101
|
Zhang D, Huang T, Lukeman PS, Paukstelis PJ. Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad. Nucleic Acids Res 2014; 42:13422-9. [PMID: 25389267 PMCID: PMC4245957 DOI: 10.1093/nar/gku1122] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.
Collapse
Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - Terry Huang
- Chemistry and Biochemistry Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Philip S. Lukeman
- Chemistry Department, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA,To whom correspondence should be addressed. Tel: 301.405.9933; Fax: 301.314.0386;
| |
Collapse
|
102
|
Sun H, Fan H, Peng X. Quantitative DNA interstrand cross-link formation by coumarin and thymine: structure determination, sequence effect, and fluorescence detection. J Org Chem 2014; 79:11359-69. [PMID: 25372021 DOI: 10.1021/jo5014756] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The coumarin analogues have been widely utilized in medicine, biology, biochemistry, and material sciences. Here, we report a detailed study on the reactivity of coumarins toward DNA. A series of coumarin analogues were synthesized and incorporated into oligodeoxynucleotides. A photoinduced [2 + 2] cycloaddition occurs between the coumarin moiety and the thymidine upon 350 nm irradiation forming both syn- and anti-cyclobutane adducts (17 and 18), which are photoreversible by 254/350 nm irradiation in DNA. Quantitative DNA interstrand cross-link (ICL) formation was observed with the coumarin moieties containing a flexible two-carbon or longer chain. DNA cross-linking by coumarins shows a kinetic preference when flanked by an A:T base pair as opposed to a G:C pair. An efficient photoinduced electron transfer between coumarin and dG slows down ICL formation. ICL formation quenches the fluorescence of coumarin, which, for the first time, enables fast, easy, and real-time monitoring of DNA cross-linking and photoreversibility via fluorescence spectroscopy. It can be used to detect the transversion mutation between pyrimidines and purines. Overall, this work provides new insights into the biochemical properties and possible toxicity of coumarins. A quantitative, fluorescence-detectable, and photoswitchable DNA cross-linking reaction of the coumarin moieties can potentially serve as mechanistic probes and tools for bioresearch without disrupting native biological environment.
Collapse
Affiliation(s)
- Huabing Sun
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | | | | |
Collapse
|
103
|
Hagiya M, Konagaya A, Kobayashi S, Saito H, Murata S. Molecular robots with sensors and intelligence. Acc Chem Res 2014; 47:1681-90. [PMID: 24905779 DOI: 10.1021/ar400318d] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONSPECTUS: What we can call a molecular robot is a set of molecular devices such as sensors, logic gates, and actuators integrated into a consistent system. The molecular robot is supposed to react autonomously to its environment by receiving molecular signals and making decisions by molecular computation. Building such a system has long been a dream of scientists; however, despite extensive efforts, systems having all three functions (sensing, computation, and actuation) have not been realized yet. This Account introduces an ongoing research project that focuses on the development of molecular robotics funded by MEXT (Ministry of Education, Culture, Sports, Science and Technology, Japan). This 5 year project started in July 2012 and is titled "Development of Molecular Robots Equipped with Sensors and Intelligence". The major issues in the field of molecular robotics all correspond to a feedback (i.e., plan-do-see) cycle of a robotic system. More specifically, these issues are (1) developing molecular sensors capable of handling a wide array of signals, (2) developing amplification methods of signals to drive molecular computing devices, (3) accelerating molecular computing, (4) developing actuators that are controllable by molecular computers, and (5) providing bodies of molecular robots encapsulating the above molecular devices, which implement the conformational changes and locomotion of the robots. In this Account, the latest contributions to the project are reported. There are four research teams in the project that specialize on sensing, intelligence, amoeba-like actuation, and slime-like actuation, respectively. The molecular sensor team is focusing on the development of molecular sensors that can handle a variety of signals. This team is also investigating methods to amplify signals from the molecular sensors. The molecular intelligence team is developing molecular computers and is currently focusing on a new photochemical technology for accelerating DNA-based computations. They also introduce novel computational models behind various kinds of molecular computers necessary for designing such computers. The amoeba robot team aims at constructing amoeba-like robots. The team is trying to incorporate motor proteins, including kinesin and microtubules (MTs), for use as actuators implemented in a liposomal compartment as a robot body. They are also developing a methodology to link DNA-based computation and molecular motor control. The slime robot team focuses on the development of slime-like robots. The team is evaluating various gels, including DNA gel and BZ gel, for use as actuators, as well as the body material to disperse various molecular devices in it. They also try to control the gel actuators by DNA signals coming from molecular computers.
