanosine, and guanine nucleotide binding motifs is far from being fully explored. Szostak and coworkers have derived a large set of different GTP-binding aptamer families differing widely in sequence, secondary structure, and ligand specificity. The so-called class V-GTP aptamer from this set binds GTP with very high affinity and has a complex secondary structure. Here we use solution NMR spectroscopy to demonstrate that the class V aptamer binds GTP through the formation of an intermolecular two-layered G-quadruplex structure that directly incorporates the ligand and folds only upon ligand addition. Ligand binding and G-quadruplex formation depend strongly on the identity of monovalent cations present with a clear preference for potassium ions. GTP binding through direct insertion into an intermolecular G-quadruplex is a previously unobserved structural variation for ligand-binding RNA motifs and rationalizes the previously observed specificity pattern of the class V aptamer for GTP analogs.
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Affiliation(s)
- Amir H Nasiri
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Philip Wurm
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carina Immer
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Anna Katharina Weickhmann
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
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25
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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26
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Balaratnam S, Basu S. Divalent cation-aided identification of physico-chemical properties of metal ions that stabilize RNA G-quadruplexes. Biopolymers 2016; 103:376-86. [PMID: 25807937 DOI: 10.1002/bip.22628] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 02/02/2023]
Abstract
DNA and RNA sequences rich in guanosines (G) can form a four-stranded secondary structure known as a G-quadruplex (GQ), which plays a role in regulation of gene expression at the transcription and translation level. Both DNA and RNA GQs typically use the monovalent K(+) ion for stabilization of the structures. However, the fundamental reasons for K(+) acting as the most stabilizing metal ion for RNA GQs are not known. To identify the properties of a metal ion that stabilizes an RNA GQ we investigated the effect of alkaline earth metal cations and a set of divalent transition metal ions on two previously identified highly stable RNA GQs. Our results based upon circular dichroism and RNase T1 structure mapping data reveal that the RNA GQs are destabilized in the presence of the tested divalent metal cations. The destabilizing effect of a divalent metal cation is reversible upon increasing K(+) concentration. Results show that ionic radius, hydration energy, and binding strength towards the hard ligand (guanine O(6)) are important factors that determine a metal ion's ability to stabilize an RNA GQ. Additionally, the tested set of divalent metal cations incongruously affects RNA and DNA GQs.
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Affiliation(s)
- Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242
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27
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Sponer J, Berger I, Spačková N, Leszczynski J, Hobza P. Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations. J Biomol Struct Dyn 2016; 17 Suppl 1:1-24. [PMID: 22607400 DOI: 10.1080/07391102.2000.10506597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.
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Affiliation(s)
- J Sponer
- a J. Heyrovský Institute of Physical Chemistiy, Academy of Sciences of the Czech Republic , Dolejškova 3 , 182 23 , Prague , Czech Republic
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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Chaubey AK, Dubey KD, Ojha RP. MD simulation of LNA-modified human telomeric G-quadruplexes: a free energy calculation. Med Chem Res 2015. [DOI: 10.1007/s00044-014-1182-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Li Y, Wang C, Hao J, Cheng M, Jia G, Li C. Higher-order human telomeric G-quadruplex DNA metalloenzyme catalyzed Diels–Alder reaction: an unexpected inversion of enantioselectivity modulated by K+ and NH4+ ions. Chem Commun (Camb) 2015; 51:13174-7. [DOI: 10.1039/c5cc05215g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
K+ and NH4+, bearing approximately equal ionic radius, present different allosteric activation for higher-order human telomeric G-quadruplex DNA metalloenzyme.
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Affiliation(s)
- Yinghao Li
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Changhao Wang
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Jingya Hao
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Guoqing Jia
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Can Li
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
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Martín-Hidalgo M, García-Arriaga M, González F, Rivera JM. Tuning supramolecular G-quadruplexes with mono- and divalent cations. Supramol Chem 2015; 27:174-180. [PMID: 27708503 DOI: 10.1080/10610278.2014.924626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Supramolecular G-quadruplexes (SGQs) are formed via the cation promoted self-assembly of guanine derivatives into stacks of planar hydrogen-bonded tetramers. Here, we present results on the formation of SGQs made from the 8-(m-acetylphenyl)-2'-deoxyguanosine (mAGi) derivative in the presence of various mono- and divalent cations. NMR and HR ESI-MS data indicate that varying the cation can efficiently tune the molecularity, the fidelity and stability (thermal and kinetic) of the resulting SGQs. The results show that, parallel to the previously reported potassium-templated hexadecamer (mAGi16·3K+), Na+, Rb+ and [Formula: see text] also promote the formation of similar supramolecules with high fidelity and molecularity. In contrast, the divalent cations Pb2+, Sr2+ and Ba2+ template the formation of octamers (mAGi8), with the latter two inducing higher thermal stabilities. Molecular dynamics simulations for the hexadecamers containing monovalent cations enabled critical insights that help explain the experimental observations.
