101
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Assessing the potential of surface-immobilized molecular logic machines for integration with solid state technology. Biosystems 2016; 146:3-9. [PMID: 27208444 DOI: 10.1016/j.biosystems.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 01/22/2023]
Abstract
Molecular computation with DNA has great potential for low power, highly parallel information processing in a biological or biochemical context. However, significant challenges remain for the field of DNA computation. New technology is needed to allow multiplexed label-free readout and to enable regulation of molecular state without addition of new DNA strands. These capabilities could be provided by hybrid bioelectronic systems in which biomolecular computing is integrated with conventional electronics through immobilization of DNA machines on the surface of electronic circuitry. Here we present a quantitative experimental analysis of a surface-immobilized OR gate made from DNA and driven by strand displacement. The purpose of our work is to examine the performance of a simple representative surface-immobilized DNA logic machine, to provide valuable information for future work on hybrid bioelectronic systems involving DNA devices. We used a quartz crystal microbalance to examine a DNA monolayer containing approximately 5×10(11)gatescm(-2), with an inter-gate separation of approximately 14nm, and we found that the ensemble of gates took approximately 6min to switch. The gates could be switched repeatedly, but the switching efficiency was significantly degraded on the second and subsequent cycles when the binding site for the input was near to the surface. Otherwise, the switching efficiency could be 80% or better, and the power dissipated by the ensemble of gates during switching was approximately 0.1nWcm(-2), which is orders of magnitude less than the power dissipated during switching of an equivalent array of transistors. We propose an architecture for hybrid DNA-electronic systems in which information can be stored and processed, either in series or in parallel, by a combination of molecular machines and conventional electronics. In this architecture, information can flow freely and in both directions between the solution-phase and the underlying electronics via surface-immobilized DNA machines that provide the interface between the molecular and electronic domains.
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Affiliation(s)
- Katherine E Dunn
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK.
| | - Martin A Trefzer
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - Steven Johnson
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - Andy M Tyrrell
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
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102
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Dembska A. The analytical and biomedical potential of cytosine-rich oligonucleotides: A review. Anal Chim Acta 2016; 930:1-12. [PMID: 27265899 DOI: 10.1016/j.aca.2016.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 02/04/2023]
Abstract
Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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103
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Xu B, Wu X, Yeow EKL, Shao F. A single thiazole orange molecule forms an exciplex in a DNA i-motif. Chem Commun (Camb) 2016; 50:6402-5. [PMID: 24811922 DOI: 10.1039/c4cc01147c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A fluorescent exciplex of thiazole orange (TO) is formed in a single-dye conjugated DNA i-motif. The exciplex fluorescence exhibits a large Stokes shift, high quantum yield, robust response to pH oscillation and little structural disturbance to the DNA quadruplex, which can be used to monitor the folding of high-order DNA structures.
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Affiliation(s)
- Baochang Xu
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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104
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Xu B, Devi G, Shao F. Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification. Org Biomol Chem 2016; 13:5646-51. [PMID: 25886653 DOI: 10.1039/c4ob02646b] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The two important epigenetic markers in the human genome, 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), are involved in gene regulation processes. As a major epigenetic target, cytosines in a C-rich DNA sequence were substituted with mC and hmC to investigate the thermal stability and pH sensitivity of the corresponding i-motifs. Circular Dichroism (CD) studies indicate the formation of i-motifs at acidic pH (<6.5) for mC- and hmC-modified DNA sequences. Thermal denaturation results suggest that DNA i-motifs are stabilized when modified with one or two mCs. However, hypermethylation with mC and single modification with hmC cause destabilization of the structure. A biomimetic crowding agent does not alter the stability effect trends resulting from mC and hmC modifications, though the corresponding i-motifs show elevated melting temperatures without significant changes in pKa values.
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Affiliation(s)
- Baochang Xu
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371.
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105
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Gao J, Berden G, Rodgers MT, Oomens J. Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals. Phys Chem Chem Phys 2016; 18:7269-77. [PMID: 26894838 DOI: 10.1039/c6cp00234j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.
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Affiliation(s)
- Juehan Gao
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.
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106
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El-Sayed AA, Pedersen EB, Khaireldin NY. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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107
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Ren J, Wang T, Wang E, Wang J. I-motif-stapled and spacer-dependent multiple DNA nanostructures. RSC Adv 2016. [DOI: 10.1039/c6ra15201e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The DNA spacers between duplexes and i-motif structures are critical for the morphology of assembled pH-responsive DNA nanostructures, which is very instructive for fabrication of distinct-scale molecular devices in the future.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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108
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Li G, Sun L, Ji L, Chao H. Ruthenium(ii) complexes with dppz: from molecular photoswitch to biological applications. Dalton Trans 2016; 45:13261-76. [DOI: 10.1039/c6dt01624c] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present article describes the recent advances in biological applications of the Ru-dppz systems in DNA binding, cellular imaging, anticancer drugs, phototherapy, protein aggregation detecting and chemosensors.