Collapse
Affiliation(s)
- Masami Hagiya
- Department
of Computer Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan,
| | - Akihiko Konagaya
- Department
of Computational Intelligence and Systems Science, Tokyo Institute of Technology, 4259 Nagatsuda, Midori-ku, Yokohama 226-8502 Japan
| | - Satoshi Kobayashi
- Department
of Communication Engineering and Informatics, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu,
Tokyo 182-8585, Japan
| | - Hirohide Saito
- Center
for iPS Cell Research and Application/The Hakubi Center for Advanced
Research, Kyoto University, 53 Shyogoin-kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Satoshi Murata
- Department
of Bioengineering and Robotics, Tohoku University, 6-6-1 Aobayama, Sendai 980-8579, Japan
| |
Collapse
|
104
|
Nakamura S, Fujimoto K. Rapid Photopolymerization of Oligodeoxynucleotides by 3-Cyanovinylcarbazole mediated DNA Photocrosslinking. J PHOTOPOLYM SCI TEC 2014. [DOI: 10.2494/photopolymer.27.485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
105
|
Sakamoto T, Shigeno A, Ohtaki Y, Fujimoto K. Photo-regulation of constitutive gene expression in living cells by using ultrafast photo-cross-linking oligonucleotides. Biomater Sci 2014; 2:1154-1157. [DOI: 10.1039/c4bm00117f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We clearly demonstrated that photoreactive AS-ODNs having CNVK act as effective photo-regulators of constitutive GFP gene expression in living cells with only 10 s of 366 nm irradiation.
Collapse
Affiliation(s)
- Takashi Sakamoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Atsuo Shigeno
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Yuichi Ohtaki
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
| | - Kenzo Fujimoto
- School of Materials Science
- Japan Advanced Institute of Science and Technology
- Nomi, Japan
- Research Center for Bio-Architecture
- Japan Advanced Institute of Science and Technology
| |
Collapse
|
106
|
Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T. Details of the Ultrafast DNA Photo-Cross-Linking Reaction of 3-Cyanovinylcarbazole Nucleoside: Cis–Trans Isomeric Effect and the Application for SNP-Based Genotyping. J Am Chem Soc 2013; 135:16161-7. [DOI: 10.1021/ja406965f] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Tadashi Tsukaguchi
- Faculty
of Bioresources and Environmental Sciences, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan
| | | |
Collapse
|
107
|
Abstract
We report an approach for generating immobilized monoclonal templates for next- generation sequencing applications. Our isothermal amplification method is based on a template walking mechanism using a pair of low-melting temperature (Tm) solid-surface homopolymer primers and a low-Tm solution phase primer. The method can generate more than one billion submicrometer-sized colonies in a single lane of a next-generation sequencing flowchip. An alternative paired-end sequencing method using interstrand DNA photo cross-linking to covalently link the complementary strands of the original templates to the solid surface is also demonstrated.