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Affiliation(s)
- Mariana Martín-Hidalgo
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras 00931, Puerto Rico
| | - Marilyn García-Arriaga
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras 00931, Puerto Rico
| | - Fernando González
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras 00931, Puerto Rico
| | - José M Rivera
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras 00931, Puerto Rico
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Wang F, Liu X, Willner I. DNA switches: from principles to applications. Angew Chem Int Ed Engl 2014; 54:1098-129. [PMID: 25521588 DOI: 10.1002/anie.201404652] [Citation(s) in RCA: 356] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Indexed: 12/13/2022]
Abstract
The base sequence of nucleic acid encodes structural and functional properties into the biopolymer. Structural information includes the formation of duplexes, G-quadruplexes, i-motif, and cooperatively stabilized assemblies. Functional information encoded in the base sequence involves the strand-displacement process, the recognition properties by aptamers, and the catalytic functions of DNAzymes. This Review addresses the implementation of the information encoded in nucleic acids to develop DNA switches. A DNA switch is a supramolecular nucleic acid assembly that undergoes cyclic, switchable, transitions between two distinct states in the presence of appropriate triggers and counter triggers, such as pH value, metal ions/ligands, photonic and electrical stimuli. Applications of switchable DNA systems to tailor switchable DNA hydrogels, for the controlled drug-release and for the activation of switchable enzyme cascades, are described, and future perspectives of the systems are addressed.
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Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel) http://chem.ch.huji.ac.il/willner/
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Cerofolini L, Amato J, Giachetti A, Limongelli V, Novellino E, Parrinello M, Fragai M, Randazzo A, Luchinat C. G-triplex structure and formation propensity. Nucleic Acids Res 2014; 42:13393-404. [PMID: 25378342 PMCID: PMC4245950 DOI: 10.1093/nar/gku1084] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/17/2022] Open
Abstract
The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3' end TBA-truncated 11-mer oligonucleotide (11-mer-3'-t-TBA). Here we present the solution structure of 11-mer-3'-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3'-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3'-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3' and the 5' ends show that only the 11-mer-3'-t-TBA yields a relatively stable G-triplex.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence 50019, Italy Giotto Biotech, Via Madonna del Piano 6, Sesto Fiorentino, Florence 50019, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples 'Federico II', Naples I-80131, Italy
| | - Andrea Giachetti
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Vittorio Limongelli
- Department of Pharmacy, University of Naples 'Federico II', Naples I-80131, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples 'Federico II', Naples I-80131, Italy
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8006, Swizerland Facoltà di Informatica, Istituto di Scienze Computazionali (ICS), Università della Svizzera Italiana, Lugano CH-6900, Switzerland
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence 50019, Italy Department of Chemistry, University of Florence, Sesto Fiorentino, Florence 50019, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples 'Federico II', Naples I-80131, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Florence 50019, Italy Department of Chemistry, University of Florence, Sesto Fiorentino, Florence 50019, Italy
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Yurenko YP, Novotný J, Mitoraj MP, Sklenář V, Michalak A, Marek R. Nucleic Acid Quadruplexes Based on 8-Halo-9-deazaxanthines: Energetics and Noncovalent Interactions in Quadruplex Stems. J Chem Theory Comput 2014; 10:5353-65. [DOI: 10.1021/ct5007554] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yevgen P. Yurenko
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
| | - Jan Novotný
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mariusz P. Mitoraj
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Vladimir Sklenář
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
| | - Artur Michalak
- Department
of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Krakow PL-30060, Poland
| | - Radek Marek
- CEITEC
− Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ − 62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, 625 00 Brno, Czech Republic
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Šket P, Korbar T, Plavec J. Influence of 3′–3′ inversion of polarity site within d(TGGGGT) on inter quartet cation binding. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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37
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Schulze-Adams M, Bernet B, Touboul D, Egli D, Herdeis L, Vasella A. Oligonucleotide Analogues with Integrated Bases and Backbone. Part 32. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201400175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Werbeck ND, Hansen DF. Heteronuclear transverse and longitudinal relaxation in AX4 spin systems: application to (15)N relaxations in (15)NH4(+). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:136-148. [PMID: 25128779 PMCID: PMC4283223 DOI: 10.1016/j.jmr.2014.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 06/03/2023]
Abstract
The equations that describe the time-evolution of transverse and longitudinal (15)N magnetisations in tetrahedral ammonium ions, (15)NH4(+), are derived from the Bloch-Wangsness-Redfield density operator relaxation theory. It is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular (15)N-(1)H and (1)H-(1)H dipole-dipole interactions and (2) interactions of the ammonium protons with remote spins, which also include the contribution to the relaxations that arise from the exchange of the ammonium protons with the bulk solvent. The dipole-dipole cross-correlated relaxation mechanisms between each of the (15)N-(1)H and (1)H-(1)H interactions are explicitly taken into account in the derivations. An application to (15)N-ammonium bound to a 41kDa domain of the protein DnaK is presented, where a comparison between experiments and simulations show that the ammonium ion rotates rapidly within its binding site with a local correlation time shorter than approximately 1ns. The theoretical framework provided here forms the basis for further investigations of dynamics of AX4 spin systems, with ammonium ions in solution and bound to proteins of particular interest.