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Affiliation(s)
- Guanying Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Lingli Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
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109
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Russo Krauss I, Spiridonova V, Pica A, Napolitano V, Sica F. Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding. Nucleic Acids Res 2015; 44:983-91. [PMID: 26673709 PMCID: PMC4737158 DOI: 10.1093/nar/gkv1384] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 11/26/2022] Open
Abstract
Mixed duplex/quadruplex oligonucleotides have attracted great interest as therapeutic targets as well as effective biomedical aptamers. In the case of thrombin-binding aptamer (TBA), the addition of a duplex motif to the G-quadruplex module improves the aptamer resistance to biodegradation and the affinity for thrombin. In particular, the mixed oligonucleotide RE31 is significantly more effective than TBA in anticoagulation experiments and shows a slower disappearance rate in human plasma and blood. In the crystal structure of the complex with thrombin, RE31 adopts an elongated structure in which the duplex and quadruplex regions are perfectly stacked on top of each other, firmly connected by a well-structured junction. The lock-and-key shape complementarity between the TT loops of the G-quadruplex and the protein exosite I gives rise to the basic interaction that stabilizes the complex. However, our data suggest that the duplex motif may have an active role in determining the greater anti-thrombin activity in biological fluids with respect to TBA. This work gives new information on mixed oligonucleotides and highlights the importance of structural data on duplex/quadruplex junctions, which appear to be varied, unpredictable, and fundamental in determining the aptamer functional properties.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples 'Federico II', Naples, Italy Institute of Biostructures and Bioimages, C.N.R, Naples, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Andrea Pica
- Department of Chemical Sciences, University of Naples 'Federico II', Naples, Italy Institute of Biostructures and Bioimages, C.N.R, Naples, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples 'Federico II', Naples, Italy Institute of Biostructures and Bioimages, C.N.R, Naples, Italy
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110
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Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene. CHEMOSENSORS 2015. [DOI: 10.3390/chemosensors3030211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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111
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Surana S, Shenoy AR, Krishnan Y. Designing DNA nanodevices for compatibility with the immune system of higher organisms. NATURE NANOTECHNOLOGY 2015; 10:741-7. [PMID: 26329110 PMCID: PMC4862568 DOI: 10.1038/nnano.2015.180] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/17/2015] [Indexed: 05/05/2023]
Abstract
DNA is proving to be a powerful scaffold to construct molecularly precise designer DNA devices. Recent trends reveal their ever-increasing deployment within living systems as delivery devices that not only probe but also program and re-program a cell, or even whole organisms. Given that DNA is highly immunogenic, we outline the molecular, cellular and organismal response pathways that designer nucleic acid nanodevices are likely to elicit in living systems. We address safety issues applicable when such designer DNA nanodevices interact with the immune system. In light of this, we discuss possible molecular programming strategies that could be integrated with such designer nucleic acid scaffolds to either evade or stimulate the host response with a view to optimizing and widening their applications in higher organisms.
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Affiliation(s)
- Sunaina Surana
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, 60637 Illinois, USA
| | - Avinash R. Shenoy
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
- ;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, 60637 Illinois, USA
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bellary Road, Bangalore 560065, India
- ;
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112
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Wunnicke D, Ding P, Yang H, Seela F, Steinhoff HJ. DNA with Parallel Strand Orientation: A Nanometer Distance Study with Spin Labels in the Watson-Crick and the Reverse Watson-Crick Double Helix. J Phys Chem B 2015; 119:13593-9. [PMID: 26121221 DOI: 10.1021/acs.jpcb.5b02935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel-stranded (ps) DNA characterized by its sugar-phosphate backbones pointing in the same direction represents an alternative pairing system to antiparallel-stranded (aps) DNA with the potential to inhibit transcription and translation. 25-mer oligonucleotides were selected containing only dA·dT base pairs to compare spin-labeled nucleobase distances over a range of 10 or 15 base pairs in ps DNA with those in aps DNA. By means of the copper(I)-catalyzed Huisgen-Meldal-Sharpless alkyne-azide cycloaddition, the spin label 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl was clicked to 7-ethynyl-7-deaza-2'-deoxyadenosine or 5-ethynyl-2'-deoxyuridine to yield 25-mer oligonucleotides incorporating two spin labels. The interspin distances between spin labeled residues were determined by pulse EPR spectroscopy. The results reveal that in ps DNA these distances are between 5 and 10% longer than in aps DNA when the labeled DNA segment is located near the center of the double helix. The interspin distance in ps DNA becomes shorter compared with aps DNA when one of the spin labels occupies a position near the end of the double helix.
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Affiliation(s)
| | - Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
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113
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Dembska A, Juskowiak B. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:928-933. [PMID: 26123509 DOI: 10.1016/j.saa.2015.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).
