1
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Cheng M, Chen J, Ju H, Zhou J, Mergny JL. Drivers of i-DNA Formation in a Variety of Environments Revealed by Four-Dimensional UV Melting and Annealing. J Am Chem Soc 2021; 143:7792-7807. [PMID: 33988990 DOI: 10.1021/jacs.1c02209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
i-DNA is a four-stranded, pH-sensitive structure formed by cytosine-rich DNA sequences. Previous reports have addressed the conditions for formation of this motif in DNA in vitro and validated its existence in human cells. Unfortunately, these in vitro studies have often been performed under different experimental conditions, making comparisons difficult. To overcome this, we developed a four-dimensional UV melting and annealing (4DUVMA) approach to analyze i-DNA formation under a variety of conditions (e.g., pH, temperature, salt, crowding). Analysis of 25 sequences provided a global understanding of i-DNA formation under disparate conditions, which should ultimately allow the design of accurate prediction tools. For example, we found reliable linear correlations between the midpoint of pH transition and temperature (-0.04 ± 0.003 pH unit per 1.0 °C temperature increment) and between the melting temperature and pH (-23.8 ± 1.1 °C per pH unit increment). In addition, by analyzing the hysteresis between denaturing and renaturing profiles in both pH and thermal transitions, we found that loop length, nature of the C-tracts, pH, temperature, and crowding agents all play roles in i-DNA folding kinetics. Interestingly, our data indicate which conformer is more favorable for the sequences with an odd number of cytosine base pairs. Then the thermal and pH stabilities of "native" i-DNAs from human promoter genes were measured under near physiological conditions (pH 7.0, 37 °C). The 4DUVMA method can become a universal resource to analyze the properties of any i-DNA-prone sequence.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Université de Bordeaux, INSERM U1212, CNRS UMR5320, IECB, Pessac 33607, France.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau Cedex 91128, France
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2
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Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (Δ Cp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. J Phys Chem B 2020; 124:5614-5625. [PMID: 32531155 DOI: 10.1021/acs.jpcb.0c04065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Knowledge of differences in heat capacity changes (ΔCp) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔCp of 61 ± 7 cal molbp -1 K -1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - G Eric Plum
- UNICON International, Inc. 241 Outerbelt Street, Columbus, Ohio 43213, United States
| | - Kenneth J Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States.,The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey 08901, United States
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3
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Takahashi S, Bhattacharjee S, Ghosh S, Sugimoto N, Bhowmik S. Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications. Sci Rep 2020; 10:2504. [PMID: 32054927 PMCID: PMC7018961 DOI: 10.1038/s41598-020-59343-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 01/14/2020] [Indexed: 12/01/2022] Open
Abstract
The relationship of i-motif DNAs with cancer has prompted the development of specific ligands to detect and regulate their formation. Some plant flavonols show unique fluorescence and anti-cancer properties, which suggest the utility of the theranostics approach to cancer therapy related to i-motif DNA. We investigated the effect of the plant flavonol, fisetin (Fis), on the physicochemical property of i-motif DNAs. Binding of Fis to the i-motif from the promoter region of the human vascular endothelial growth factor (VEGF) gene dramatically induced the excited state intramolecular proton transfer (ESIPT) reaction that significantly enhanced the intensity of the tautomer emission band of Fis. This unique response was due to the coincidence of the structural change from i-motif to the hairpin-like structure which is stabilized via putative Watson-Crick base pairs between some guanines within the loop region of the i-motif and cytosines in the structure. As a result, the VEGF i-motif did not act as a replication block in the presence of Fis, which indicates the applicability of Fis for the regulation of gene expression of VEGF. The fluorescence and biological properties of Fis may be utilised for theranostics applications for cancers related to a specific cancer-related gene, such as VEGF.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, University College of Science, 92, A.P.C. Road, Kolkata, 700009, India
| | - Saptarshi Ghosh
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan. .,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, University College of Science, 92, A.P.C. Road, Kolkata, 700009, India.