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Affiliation(s)
- Nicolas D Werbeck
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
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Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 2014; 10:686-91. [PMID: 24952597 PMCID: PMC4104137 DOI: 10.1038/nchembio.1561] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 05/21/2014] [Indexed: 01/30/2023]
Abstract
Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.
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Affiliation(s)
- Hao Huang
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sandip A. Shelke
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Molly E. Evans
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Phoebe A. Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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Zhu H, Xiao S, Wang L, Liang H. Communication: Asymmetrical cation movements through G-quadruplex DNA. J Chem Phys 2014; 141:041103. [DOI: 10.1063/1.4891218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hong Zhu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Lei Wang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
- Hefei National Laboratory for Physical Sciences at Microscale, Collaborative Innovation Center of Chemistry for Energy Materials, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Werbeck ND, Kirkpatrick J, Reinstein J, Hansen DF. Using ¹⁵N-ammonium to characterise and map potassium binding sites in proteins by NMR spectroscopy. Chembiochem 2014; 15:543-8. [PMID: 24520048 PMCID: PMC4016748 DOI: 10.1002/cbic.201300700] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Indexed: 11/05/2022]
Abstract
A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the (1) H,(15) N spin-pair of enzyme-bound (15) NH4 (+) can be probed by (15) N-edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non-invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances.
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Affiliation(s)
- Nicolas D Werbeck
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT (UK).
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Ngo VA, Di Felice R, Haas S. Is the G-Quadruplex an Effective Nanoconductor for Ions? J Phys Chem B 2014; 118:864-72. [DOI: 10.1021/jp408071h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Van A. Ngo
- Department
of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Rosa Di Felice
- Department
of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Stephan Haas
- Department
of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
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43
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Stewart M, Dunlap T, Dourlain E, Grant B, McFail-Isom L. Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions. PLoS One 2013; 8:e71420. [PMID: 23940752 PMCID: PMC3735504 DOI: 10.1371/journal.pone.0071420] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 07/02/2013] [Indexed: 11/19/2022] Open
Abstract
The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.
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Affiliation(s)
- Mikaela Stewart
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Tori Dunlap
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Elizabeth Dourlain
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Bryce Grant
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Lori McFail-Isom
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
- * E-mail:
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Shibata T, Dohno C, Nakatani K. G-quadruplex formation of entirely hydrophobic DNA in organic solvents. Chem Commun (Camb) 2013; 49:5501-3. [PMID: 23660830 DOI: 10.1039/c3cc42221f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report herein a novel hydrophobic G-quadruplex DNA consisting of dodecyl phosphotriester linkages. The 6-mer hydrophobic DNA having a TG4T sequence binds to monovalent cations to form a tetramolecular G-quadruplex in low polarity organic solvents.
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Affiliation(s)
- Tomonori Shibata
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
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Sjoberg J. Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1-8. [PMID: 23132414 PMCID: PMC5110665 DOI: 10.1007/s13361-012-0499-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/04/2012] [Accepted: 09/04/2012] [Indexed: 06/01/2023]
Abstract
G-quadruplex nucleic acids can bind ammonium ions in solution, and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG(4)T(4)G(4))(2), (dG(4)T(3)G(4))(2), and (dG(3)T(4)G(4))(2), and the intramolecular G-quadruplexes dG(4)(T(4)G(4))(3) and dG(2)T(2)G(2)TGTG(2)T(2)G(2) (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure traveling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets, can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments, therefore, help assign the number of inner ammonium ions in the solution phase structure.