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Affiliation(s)
- 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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114
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Potempa M, Nalivaika E, Ragland D, Lee SK, Schiffer CA, Swanstrom R. A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro. J Mol Biol 2015; 427:2360-78. [PMID: 25986307 DOI: 10.1016/j.jmb.2015.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 01/09/2023]
Abstract
Though the steps of human immunodeficiency virus type 1 (HIV-1) virion maturation are well documented, the mechanisms regulating the proteolysis of the Gag and Gag-Pro-Pol polyproteins by the HIV-1 protease (PR) remain obscure. One proposed mechanism argues that the maturation intermediate p15NC must interact with RNA for efficient cleavage by the PR. We investigated this phenomenon and found that processing of multiple substrates by the HIV-1 PR was enhanced in the presence of RNA. The acceleration of proteolysis occurred independently from the substrate's ability to interact with nucleic acid, indicating that a direct interaction between substrate and RNA is not necessary for enhancement. Gel-shift assays demonstrated the HIV-1 PR is capable of interacting with nucleic acids, suggesting that RNA accelerates processing reactions by interacting with the PR rather than the substrate. All HIV-1 PRs examined have this ability; however, the HIV-2 PR does not interact with RNA and does not exhibit enhanced catalytic activity in the presence of RNA. No specific sequence or structure was required in the RNA for a productive interaction with the HIV-1 PR, which appears to be principally, though not exclusively, driven by electrostatic forces. For a peptide substrate, RNA increased the kinetic efficiency of the HIV-1 PR by an order of magnitude, affecting both turnover rate (k(cat)) and substrate affinity (K(m)). These results suggest that an allosteric binding site exists on the HIV-1 PR and that HIV-1 PR activity during maturation could be regulated in part by the juxtaposition of the enzyme with virion-packaged RNA.
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Affiliation(s)
- Marc Potempa
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellen Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Debra Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ronald Swanstrom
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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115
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Petty JT, Sergev OO, Kantor AG, Rankine IJ, Ganguly M, David FD, Wheeler SK, Wheeler JF. Ten-atom silver cluster signaling and tempering DNA hybridization. Anal Chem 2015; 87:5302-9. [PMID: 25923963 DOI: 10.1021/acs.analchem.5b01265] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Silver clusters with ∼10 atoms are molecules, and specific species develop within DNA strands. These molecular metals have sparsely organized electronic states with distinctive visible and near-infrared spectra that vary with cluster size, oxidation, and shape. These small molecules also act as DNA adducts and coordinate with their DNA hosts. We investigated these characteristics using a specific cluster-DNA conjugate with the goal of developing a sensitive and selective biosensor. The silver cluster has a single violet absorption band (λ(max) = 400 nm), and its single-stranded DNA host has two domains that stabilize this cluster and hybridize with target oligonucleotides. These target analytes transform the weakly emissive violet cluster to a new chromophore with blue-green absorption (λ(max) = 490 nm) and strong green emission (λ(max) = 550 nm). Our studies consider the synthesis, cluster size, and DNA structure of the precursor violet cluster-DNA complex. This species preferentially forms with relatively low amounts of Ag(+), high concentrations of the oxidizing agent O2, and DNA strands with ≳20 nucleotides. The resulting aqueous and gaseous forms of this chromophore have 10 silvers that coalesce into a single cluster. This molecule is not only a chromophore but also an adduct that coordinates multiple nucleobases. Large-scale DNA conformational changes are manifested in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking. Multidentate coordination also stabilizes the single-stranded DNA and thereby inhibits hybridization with target complements. These observations suggest that the silver cluster-DNA conjugate acts like a molecular beacon but is distinguished because the cluster chromophore not only sensitively signals target analytes but also stringently discriminates against analogous competing analytes.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Orlin O Sergev
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Andrew G Kantor
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Ian J Rankine
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Mainak Ganguly
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Frederic D David
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sandra K Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - John F Wheeler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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116
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Wu F, Zhang Y, Yang Z. An Overview of Self-Assembly and Morphological Regulation of Amphiphilic DNA Organic Hybrids. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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117
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Yan Y, Sun Y, Yu H, Xu H, Lu JR. Self-assembly and nanoaggregation of a pH responsive DNA hybrid amphiphile. SOFT MATTER 2015; 11:1748-1754. [PMID: 25603356 DOI: 10.1039/c4sm02499k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This work describes the design and preparation of a simple but novel hybrid amphiphile containing a pH-responsive DNA sequence. The formation of a bimolecular i-motif structure allows the control of reversible switching of the hybrid amphiphile between the dimer and unimer by pH. Thus, spherical aggregates with distinct self-assembly pathways, sizes and structures are obtained at pH 4.5 and pH 9.0, and the structures can be switched by the change of pH and thermal annealing. This work reports different self-assembled nanostructures and their transitions that give this amphiphile potential for the design of controllable drug delivery systems.
