1
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Kim SE, Hong SC. Two Opposing Effects of Monovalent Cations on the Stability of i-Motif Structure. J Phys Chem B 2023; 127:1932-1939. [PMID: 36811958 DOI: 10.1021/acs.jpcb.2c07069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
At acidic pH, cytosine-rich single-stranded DNA can be folded into a tetraplex structure called i-motif (iM). In recent studies, the effect of monovalent cations on the stability of iM structure has been addressed, but a consensus about the issue has not been reached yet. Thus, we investigated the effects of various factors on the stability of iM structure using fluorescence resonance energy transfer (FRET)-based analysis for three types of iM derived from human telomere sequences. We confirmed that the protonated cytosine-cytosine (C:C+) base pair is destabilized as the concentration of monovalent cations (Li+, Na+, K+) increases and that Li+ has the greatest tendency of destabilization. Intriguingly, monovalent cations would play an ambivalent role in iM formation by making single-stranded DNA flexible and pliant for an iM structure. In particular, we found that Li+ has a notably greater flexibilizing effect than Na+ and K+. All taken together, we conclude that the stability of iM structure is controlled by the subtle balance of the two counteractive effects of monovalent cations: electrostatic screening and disruption of cytosine base pairing.
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Affiliation(s)
- Sung Eun Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Korea, Department of Physics, Korea University, Seoul 02841, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul, Korea, Department of Physics, Korea University, Seoul 02841, Korea
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2
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Greco F, Marzano M, Falanga AP, Terracciano M, Piccialli G, Roviello GN, D'Errico S, Borbone N, Oliviero G. Cytosine-rich oligonucleotides incorporating a non-nucleotide loop: A further step towards the obtainment of physiologically stable i-motif DNA. Int J Biol Macromol 2022; 219:626-636. [PMID: 35952813 DOI: 10.1016/j.ijbiomac.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/02/2022] [Indexed: 11/05/2022]
Abstract
i-Motifs, also known as i-tetraplexes, are secondary structures of DNA occurring in cytosine-rich oligonucleotides (CROs) that recall increasing interest in the scientific community for their relevance in various biological processes and DNA nanotechnology. This study reports the design of new structurally modified CROs, named Double-Ended-Linker-CROs (DEL-CROs), capable of forming stable i-motif structures. Here, two C-rich strands having sequences d(AC4A) and d(C6) have been attached, in a parallel fashion, to the two linker's edges by their 3' or 5' ends. The resulting DEL-CROs have been investigated for their capability to form i-motif structures by circular dichroism, poly-acrylamide gel electrophoresis, HPLC-size-exclusion chromatography, and NMR studies. This investigation established that DEL-CROs could form more stable i-motif structures than the corresponding unmodified CROs. In particular, the i-motif formed by DEL-5'-d(C6)2 resulted stable enough to be detected even at near physiological conditions (37 °C, pH 7.0). The results open the way to developing pH-switchable nanocarriers and aptamers based on suitably functionalized DEL-CROs.
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Affiliation(s)
- Francesca Greco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Maria Marzano
- Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Monica Terracciano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy
| | - Giovanni Nicola Roviello
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy; Istituto di Scienze Applicate e Sistemi Intelligenti - Unità di Napoli, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Napoli, Italy; ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy.
| | - Giorgia Oliviero
- ISBE Italy, Università degli Studi di Napoli Federico II, 80138 Napoli, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
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3
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Yang N, Wang Y, Wang X, Zhang F, Xiao Y, Yan B, Zhang T, Liu X, Li Y. Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2022; 13:6208-6214. [PMID: 35770782 DOI: 10.1021/acs.jpclett.2c01461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.