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4
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Habibian M, Yahyaee-Anzahaee M, Lucic M, Moroz E, Martín-Pintado N, Di Giovanni LD, Leroux JC, Hall J, González C, Damha MJ. Structural properties and gene-silencing activity of chemically modified DNA-RNA hybrids with parallel orientation. Nucleic Acids Res 2019; 46:1614-1623. [PMID: 29373740 PMCID: PMC5829573 DOI: 10.1093/nar/gky024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/12/2018] [Indexed: 01/24/2023] Open
Abstract
We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reverse Watson-Crick base pairs in ps-DNA:DNA, ps-DNA:RNA, ps-(DNA-2'F-ANA):RNA, and ps-DNA:2'F-RNA duplexes. The formation of these duplexes was confirmed by UV melting experiments, FRET and CD studies. In addition, NMR structural studies were conducted on a ps-DNA:RNA hybrid for the first time. Finally, we provide evidence for the unprecedented finding that ps-DNA:RNA and ps-DNA:2'F-RNA hybrids can engage the RNAi pathway to silence gene expression in vitro.
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Affiliation(s)
- Maryam Habibian
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Maryam Yahyaee-Anzahaee
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Matije Lucic
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Elena Moroz
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Nerea Martín-Pintado
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Logan Dante Di Giovanni
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Jean-Christophe Leroux
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5, 8093 Zurich, Switzerland
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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5
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Bielecka P, Dembska A, Juskowiak B. Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC. Molecules 2019; 24:molecules24050952. [PMID: 30857134 PMCID: PMC6429216 DOI: 10.3390/molecules24050952] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023] Open
Abstract
The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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6
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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7
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Ma C, Chan RCT, Chan CTL, Wong AKW, Chung BPY, Kwok WM. Fluorescence and Ultrafast Fluorescence Unveil the Formation, Folding Molecularity, and Excitation Dynamics of Homo-Oligomeric and Human Telomeric i-Motifs at Acidic and Neutral pH. Chem Asian J 2018; 13:3706-3717. [PMID: 30230251 DOI: 10.1002/asia.201801117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/28/2018] [Indexed: 01/07/2023]
Abstract
i-Motifs are tetraplex DNAs known to be stable at acidic pH. The structure of i-motifs is important in DNA nanotechnology; i-motif-forming sequences with consecutive cytosine (C) molecules are abundant throughout the human genome. There is, however, little information on the structure of C-rich DNAs under physiologically relevant neutral conditions. The electron dynamics of i-motifs, crucial to both biology and materials applications, also remains largely unexplored. In this work, we report a combined femtosecond and nanosecond broadband time-resolved fluorescence (TRF) and steady-state fluorescence investigation on homo-oligomer dC20 , a human telomeric sequence (HTS) 5'-dC3 (TA2 C3 )3 , and its analogue performed with different excitation at both acidic and neutral pH. Our study provides direct observation of intrinsic fluorescence and the first full probe of the real-time dynamics of the intrinsic fluorescence from i-motifs formed from varied sequences and pH conditions. The results obtained demonstrate concrete evidence for the existence at neutral pH of i-motifs from both dC20 and the HTS. It also identifies that, under neutral conditions, the i-motif from dC20 adopting the bimolecular folding structure is significantly more stable than the HTS i-motif featuring the unimolecular topology. Our femtosecond and nanosecond TRF study unveils excitation dynamics distinctive of the interdigitated architecture of i-motifs with the excited states involved exhibiting deactivation over a remarkably broad timescale through multiple channels involving proton-coupled electron transfer lasting tens of picoseconds, as signified by the solvent kinetic isotope effect, and structure-dependent charge recombination in the hundreds of picoseconds to tens of nanoseconds time regime.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Ruth Chau-Ting Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Chris Tsz-Leung Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Bowie Po-Yee Chung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
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8
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Linking Temperature, Cation Concentration and Water Activity for the B to Z Conformational Transition in DNA. Molecules 2018; 23:molecules23071806. [PMID: 30037061 PMCID: PMC6099936 DOI: 10.3390/molecules23071806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/05/2022] Open
Abstract
High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models can allow a thermodynamic characterization of the transition. Both form right handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na+ at 25 °C. However, at 2.0 M Na+ or 200 μM [Co(NH3)6]3+, (dm5C-dG)4 assumes a left handed double helical structure (Z-DNA) while the unmethylated (dC-dG)4 analogue remains right handed under those conditions. We have previously demonstrated that the enthalpy of the transition at 25 °C for either inducer can be determined using isothermal titration calorimetry (ITC). Here, ITC is used to investigate the linkages between temperature, water activity and DNA conformation. We found that the determined enthalpy for each titration varied linearly with temperature allowing determination of the heat capacity change (ΔCp) between the initial and final states. As expected, the ΔCp values were dependent upon the cation (i.e., Na+ vs. [Co(NH3)6]3+) as well as the sequence of the DNA oligomer (i.e., methylated vs. unmethylated). Osmotic stress experiments were carried out to determine the gain or loss of water by the oligomer induced by the titration. The results are discussed in terms of solvent accessible surface areas, electrostatic interactions and the role of water.