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Affiliation(s)
- Yongfeng Yan
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao 266580, China.
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118
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Mata G, Luedtke NW. Fluorescent Probe for Proton-Coupled DNA Folding Revealing Slow Exchange of i-Motif and Duplex Structures. J Am Chem Soc 2015; 137:699-707. [DOI: 10.1021/ja508741u] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Guillaume Mata
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
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119
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Ren J, Wang T, Wang E, Wang J. Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems. Analyst 2015; 140:2556-72. [DOI: 10.1039/c4an02282c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.
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Affiliation(s)
- Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Tianshu Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- China
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120
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Fu B, Huang J, Bai D, Xie Y, Wang Y, Wang S, Zhou X. Label-free detection of pH based on the i-motif using an aggregation-caused quenching strategy. Chem Commun (Camb) 2015; 51:16960-3. [DOI: 10.1039/c5cc04784f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A label-free and biocompatible pH sensor system based on the aggregation-caused quenching (ACQ) probe has been reported herein.
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Affiliation(s)
- Boshi Fu
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Jinguo Huang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Dongsheng Bai
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Yalun Xie
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Yang Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biomedical Polymers of Ministry of Education
- Institute of Advanced Studies - 68756663
- China
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121
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Manukyan A, Tekin A. First principles potential for the cytosine dimer. Phys Chem Chem Phys 2015; 17:14685-701. [DOI: 10.1039/c5cp00553a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new first principles potential for the cytosine dimer.
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Affiliation(s)
- Artür Manukyan
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| | - Adem Tekin
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
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122
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Takahashi S, Sugimoto N. Pressure-dependent formation of i-motif and G-quadruplex DNA structures. Phys Chem Chem Phys 2015; 17:31004-10. [DOI: 10.1039/c5cp04727g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pressure is an important physical stimulus that can influence the fate of cells by causing structural changes in biomolecules such as DNA.
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Affiliation(s)
- S. Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
| | - N. Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe 650-0047
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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123
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Wu J, Tan LH, Hwang K, Xing H, Wu P, Li W, Lu Y. DNA Sequence-Dependent Morphological Evolution of Silver Nanoparticles and Their Optical and Hybridization Properties. J Am Chem Soc 2014; 136:15195-202. [DOI: 10.1021/ja506150s] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jiangjiexing Wu
- Collaborative Innovation Center
of Chemical Science and
Chemical Engineering (Tianjin) and Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Li Huey Tan
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kevin Hwang
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Hang Xing
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Peiwen Wu
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wei Li
- Collaborative Innovation Center
of Chemical Science and
Chemical Engineering (Tianjin) and Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Yi Lu
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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124
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Kim J, Lee YM, Kang Y, Kim WJ. Tumor-homing, size-tunable clustered nanoparticles for anticancer therapeutics. ACS NANO 2014; 8:9358-9367. [PMID: 25184691 DOI: 10.1021/nn503349g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present herein a pH-responsive dynamic DNA nanocluster based on gold nanoparticles with highly packed nucleic acid assembly and evaluate its potential as a drug delivery vehicle with tumor-specific accumulation. Each gold nanoparticle was readily functionalized with various functional DNA sequences; in particular, we modified the surface of gold nanoparticles with bcl-2 antisense and i-motif binding sequences. Clustering of the gold nanoparticles induced by hybridization of each DNA sequence via i-motif DNA provided tumor targeting and drug loading capabilities. After cellular uptake, the drug was released by disassembly of the gold nanoparticle cluster into single gold nanoparticles in response to the pH decrease in the late endosome. Furthermore, the antiapoptotic Bcl-2 protein was down-regulated by the antisense-modified gold nanoparticles; thus, drug-mediated apoptosis was significantly accelerated by sensitizing the cancer cells to the drug. Our size-tunable clustered nucleic acid-grafted gold nanoparticles provide tumor homing in the blood circulation and are thus a potential multifunctional therapeutic agent in vivo as well as in vitro.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS) , Pohang 790-784, Korea
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125
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Petty JT, Nicholson D, Sergev OO, Graham SK. Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts. Anal Chem 2014; 86:9220-8. [PMID: 25157472 PMCID: PMC4165452 DOI: 10.1021/ac502192w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Silver clusters with ~10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5'-cluster domain that complexes silver clusters and a 3'-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ~11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (~5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.