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Affiliation(s)
- Ni Yang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yunpeng Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xiaotong Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Fenghai Zhang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Bingdi Yan
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Ting Zhang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xin Liu
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
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4
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Trnkova L, Triskova I, Vorlickova M, Kejnovska I, Dvorakova Z, Pivonkova H, Fiala R. Comparative Electrochemical and Spectroscopic Studies of I‐Motif‐forming DNA Nonamers. ELECTROANAL 2019. [DOI: 10.1002/elan.201900323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Libuse Trnkova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Iveta Triskova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Michaela Vorlickova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Iva Kejnovska
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Zuzana Dvorakova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Hana Pivonkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Radovan Fiala
- CEITEC MU – Central European Institute of Technology, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
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5
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Rogers RA, Fleming AM, Burrows CJ. Unusual Isothermal Hysteresis in DNA i-Motif pH Transitions: A Study of the RAD17 Promoter Sequence. Biophys J 2019; 114:1804-1815. [PMID: 29694860 DOI: 10.1016/j.bpj.2018.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 11/15/2022] Open
Abstract
We have interrogated the isothermal folding behavior of the DNA i-motif of the human telomere, dC19, and a high-stability i-motif-forming sequence in the promoter of the human DNA repair gene RAD17 using human physiological solution and temperature conditions. We developed a circular-dichroism-spectroscopy-based pH titration method that is followed by analysis of titration curves in the derivative domain and found that the observed pH-dependent folding behavior can be significantly different and, in some cases, multiphasic, with a dependence on how rapidly i-motif folding is induced. Interestingly, the human telomere sequence exhibits unusual isothermal hysteresis in which the unfolding process always occurs at a higher pH than the folding process. For the RAD17 i-motif, rapid folding by injection into a low-pH solution results in triphasic unfolding behavior that is completely diminished when samples are slowly folded in a stepwise manner via pH titration. Chemical footprinting of the RAD17 sequence and pH titrations of dT-substituted mutants of the RAD17 sequence were used to develop a model of RAD17 folding and unfolding. These results may provide valuable information pertinent to i-motif use in sensors and materials, as well as insight into the potential biological activity of i-motif-forming sequences under stepwise or instantaneous changes in pH.
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Affiliation(s)
- R Aaron Rogers
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
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6
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Biochemical characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4. Protein Expr Purif 2018; 150:100-108. [PMID: 29807140 DOI: 10.1016/j.pep.2018.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/22/2022]
Abstract
Cytosine-specific DNA methyltransferases are important enzymes in most living organisms. In prokaryotes, most DNA methyltransferases are members of the type II restriction-modification system where they methylate host DNA, thereby protecting it from digestion by the accompanying restriction endonucleases. DNA methyltransferases can also act as solitary enzymes having important roles in controlling gene expression, DNA replication, cell cycle and DNA post-replicative mismatch repair. They have potential applications in biotechnology, such as in labeling of biopolymers, DNA mapping or epigenetic analysis, as well as for general DNA-protein interaction studies. The parI gene from the psychrophilic bacterium Psychrobacter arcticus 273-4 encodes a cytosine-specific DNA methyltransferase. In this work, recombinant ParI was expressed and purified in fusion to either an N-terminal hexahistidine affinity tag, or a maltose binding protein following the hexahistidine affinity tag, for solubility improvement. After removal of the fusion partners, recombinant ParI was found to be monomeric by size exclusion chromatography, with its molecular mass estimated to be 54 kDa. The apparent melting temperature of the protein was 53 °C with no detectable secondary structures above 65 °C. Both recombinant and native ParI showed methyltransferase activity in vivo. In addition, MBP- and His-tagged ParI also demonstrated in vitro activity. Although the overall structure of ParI exhibits high thermal stability, the loss of in vitro activity upon removal of solubility tags or purification from the cellular milieu indicates that the catalytically active form is more labile. Horizontal gene transfer may explain the acquisition of a protein-encoding gene that does not display common cold-adapted features.
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7
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Protopopova AD, Tsvetkov VB, Varizhuk AM, Barinov NA, Podgorsky VV, Klinov DV, Pozmogova GE. The structural diversity of C-rich DNA aggregates: unusual self-assembly of beetle-like nanostructures. Phys Chem Chem Phys 2018; 20:3543-3553. [PMID: 29336444 DOI: 10.1039/c7cp05380k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We studied the ability of oligonucleotides CnT25 (n = 2, 5, 7, 9, 12, 25) to form an intermolecular i-motif using circular dichroism, ultra-violet spectroscopy, nuclear magnetic resonance, high-resolution atomic force microscopy, high-performance liquid chromatography, and molecular dynamics simulations. The arrangement of single-stranded oligonucleotides in multimer i-motifs was very unusual: C-tracts of different oligonucleotides followed each other consecutively in order to fold into a closed intermolecular i-motif core with minimal loops (one cytidine in a loop spanning over a minor groove, three cytidines in a loop over a major groove); intact T-tracts protruded from predefined loci allowing visualization of beetle-like nanostructures by atomic force microscopy. The same structures were formed from analogous biotinylated oligonucleotides demonstrating one of the potential applications of such structures as carriers of multiple functional groups. Our findings open up possibilities for the rational design of pH-sensitive DNA aggregates and evaluation of the efficiency of their assembly.