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9
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del Villar-Guerra R, Gray RD, Trent JO, Chaires JB. A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity. Nucleic Acids Res 2018; 46:e41. [PMID: 29361140 PMCID: PMC6283418 DOI: 10.1093/nar/gky019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/12/2017] [Accepted: 01/09/2018] [Indexed: 12/23/2022] Open
Abstract
We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal component analysis and hierarchical clustering analysis to interpret the results obtained. This analysis classified compounds based on selectivity for AT-rich, GC-rich and G4 structures. We used the FID assay as a secondary screen to test the binding selectivity of an additional 20 compounds selected from the NCI Diversity Set III library that were identified as G4 binders using a thermal shift assay. The results showed G4 binding selectivity for only a few of the 20 compounds. Overall, we show that this R-FID assay, coupled with PCA and HCA, provides a useful tool for the discovery of ligands selective for particular nucleic acid structures.
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Affiliation(s)
- Rafael del Villar-Guerra
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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10
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Adam C, Olmos JM, Doneux T. Electrochemical Monitoring of the Reversible Folding of Surface-Immobilized DNA i-Motifs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:3112-3118. [PMID: 29481095 DOI: 10.1021/acs.langmuir.7b04088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two cytosine (C) rich DNA sequences folding in i-motif upon protonation of C at low pH have been immobilized at gold electrodes to study the impact of the electrode|electrolyte interface on the stability of the noncanonical DNA secondary structure. The effects of the molecular composition and environment on the melting and folding of the structures immobilized at the gold surface have been compared to the properties of the DNA strands in solution. The DNA folding into i-motif upon protonation, both at the surface and in solution, results in a significant variation of the charge density which is monitored electrochemically through the electrostatic interactions between the DNA strand and the electroactive hexaammineruthenium(III). This method is shown to be sufficiently sensitive to distinguish hemiprotonated folded state and single strand unfolded state of i-motif. The pH of melting has been determined for both sequences in the bulk and at the gold|electrolyte interface. The results evidence a stabilizing effect of the interface on i-motif structure, whereby the pH of melting is higher for the sequences immobilized at the surface. The reversibility and precision of the electrochemical model described here allows a clear and simple characterization of DNA structures and does not require any labeling of the sequence.
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Affiliation(s)
- Catherine Adam
- Chimie Analytique et Chimie des Interfaces , Université libre de Bruxelles (ULB) , Boulevard du Triomphe, 2, CP255 , B-1050 Bruxelles , Belgium
| | - José Manuel Olmos
- Chimie Analytique et Chimie des Interfaces , Université libre de Bruxelles (ULB) , Boulevard du Triomphe, 2, CP255 , B-1050 Bruxelles , Belgium
- Departamento de Química Física, Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum" , Universidad de Murcia , 30100 Murcia , Spain
| | - Thomas Doneux
- Chimie Analytique et Chimie des Interfaces , Université libre de Bruxelles (ULB) , Boulevard du Triomphe, 2, CP255 , B-1050 Bruxelles , Belgium
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11
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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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12
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Keane PM, Baptista FR, Gurung SP, Devereux SJ, Sazanovich IV, Towrie M, Brazier JA, Cardin CJ, Kelly JM, Quinn SJ. Long-Lived Excited-State Dynamics of i-Motif Structures Probed by Time-Resolved Infrared Spectroscopy. Chemphyschem 2016; 17:1281-7. [PMID: 26879336 DOI: 10.1002/cphc.201501183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Indexed: 01/22/2023]
Abstract
UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ∼300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.
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Affiliation(s)
- Páraic M Keane
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK.