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Affiliation(s)
| | - David
A. Nicholson
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
| | - Orlin O. Sergev
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
| | - Stuart K. Graham
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
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126
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Pilarova I, Kejnovska I, Vorlickova M, Trnkova L. Dynamic Structures of DNA Heptamers with Different Central Trinucleotide Sequences Studied by Electrochemical and Spectral Methods. ELECTROANAL 2014. [DOI: 10.1002/elan.201400288] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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127
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Largy E, Mergny JL. Shape matters: size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Res 2014; 42:e149. [PMID: 25143531 PMCID: PMC4231728 DOI: 10.1093/nar/gku751] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In recent years, an increasing number of reports have been focused on the structure and biological role of non-canonical nucleic acid secondary structures. Many of these studies involve the use of oligonucleotides that can often adopt a variety of structures depending on the experimental conditions, and hence change the outcome of an assay. The knowledge of the structure(s) formed by oligonucleotides is thus critical to correctly interpret the results, and gain insight into the biological role of these particular sequences. Herein we demonstrate that size-exclusion HPLC (SE-HPLC) is a simple yet surprisingly powerful tool to quickly and effortlessly assess the secondary structure(s) formed by oligonucleotides. For the first time, an extensive calibration and validation of the use of SE-HPLC to confidently detect the presence of different species displaying various structure and/or molecularity, involving >110 oligonucleotides forming a variety of secondary structures (antiparallel, parallel, A-tract bent and mismatched duplexes, triplexes, G-quadruplexes and i-motifs, RNA stem loops), is performed. Moreover, we introduce simple metrics that allow the use of SE-HPLC without the need for a tedious calibration work. We show that the remarkable versatility of the method allows to quickly establish the influence of a number of experimental parameters on nucleic acid structuration and to operate on a wide range of oligonucleotide concentrations. Case studies are provided to clearly illustrate the all-terrain capabilities of SE-HPLC for oligonucleotide secondary structure analysis. Finally, this manuscript features a number of important observations contributing to a better understanding of nucleic acid structural polymorphism.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
| | - Jean-Louis Mergny
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
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128
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Chen YW, Jhan CR, Neidle S, Hou MH. Structural Basis for the Identification of an i-Motif Tetraplex Core with a Parallel-Duplex Junction as a Structural Motif in CCG Triplet Repeats. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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129
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Chen YW, Jhan CR, Neidle S, Hou MH. Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats. Angew Chem Int Ed Engl 2014; 53:10682-6. [PMID: 25139267 DOI: 10.1002/anie.201405637] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Indexed: 11/12/2022]
Abstract
CCG triplet repeats can fold into tetraplex structures, which are associated with the expansion of (CCG)n trinucleotide sequences in certain neurological diseases. These structures are stabilized by intertwining i-motifs. However, the structural basis for tetraplex i-motif formation in CCG triplet repeats remains largely unknown. We report the first crystal structure of a CCG-repeat sequence, which shows that two dT(CCG)3 A strands can associate to form a tetraplex structure with an i-motif core containing four C:C(+) pairs flanked by two G:G homopurine base pairs as a structural motif. The tetraplex core is attached to a short parallel-stranded duplex. Each hairpin itself contains a central CCG loop in which the nucleotides are flipped out and stabilized by stacking interactions. The helical twists between adjacent cytosine residues of this structure in the i-motif core have an average value of 30°, which is greater than those previously reported for i-motif structures.
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Affiliation(s)
- Yi-Wen Chen
- Institute of Genomics and Bioinformatics and Institute of Biochemistry, National Chung Hsing University, No. 250 Kuo-Kuang Road, Taichung (Taiwan)
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130
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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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131
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Gottstein-Schmidtke SR, Duchardt-Ferner E, Groher F, Weigand JE, Gottstein D, Suess B, Wöhnert J. Building a stable RNA U-turn with a protonated cytidine. RNA (NEW YORK, N.Y.) 2014; 20:1163-72. [PMID: 24951555 PMCID: PMC4105743 DOI: 10.1261/rna.043083.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/16/2014] [Indexed: 05/28/2023]
Abstract
The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
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Affiliation(s)
- Sina R Gottstein-Schmidtke
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Daniel Gottstein
- Institute for Biophysical Chemistry, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
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132
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Amato J, Iaccarino N, Randazzo A, Novellino E, Pagano B. Noncanonical DNA Secondary Structures as Drug Targets: the Prospect of the i-Motif. ChemMedChem 2014; 9:2026-30. [DOI: 10.1002/cmdc.201402153] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 11/06/2022]
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133
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Nesterova IV, Nesterov EE. Rational Design of Highly Responsive pH Sensors Based on DNA i-Motif. J Am Chem Soc 2014; 136:8843-6. [DOI: 10.1021/ja501859w] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Irina V. Nesterova
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Evgueni E. Nesterov
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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134
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Yuan Z, Chen YC, Li HW, Chang HT. Fluorescent silver nanoclusters stabilized by DNA scaffolds. Chem Commun (Camb) 2014; 50:9800-15. [DOI: 10.1039/c4cc02981j] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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135
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Day HA, Pavlou P, Waller ZAE. i-Motif DNA: structure, stability and targeting with ligands. Bioorg Med Chem 2014; 22:4407-18. [PMID: 24957878 DOI: 10.1016/j.bmc.2014.05.047] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 10/25/2022]
Abstract
i-Motifs are four-stranded DNA secondary structures which can form in sequences rich in cytosine. Stabilised by acidic conditions, they are comprised of two parallel-stranded DNA duplexes held together in an antiparallel orientation by intercalated, cytosine-cytosine(+) base pairs. By virtue of their pH dependent folding, i-motif forming DNA sequences have been used extensively as pH switches for applications in nanotechnology. Initially, i-motifs were thought to be unstable at physiological pH, which precluded substantial biological investigation. However, recent advances have shown that this is not always the case and that i-motif stability is highly dependent on factors such as sequence and environmental conditions. In this review, we discuss some of the different i-motif structures investigated to date and the factors which affect their topology, stability and dynamics. Ligands which can interact with these structures are necessary to aid investigations into the potential biological functions of i-motif DNA and herein we review the existing i-motif ligands and give our perspective on the associated challenges with targeting this structure.