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Affiliation(s)
- A D Protopopova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia.
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8
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Cao Y, Gao S, Yan Y, Bruist MF, Wang B, Guo X. Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs. Nucleic Acids Res 2016; 45:26-38. [PMID: 27899568 PMCID: PMC5224476 DOI: 10.1093/nar/gkw1049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TGiAC5) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG4AC7) and d(TGBrGGBrGAC7) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG4AC7) forms supramolecules under acidic conditions in the presence of K+ that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TGBrGGBrGAC7) forms long linear quadruplex wires under acidic conditions in the presence of Na+ that consist of both antiparallel G4s and i-motifs.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Shang Gao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yuting Yan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Michael F Bruist
- Department of Chemistry & Biochemistry, University of the Sciences, 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
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9
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Cao Y, Gao S, Li C, Yan Y, Wang B, Guo X. Structural varieties of selectively mixed G- and C-rich short DNA sequences studied with electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:931-937. [PMID: 27378414 DOI: 10.1002/jms.3804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 05/09/2023]
Abstract
Short guanine(G)-repeat and cytosine(C)-repeat DNA strands can self-assemble to form four-stranded G-quadruplexes and i-motifs, respectively. Herein, G-rich and C-rich strands with non-G or non-C terminal bases and different lengths of G- or C-repeats are mixed selectively in pH 4.5 and 6.7 ammonium acetate buffer solutions and studied by electrospray ionization mass spectrometry (ESI-MS). Various strand associations corresponding to bi-, tri- and tetramolecular ions are observed in mass spectra, indicating that the formation of quadruplex structures is a random strand by strand association process. However, with increasing incubation time for the mixtures, initially associated hybrid tetramers will transform into self-assembled conformations, which is mainly driven by the structural stability. The melting temperature values of self-assembled quadruplexes suggest that the length of G-repeats or C-repeats shows more significant effect on the stability of quadruplex structures than that of terminal residues. Accordingly, we can obtain the self-associated tetrameric species generated from the mixtures of various homologous G- or C-strands efficiently by altering the length of G- or C-repeats. Our studies demonstrate that ESI-MS is a very direct, fast and sensitive tool to provide significant information on DNA strand associations and stoichiometric transitions, particularly for complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Shang Gao
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Caijin Li
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yuting Yan
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Bing Wang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xinhua Guo
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
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10
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Nakano SI, Oka H, Fujii M, Sugimoto N. Use of a Ureido-Substituted Deoxycytidine Module for DNA Assemblies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:370-8. [PMID: 27152551 DOI: 10.1080/15257770.2016.1174262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Ureido-substituted cytosine derivatives are promising for constructing self-assembly structures that can be applied to nanotechnology research. However, conventional cytosine modules achieve assembly in organic solvents. In this study, an N-phenylcarbamoyl deoxycytidine nucleoside was incorporated into a C-rich oligonucleotide to achieve self-assembly in aqueous solution. The results show that the capability of the module to form DNA assemblies varied depending on the number of modules incorporated. The deoxycytidine derivative has a potential application in the development of smart materials based on DNA assembly.
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Affiliation(s)
- Shu-Ichi Nakano
- a Department of Nanobiochemistry , Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan
| | - Hirohito Oka
- b Department of Chemistry , Faculty of Science and Engineering, Konan University , Kobe , Japan
| | - Masayuki Fujii
- c Molecular Engineering Institute (MEI), Kinki University , Fukuoka , Japan.,d Department of Environmental and Biological Chemistry , Kinki University , Fukuoka , Japan
| | - Naoki Sugimoto
- a Department of Nanobiochemistry , Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan.,e Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , Kobe , Japan
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11
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Cao Y, Qin Y, Bruist M, Gao S, Wang B, Wang H, Guo X. Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC 4Y m) Monitored with Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:994-1003. [PMID: 25862186 DOI: 10.1007/s13361-015-1093-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(X(n)C(4)Y(m)) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (Tm) obtained in solution show that a non-C base residue located at 5' end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3' end. Detection of penta- and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH = 4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
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12
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Singh RP, Blossey R, Cleri F. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation. Biophys J 2014; 105:2820-31. [PMID: 24359754 DOI: 10.1016/j.bpj.2013.10.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022] Open
Abstract
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual C⋅C(+) stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression, and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.