| | | | - Sarah P Gurung
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
- Diamond Light Source, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Stephen J Devereux
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - John A Brazier
- Department of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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13
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Bielecka P, Juskowiak B. Fluorescent Sensor for PH Monitoring Based on an i-Motif---Switching Aptamer Containing a Tricyclic Cytosine Analogue (tC). Molecules 2015; 20:18511-25. [PMID: 26473815 PMCID: PMC6332284 DOI: 10.3390/molecules201018511] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/24/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
There are cytosine-rich regions in the genome that bind protons with high specificity. Thus protonated C-rich sequence may undergo folding to tetraplex structures called i-motifs. Therefore, one can regard such specific C-rich oligonucleotides as aptamers that recognize protons and undergo conformational transitions. Proper labeling of the aptamer with a fluorescent tag constitutes a platform to construct a pH-sensitive aptasensor. Since the hemiprotonated C-C⁺ base pairs are responsible for the folded tetraplex structure of i-motif, we decided to substitute one of cytosines in an aptamer sequence with its fluorescent analogue, 1,3-diaza-2-oxophenothiazine (tC). In this paper we report on three tC-modified fluorescent probes that contain RET related sequences as a proton recognizing aptamer. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of these tC-modified i-motif probes are presented and discussed. The pH-induced i-motif formation by the probes resulted in fluorescence quenching of tC fluorophore. Efficiency of quenching was related to the pH variations. Suitability of the sensor for monitoring pH changes was also demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
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14
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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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15
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Völker J, Plum GE, Gindikin V, Klump HH, Breslauer KJ. Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers 2014; 101:1-12. [PMID: 23494673 PMCID: PMC3920904 DOI: 10.1002/bip.22236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 03/05/2013] [Indexed: 11/12/2022]
Abstract
Repetitive DNA sequences exhibit complex structural and energy landscapes, populated by metastable, noncanonical states, that favor expansion and deletion events correlated with disease phenotypes. To probe the origins of such genotype-phenotype linkages, we report the impact of sequence and repeat number on properties of (CNG) repeat bulge loops. We find the stability of duplexes with a repeat bulge loop is controlled by two opposing effects; a loop junction-dependent destabilization of the underlying double helix, and a self-structure dependent stabilization of the repeat bulge loop. For small bulge loops, destabilization of the underlying double helix overwhelms any favorable contribution from loop self-structure. As bulge loop size increases, the stabilizing loop structure contribution dominates. The role of sequence on repeat loop stability can be understood in terms of its impact on the opposing influences of junction formation and loop structure. The nature of the bulge loop affects the thermodynamics of these two contributions differently, resulting in unique differences in repeat size-dependent minima in the overall enthalpy, entropy, and free energy changes. Our results define factors that control repeat bulge loop formation; knowledge required to understand how this helix imperfection is linked to DNA expansion, deletion, and disease phenotypes.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - G. Eric Plum
- IBET, Inc., 1507 Chambers Road, Suite 301, Columbus, OH
43212
| | - Vera Gindikin
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
| | - Horst H. Klump
- Department of Molecular and Cell Biology,
University of Cape Town, Private Bag, Rondebosch 7800, South Africa
| | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers, The
State University of New Jersey, 610 Taylor Rd, Piscataway, NJ 08854
- The Cancer Institute of New Jersey, New Brunswick,
NJ 08901
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16
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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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17
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Nesterova IV, Elsiddieg SO, Nesterov EE. Design and evaluation of an i-motif-based allosteric control mechanism in DNA-hairpin molecular devices. J Phys Chem B 2013; 117:10115-21. [PMID: 23941235 DOI: 10.1021/jp405230g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular devices designed to assess and manipulate biologically relevant conditions with required accuracy and precision play an essential role in life sciences research. Incorporating allosteric regulation mechanism is an attractive strategy toward more efficient artificial sensing and switching systems. Herein, we report on a new principle of regulating switching parameters of a DNA-based molecular device based on allosteric interaction between spatially separated hairpin stem and a tetraplexed fragment (i.e., i-motif). We characterized thermodynamic and kinetic effects arising from interaction between functional domains of the device and demonstrated the potential of applying the allosteric control principle for rational design of sensors and switches with precisely defined operational characteristics.
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Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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18
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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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19
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Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. J Am Chem Soc 2012; 134:6033-44. [PMID: 22397401 PMCID: PMC3318849 DOI: 10.1021/ja3010896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/30/2022]
Abstract
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.