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Affiliation(s)
- Henry A Day
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Pavlos Pavlou
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
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136
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Agarwal T, Roy S, Kumar S, Chakraborty TK, Maiti S. In the Sense of Transcription Regulation by G-Quadruplexes: Asymmetric Effects in Sense and Antisense Strands. Biochemistry 2014; 53:3711-8. [DOI: 10.1021/bi401451q] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tani Agarwal
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
| | - Saumya Roy
- CSIR-Indian Institute
of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India
| | - Santosh Kumar
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
| | - Tushar Kanti Chakraborty
- CSIR-Indian Institute
of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Souvik Maiti
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
- CSIR-National
Chemical Laboratory, Dr. Homi Bhabha
Road, Pune 411008, India
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137
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Ruedas-Rama MJ, Orte A, Martin-Domingo MC, Castello F, Talavera EM, Alvarez-Pez JM. Interaction of YOYO-3 with Different DNA Templates to Form H-Aggregates. J Phys Chem B 2014; 118:6098-106. [DOI: 10.1021/jp5022888] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria J. Ruedas-Rama
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
| | - Angel Orte
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
| | - Maria C. Martin-Domingo
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
| | - F. Castello
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
| | - Eva. M. Talavera
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
| | - Jose M. Alvarez-Pez
- Department of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada,Spain
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138
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Berdakin M, Steinmetz V, Maitre P, Pino GA. Gas Phase Structure of Metal Mediated (Cytosine)2Ag+ Mimics the Hemiprotonated (Cytosine)2H+ Dimer in i-Motif Folding. J Phys Chem A 2014; 118:3804-3809. [DOI: 10.1021/jp5038969] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET
− Universidad Nacional de Córdoba), Departamento de
Fisicoquímica, Facultad de Ciencias Químicas, Centro
Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Córdoba, Argentina
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR8000 CNRS, Faculté des Sciences, 91405 Orsay Cedex, France
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris Sud, UMR8000 CNRS, Faculté des Sciences, 91405 Orsay Cedex, France
| | - Gustavo A. Pino
- INFIQC (CONICET
− Universidad Nacional de Córdoba), Departamento de
Fisicoquímica, Facultad de Ciencias Químicas, Centro
Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Córdoba, Argentina
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139
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Kim SE, Lee IB, Hyeon C, Hong SC. Destabilization of i-Motif by Submolar Concentrations of a Monovalent Cation. J Phys Chem B 2014; 118:4753-60. [DOI: 10.1021/jp500120d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sung Eun Kim
- Department
of Physics, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Il-Buem Lee
- Department
of Physics, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 136-713, Republic of Korea
| | - Changbong Hyeon
- School
of Computational Sciences, Korea Institute for Advanced Study, 85
Hoegi-ro Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Seok-Cheol Hong
- Department
of Physics, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 136-713, Republic of Korea
- School
of Computational Sciences, Korea Institute for Advanced Study, 85
Hoegi-ro Dongdaemun-gu, Seoul 130-722, Republic of Korea
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140
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Charoenphol P, Bermudez H. Design and application of multifunctional DNA nanocarriers for therapeutic delivery. Acta Biomater 2014; 10:1683-91. [PMID: 23896566 DOI: 10.1016/j.actbio.2013.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/17/2013] [Accepted: 07/17/2013] [Indexed: 12/31/2022]
Abstract
The unique programmability of nucleic acids offers versatility and flexibility in the creation of self-assembled DNA nanostructures. To date, many three-dimensional DNA architectures of varying sizes and shapes have been precisely formed. Their biocompatibility, biodegradability and high intrinsic stability in physiological environments emphasize their emerging use as carriers for drug and gene delivery. Furthermore, DNA nanocarriers have been shown to enter cells efficiently and without the aid of transfection reagents. A key strength of DNA nanocarriers over other delivery systems is their modularity and their ability to control the spatial distribution of cargoes and ligands. Optimizing DNA nanocarrier properties to dictate their localization, uptake and intracellular trafficking is also possible. This review presents design considerations for DNA nanocarriers and examples of their use in the context of therapeutic delivery applications. The assembly of DNA nanocarriers and approaches for loading and releasing cargo are described. The stability and safety of DNA nanocarriers are also discussed, with particular attention to the in vivo physiological environment. Mechanisms of cellular uptake and intracellular trafficking are examined, and the paper concludes with strategies to enhance the delivery efficiency of DNA nanocarriers.