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Šket P, Virgilio A, Esposito V, Galeone A, Plavec J. Strand directionality affects cation binding and movement within tetramolecular G-quadruplexes. Nucleic Acids Res 2012; 40:11047-57. [PMID: 22977177 PMCID: PMC3510487 DOI: 10.1093/nar/gks851] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Nuclear magnetic resonance study of G-quadruplex structures formed by d(TG3T) and its modified analogs containing a 5′-5′ or 3′-3′ inversion of polarity sites, namely d(3′TG5′-5′G2T3′), d(3′T5′-5′G3T3′) and d(5′TG3′-3′G2T5’) demonstrates formation of G-quadruplex structures with tetrameric topology and distinct cation-binding preferences. All oligonucleotides are able to form quadruplex structures with two binding sites, although the modified oligonucleotides also form, in variable amounts, quadruplex structures with only one bound cation. The inter-quartet cavities at the inversion of polarity sites bind ammonium ions less tightly than a naturally occurring 5′-3′ backbone. Exchange of 15 ions between G-quadruplex and bulk solution is faster at the 3′-end in comparison to the 5′-end. In addition to strand directionality, cation movement is influenced by formation of an all-syn G-quartet. Formation of such quartet has been observed also for the parent d(TG3T) that besides the canonical quadruplex with only all-anti G-quartets, forms a tetramolecular parallel quadruplex containing one all-syn G-quartet, never observed before in unmodified quadruplex structures.
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Affiliation(s)
- Primoz Šket
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana SI-1000, Slovenia
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Nakayama S, Sintim HO. Investigating the interactions between cations, peroxidation substrates and G-quadruplex topology in DNAzyme peroxidation reactions using statistical testing. Anal Chim Acta 2012; 747:1-6. [PMID: 22986129 DOI: 10.1016/j.aca.2012.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/28/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
Cations affect the topology and enzymatic proficiency of most macromolecular catalysts but the role of cations in DNAzyme peroxidation reactions remains unresolved. Herein, we use statistical methods (ANOVA, t-test and Wilcoxon Mann-Whitney non-parametric test) to demonstrate that there are strong associations between cations, DNAzyme topology, peroxidation substrate and peroxidation rates of G-quadruplex peroxidises. Ammonium cation was found to be superior to all tested cations, including potassium. A t-test indicated that NH(4)(+) was better than K(+) with a p-value=0.05. Interestingly, the nature of the peroxidation substrate employed affected the dependence of peroxidation rate on the cation present and of the three substrates tested, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), tyramine and 3,3',5,5'-tetramethylbenzidine (TMB), ABTS was the most sensitive to the nature of cation present.
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Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Akhshi P, Acton G, Wu G. Molecular dynamics simulations to provide new insights into the asymmetrical ammonium ion movement inside of the [d(G3T4G4)]2 G-quadruplex DNA structure. J Phys Chem B 2012; 116:9363-70. [PMID: 22780684 DOI: 10.1021/jp304760k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have used both adaptive biasing force (ABF) and regular molecular dynamics (MD) simulations to investigate the asymmetrical NH(4)(+) ion movement inside of a bimolecular G-quadruplex DNA structure [d(G(3)T(4)G(4))](2). The free-energy landscapes obtained from ABF MD simulations suggest that the NH(4)(+) ion exiting the [d(G(3)T(4)G(4))](2) G-quadruplex stem in the direction toward the edge-type loop (denoted as the upper direction) experiences a lower free-energy barrier than that toward the diagonal loop (denoted as the lower direction) by approximately 3-4 kcal mol(-1). This result is in qualitative agreement with the previous discovery made by Šket and Plavec on the same G-quadruplex structure from (15)N NMR experiments (J. Am. Chem. Soc. 2007, 129, 8794). In the Na(+) form of the same G-quadruplex, Na(+) ion movement was found to be symmetrical, with a free-energy barrier of only 5-7 kcal mol(-1) to cross all three G-quartets, that is, [d(G(3)T(4)G(4))](2) still exhibits ion-channel-like behaviors for Na(+) ions. On the basis of the new computational results, we hypothesize that the stiffness of a G-quartet is primarily determined by the base stacking interactions within the G-quadruplex stem. Therefore, the structural origin for the asymmetrical NH(4)(+) ion movement in [d(G(3)T(4)G(4))](2) is the presence of two different modes of base stacking around the NH(4)(+) binding sites, a more stable 5'-syn-anti mode between lower and central G-quartets and a less stable 5'-anti-anti mode between upper and central G-quartets. Simulations also suggest that loop topology at the end of a G-quadruplex stem only controls the direction at which an exiting NH(4)(+) ion reaches bulk solution but does not impose significant free-energy barriers.
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Affiliation(s)
- Parisa Akhshi
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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Guéroult M, Boittin O, Mauffret O, Etchebest C, Hartmann B. Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One 2012; 7:e41704. [PMID: 22844516 PMCID: PMC3402463 DOI: 10.1371/journal.pone.0041704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022] Open
Abstract
This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.
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Affiliation(s)
- Marc Guéroult
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | - Olivier Boittin
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Oliver Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
| | - Catherine Etchebest
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Brigitte Hartmann
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
- * E-mail:
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