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Affiliation(s)
- Raghvendra Pratap Singh
- Institut d'Electronique Microelectronique et Nanotechnologie (IEMN UMR Cnrs 8520), University of Lille I, Villeneuve d'Ascq, France; Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France
| | - Ralf Blossey
- Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France
| | - Fabrizio Cleri
- Interdisciplinary Research Institute (IRI USR Cnrs 3078), University of Lille I, Villeneuve d'Ascq, France.
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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14
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Mei H, Budow S, Seela F. Construction and assembly of chimeric DNA: oligonucleotide hybrid molecules composed of parallel or antiparallel duplexes and tetrameric i-motifs. Biomacromolecules 2012; 13:4196-204. [PMID: 23121010 DOI: 10.1021/bm301471d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chimeric DNA containing parallel (ps) and antiparallel (aps) duplex elements as well as poly-dC tracts were designed and synthesized. Oligonucleotide duplexes with ps chain orientation containing reverse Watson-Crick dA-dT base pairs and short d(C)2 tails are stabilized under slightly acidic conditions by hemiprotonated dCH+-dC base pairs ("clamp" effect). Corresponding molecules with aps orientation containing Watson-Crick dA-dT base pairs do not show this phenomenon. Chimeric DNA with ps duplex elements and long d(C)5 tails at one or at both ends assemble to tetrameric i-motif structures. Molecules with two terminal d(C)5 tails form multimeric assemblies which have the potential to form nanoscopic scaffolds. A preorganization of the ps duplex chains stabilizes the i-motif assemblies up to almost neutral conditions as evidenced by thermal melting and gel electrophoresis. Although, ps DNA is generally less stable than aps DNA, the aps duplexes contribute less to the stability of the i-motif than ps DNA.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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15
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Abstract
The physicochemical properties of small molecules as well as macromolecules are modulated by solution pH, and DNA is no exception. Special sequences of DNA can adopt unusual conformations e.g., triplex, i-motif and A-motif, depending on solution pH. The specific range of pH for these unusual structures is dictated by the pKa of protonation of the relevant nucleobase involved in the resultant non-canonical base pairing that is required to stabilise the structure. The biological significance of these pH-dependent structures is not yet clear. However, these non-B-DNA structures have been used to design different devices to direct chemical reactions, generate mechanical force, sense pH, etc. The performance of these devices can be monitored by a photonic signal. They are autonomous and their ‘waste free’ operation cycles makes them highly processive. Applications of these devices help to increase understanding of the structural polymorphism of the motifs themselves. The design of these devices has continuously evolved to improve their performance efficiency in different contexts. In some examples, these devices have been shown to perform inside complex living systems with similar efficiencies, to report on the chemical environment there. The robust performance of these devices opens up exciting possibilities for pH-sensitive DNA devices in the study of various pH-regulated biological events.
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Affiliation(s)
- Sonali Saha
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
| | - Yamuna Krishnan*
- National Centre for Biological Sciences TIFR, GKVK, Bellary Road, Bangalore 560065 India
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16
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Guittet E, Renciuk D, Leroy JL. Junctions between i-motif tetramers in supramolecular structures. Nucleic Acids Res 2012; 40:5162-70. [PMID: 22362739 PMCID: PMC3367196 DOI: 10.1093/nar/gks161] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3'- or 5'-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms.
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Affiliation(s)
- Eric Guittet
- Laboratoire de Chimie et Biologie Structurales, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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17
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Lee IJ, Park M, Joo T, Kim BH. Using fluorescence changes of F1U units at terminal and mid-loop positions to probe i-motif structures. ACTA ACUST UNITED AC 2012; 8:486-90. [DOI: 10.1039/c1mb05343d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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18
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Lee IJ, Kim BH. Monitoring i-motif transitions through the exciplex emission of a fluorescent probe incorporating two PyA units. Chem Commun (Camb) 2012; 48:2074-6. [DOI: 10.1039/c1cc16497j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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