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Affiliation(s)
- P Charoenphol
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - H Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
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141
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Lee JD, Cang J, Chen YC, Chen WY, Ou CM, Chang HT. Detection of adenosine 5'-triphosphate by fluorescence variation of oligonucleotide-templated silver nanoclusters. Biosens Bioelectron 2014; 58:266-71. [PMID: 24657647 DOI: 10.1016/j.bios.2014.02.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/25/2014] [Indexed: 11/18/2022]
Abstract
Oligonucleotide-templated Ag nanoclusters (DNA-Ag NCs) prepared from AgNO3 using an oligonucleotide (5'-TAACCCCTAACCCCT-3') as a template and NaBH4 as a reducing agent have been used for sensing of adenosine 5'-triphosphate (ATP). The fluorescence intensity and emission wavelength of DNA-Ag NCs are dependent on the pH value and ATP concentration. At pH 3.0 and 11.0, ATP shows greater effects on fluorescence of the DNA-Ag NCs. Upon increasing ATP concentration from 10 to 50μM, their emission wavelength at pH 3.0 shifts from 525 to 585nm. At pH 11.0, their fluorescence intensity (510nm) increases upon increasing ATP concentration. The circular dichroism (CD), electrospray ionization-mass spectrometry (ESI-MS), absorption, and fluorescence results indicate that ATP and pH affect the interactions between DNAs and Ag atoms, resulting in changes in their fluorescence. The DNA-Ag NCs allow detection of ATP over a concentration range of 0.1-10μM, with a limit of detection 33nM. Practicality of the DNA-Ag NCs probe has been validated with the determination of ATP concentrations in the lysate of MDA-MB-231 breast carcinoma cells.
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Affiliation(s)
- Jennifer Daneen Lee
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jinshun Cang
- Department of Chemical Engineering, Yancheng Institute of Industry Technology, Yancheng, Jiangsu, China
| | - Ying-Chieh Chen
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Wei-Yu Chen
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chung-Mao Ou
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
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142
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Abstract
An atomistic Molecular Dynamics simulation to study the unfolding and deprotonation mechanism of a single-stranded and fully protonated DNA i-motif.
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Affiliation(s)
- Jens Smiatek
- Institut für Computerphysik
- Universität Stuttgart
- 70569 Stuttgart, Germany
| | - Andreas Heuer
- Institut für Physikalische Chemie
- Universität Münster
- 48149 Münster, Germany
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143
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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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144
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Mizielinska S, Lashley T, Norona FE, Clayton EL, Ridler CE, Fratta P, Isaacs AM. C9orf72 frontotemporal lobar degeneration is characterised by frequent neuronal sense and antisense RNA foci. Acta Neuropathol 2013; 126:845-57. [PMID: 24170096 PMCID: PMC3830745 DOI: 10.1007/s00401-013-1200-z] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/16/2013] [Accepted: 10/19/2013] [Indexed: 12/11/2022]
Abstract
An expanded GGGGCC repeat in a non-coding region of the C9orf72 gene is a common cause of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis. Non-coding repeat expansions may cause disease by reducing the expression level of the gene they reside in, by producing toxic aggregates of repeat RNA termed RNA foci, or by producing toxic proteins generated by repeat-associated non-ATG translation. We present the first definitive report of C9orf72 repeat sense and antisense RNA foci using a series of C9FTLD cases, and neurodegenerative disease and normal controls. A sensitive and specific fluorescence in situ hybridisation protocol was combined with protein immunostaining to show that both sense and antisense foci were frequent, specific to C9FTLD, and present in neurons of the frontal cortex, hippocampus and cerebellum. High-resolution imaging also allowed accurate analyses of foci number and subcellular localisation. RNA foci were most abundant in the frontal cortex, where 51 % of neurons contained foci. RNA foci also occurred in astrocytes, microglia and oligodendrocytes but to a lesser degree than in neurons. RNA foci were observed in both TDP-43- and p62-inclusion bearing neurons, but not at a greater frequency than expected by chance. RNA foci abundance in the frontal cortex showed a significant inverse correlation with age at onset of disease. These data establish that sense and antisense C9orf72 repeat RNA foci are a consistent and specific feature of C9FTLD, providing new insight into the pathogenesis of C9FTLD.