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Affiliation(s)
- Jens Völker
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Vera Gindikin
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Horst H. Klump
- Department
of Molecular and
Cell Biology, University of Cape Town,
Private Bag, Rondebosch 7800, South Africa
| | - G. Eric Plum
- IBET Inc., 1507 Chambers
Road, Suite 301, Columbus, Ohio 43212, United States
| | - Kenneth J. Breslauer
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
- The Cancer Institute
of New Jersey, New Brunswick, New Jersey 08901, United
States
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20
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Dettler JM, Buscaglia R, Cui J, Cashman D, Blynn M, Lewis EA. Biophysical characterization of an ensemble of intramolecular i-motifs formed by the human c-MYC NHE III1 P1 promoter mutant sequence. Biophys J 2010; 99:561-7. [PMID: 20643075 DOI: 10.1016/j.bpj.2010.04.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022] Open
Abstract
i-Motif-forming sequences are present in or near the regulatory regions of >40% of all genes, including known oncogenes. We report here the results of a biophysical characterization and computational study of an ensemble of intramolecular i-motifs that model the polypyrimidine sequence in the human c-MYC P1 promoter. Circular dichroism results demonstrate that the mutant sequence (5'-CTT TCC TAC CCTCCC TAC CCT AA-3') can adopt multiple "i-motif-like," classical i-motif, and single-stranded structures as a function of pH. The classical i-motif structures are predominant in the pH range 4.2-5.2. The "i-motif-like" and single-stranded structures are the most significant species in solution at pH higher and lower, respectively, than that range. Differential scanning calorimetry results demonstrate an equilibrium mixture of at least three i-motif folded conformations with Tm values of 38.1, 46.6, and 49.5 degrees C at pH 5.0. The proposed ensemble of three folded conformations includes the three lowest-energy conformations obtained by computational modeling and two folded conformers that were proposed in a previous NMR study. The NMR study did not report the most stable conformer found in this study.
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Affiliation(s)
- Jamie M Dettler
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
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21
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Jain AK, Bhattacharya S. Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA. Bioconjug Chem 2010; 21:1389-403. [DOI: 10.1021/bc900247s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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22
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Kaushik M, Prasad M, Kaushik S, Singh A, Kukreti S. Structural transition from dimeric to tetrameric i-motif, caused by the presence of TAA at the 3â²-end of human telomeric C-rich sequence. Biopolymers 2010; 93:150-60. [DOI: 10.1002/bip.21313] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases. Proc Natl Acad Sci U S A 2008; 105:18326-30. [PMID: 19015511 DOI: 10.1073/pnas.0810376105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Biopolymers exhibit rough energy landscapes, thereby allowing biological processes to access a broad range of kinetic and thermodynamic states. In contrast to proteins, the energy landscapes of nucleic acids have been the subject of relatively few experimental investigations. In this study, we use calorimetric and spectroscopic observables to detect, resolve, and selectively enrich energetically discrete ensembles of microstates within metastable DNA structures. Our results are consistent with metastable, "native" DNA states being composed of an ensemble of discrete and kinetically stable microstates of differential stabilities, rather than exclusively being a single, discrete thermodynamic species. This conceptual construct is important for understanding the linkage between biopolymer conformational/configurational space and biological function, such as in protein folding, allosteric control of enzyme activity, RNA and DNA folding and function, DNA structure and biological regulation, etc. For the specific DNA sequences and structures studied here, the demonstration of discrete, kinetically stable microstates potentially has biological consequences for understanding the development and onset of DNA expansion and triplet repeat diseases.
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24
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Abstract
The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)(18) at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.
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Affiliation(s)
| | | | - Bern Kohler
- Corresponding author: e-mail: , Telephone +1-614-688-3944, Fax +1-614-292-1685
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25
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Saxena S, Bansal A, Kukreti S. Structural polymorphism exhibited by a homopurine.homopyrimidine sequence found at the right end of human c-jun protooncogene. Arch Biochem Biophys 2008; 471:95-108. [PMID: 18262488 DOI: 10.1016/j.abb.2008.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Revised: 01/15/2008] [Accepted: 01/19/2008] [Indexed: 11/17/2022]
Abstract
Homopurine.homopyrimidine (Pu.Py) tracts are likely to play important biological role in eukaryotes. Using circular dichroism, UV-thermal denaturation and gel electrophoresis, we have analyzed the structural polymorphism of a 21-bp Pu.Py DNA segment within human c-jun protooncogene 3'-region, a potential target for triplex formation. Results show that below physiological pH and in the presence of Na+/K+ with Mg2+ the duplex is destabilized/disproportionated, resulting in strand mediated structural transitions to the self-associated structures of G- and C-rich strands separately, identified as G-quadruplex and i-motif species. A significant differential behavior of the monovalent cations was observed, accordingly the presence of Na+ in acidic as well as neutral pH facilitated the duplex formation, while K+ favored the formation of self-associated structures. In Na+ and Mg2+, under acidic and neutral pH conditions, the duplex displayed triphasic and biphasic melting profiles, respectively. This self-association property of oligonucleotides might limit their use as duplex targets in triplex formation. Study is also relevant for understanding structural and biological properties of DNA sequence containing homopurine tracts.
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Affiliation(s)
- Sarika Saxena
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India
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