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Affiliation(s)
- Sarah Mizielinska
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Tammaryn Lashley
- Department of Molecular Neuroscience, Queen Square Brain Bank, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Frances E. Norona
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Emma L. Clayton
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Charlotte E. Ridler
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Pietro Fratta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
- MRC Centre for Neuromuscular Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Adrian M. Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
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145
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de Vries JW, Zhang F, Herrmann A. Drug delivery systems based on nucleic acid nanostructures. J Control Release 2013; 172:467-83. [DOI: 10.1016/j.jconrel.2013.05.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 01/26/2023]
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146
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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147
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013; 52:12937-41. [DOI: 10.1002/anie.201306017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/11/2013] [Indexed: 11/08/2022]
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148
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Chiorcea-Paquim AM, Santos PV, Oliveira-Brett AM. Atomic force microscopy and voltammetric characterisation of synthetic homo-oligodeoxynucleotides. Electrochim Acta 2013. [DOI: 10.1016/j.electacta.2013.03.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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149
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Cui J, Waltman P, Le VH, Lewis EA. The effect of molecular crowding on the stability of human c-MYC promoter sequence I-motif at neutral pH. Molecules 2013; 18:12751-67. [PMID: 24132198 PMCID: PMC6270392 DOI: 10.3390/molecules181012751] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022] Open
Abstract
We have previously shown that c-MYC promoter sequences can form stable i-motifs in acidic solution (pH 4.5-5.5). In terms of drug targeting, the question is whether c-MYC promoter sequence i-motifs will exist in the nucleus at neutral pH. In this work, we have investigated the stability of a mutant c-MYC i-motif in solutions containing a molecular crowding agent. The crowded nuclear environment was modeled by the addition of up to 40% w/w polyethylene glycols having molecular weights up to 12,000 g/mol. CD and DSC were used to establish the presence and stability of c-MYC i-motifs in buffer solutions over the pH range 4 to 7. We have shown that the c-MYC i-motif can exist as a stable structure at pH values as high as 6.7 in crowded solutions. Generic dielectric constant effects, e.g., a shift in the pKa of cytosine by more than 2 units (e.g., 4.8 to 7.0), or the formation of non-specific PEG/DNA complexes appear to contribute insignificantly to i-motif stabilization. Molecular crowding, largely an excluded volume effect of added PEG, having a molecular weight in excess of 1,000 g/mol, appears to be responsible for stabilizing the more compact i-motif over the random coil at higher pH values.
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Affiliation(s)
- Jingjing Cui
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA.
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150
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Petty JT, Sergev OO, Nicholson DA, Goodwin PM, Giri B, McMullan DR. A silver cluster-DNA equilibrium. Anal Chem 2013; 85:9868-76. [PMID: 24032398 PMCID: PMC4532306 DOI: 10.1021/ac4028559] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA encapsulates silver clusters, and these hybrid nanomaterials form molecular sensors. We discuss a silver cluster-oligonucleotide sensor with four characteristics. First, a specific reporting cluster forms within a single-stranded DNA. This template uses the 5' cluster domain CCCCAACTCCTT with different 3' recognition sites for complementary oligonucleotides. The modular composite strand exclusively forms a cluster with λmax = 400 nm and with low emission. Conjugates were chromatographically purified, and their elemental analysis measured a cluster adduct with ∼11 silver atoms. Second, hybridization transforms the cluster. Size exclusion chromatography shows that the 3' recognition sites of the single-stranded conjugates hybridize with their complements. This secondary structural change both shifts cluster absorption from 400 to 490 nm and develops emission at 550 nm. Third, cluster size remains intact. Like their violet predecessors, purified blue-green clusters have ∼11 silver atoms. Cluster integrity is further supported by extracting the complement from the blue-green conjugate and reversing the spectral changes. Fourth, the cluster transformation is an equilibrium. Complementary strands generate an isosbestic point and thus directly link single-stranded hosts for the violet cluster and their hybridized analogs for the blue-green cluster. This equilibrium shifts with temperature. A van't Hoff analysis shows that longer and more stable duplexes favor the blue-green cluster. However, hybridized cluster hosts are less stable than their native DNA counterparts, and stability further degrades when short complements expose nucleobases within S1-S2. Duplex instability suggests that unpaired nucleobases coordinate the violet cluster and favor the single-stranded sensor. A balance between innate hybridization and exogenous folding highlights a distinct feature of silver clusters for sensing: they are both chromophoric reporters and ligands that modulate analyte-sensor interactions.
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Affiliation(s)
- Jeffrey T. Petty
- Department of Chemistry, Furman University, Greenville, SC 29613
| | - Orlin O. Sergev
- Department of Chemistry, Furman University, Greenville, SC 29613
| | | | | | - Banabihari Giri
- Department of Chemistry, Furman University, Greenville, SC 29613
| | - D. Ryan McMullan
- Department of Chemistry, Furman University, Greenville, SC 29613
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