Collapse
|
108
|
Feng L, Romulus J, Li M, Sha R, Royer J, Wu KT, Xu Q, Seeman NC, Weck M, Chaikin P. Cinnamate-based DNA photolithography. NATURE MATERIALS 2013; 12:747-53. [PMID: 23685865 PMCID: PMC3722280 DOI: 10.1038/nmat3645] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 04/02/2013] [Indexed: 05/09/2023]
Abstract
As demonstrated by means of DNA nanoconstructs, as well as DNA functionalization of nanoparticles and micrometre-scale colloids, complex self-assembly processes require components to associate with particular partners in a programmable fashion. In many cases the reversibility of the interactions between complementary DNA sequences is an advantage. However, permanently bonding some or all of the complementary pairs may allow for flexibility in design and construction. Here, we show that the substitution of a cinnamate group for a pair of complementary bases provides an efficient, addressable, ultraviolet light-based method to bond complementary DNA covalently. To show the potential of this approach, we wrote micrometre-scale patterns on a surface using ultraviolet light and demonstrated the reversible attachment of conjugated DNA and DNA-coated colloids. Our strategy enables both functional DNA photolithography and multistep, specific binding in self-assembly processes.
Collapse
Affiliation(s)
- Lang Feng
- Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, NY 10003, USA
| | - Joy Romulus
- Chemistry Department, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Minfeng Li
- Chemistry Department, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Ruojie Sha
- Chemistry Department, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - John Royer
- Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, NY 10003, USA
| | - Kun-Ta Wu
- Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, NY 10003, USA
| | - Qin Xu
- Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, NY 10003, USA
| | - Nadrian C. Seeman
- Chemistry Department, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Marcus Weck
- Chemistry Department, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Paul Chaikin
- Center for Soft Matter Research, Physics Department, New York University, 4 Washington Place, New York, NY 10003, USA
| |
Collapse
|
109
|
Fujimoto K, Kishi S, Sakamoto T. Geometric Effect on the Photocrosslinking Reaction between 3-Cyanovinylcarbazole Nucleoside and Pyrimidine Base in DNA/RNA Heteroduplex. Photochem Photobiol 2013; 89:1095-9. [DOI: 10.1111/php.12118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Satomi Kishi
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
| | - Takashi Sakamoto
- School of Materials Science; Japan Advanced Institute of Science and Technology; Nomi-shi; Japan
| |
Collapse
|
110
|
Vieregg J, Nelson HM, Stoltz BM, Pierce NA. Selective nucleic acid capture with shielded covalent probes. J Am Chem Soc 2013; 135:9691-9. [PMID: 23745667 PMCID: PMC3703666 DOI: 10.1021/ja4009216] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Indexed: 11/29/2022]
Abstract
Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2-3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1-2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo).
Collapse
Affiliation(s)
- Jeffrey
R. Vieregg
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Hosea M. Nelson
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Brian M. Stoltz
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| | - Niles A. Pierce
- Department
of Bioengineering, Department of Chemistry, Department of Computing and Mathematical Sciences, California Institute of Technology,
Pasadena, California 91125, United States
| |
Collapse
|
111
|
Shigeno A, Sakamoto T, Yoshimura Y, Fujimoto K. Quick regulation of mRNA functions by a few seconds of photoirradiation. Org Biomol Chem 2013; 10:7820-5. [PMID: 22918386 DOI: 10.1039/c2ob25883h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
3-Cyanovinylcarbazole nucleoside, which effectively photocrosslinks to the pyrimidine base in complementary RNA strands, was incorporated into antisense oligonucleotides, and we evaluated the photoreactivity and the sequence selectivity to mutated K-ras oligoRNAs, as well as the regulation of the function of K-ras mRNA. We demonstrated that the reverse transcription and the translation activity of K-ras mRNA were quickly suppressed by a few seconds of photoirradiation with the addition of the photoresponsive antisense ODN.
Collapse
Affiliation(s)
- Atsuo Shigeno
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan
| | | | | | | |
Collapse
|
112
|
Imoto S, Chikuni T, Kansui H, Kunieda T, Nagatsugi F. Fast DNA interstrand cross-linking reaction by 6-vinylpurine. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 31:752-62. [PMID: 23067126 DOI: 10.1080/15257770.2012.726756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Oligonucleotides that incorporate a reactive moiety to form an interstrand cross-link have been widely studied for their potential toward inhibiting gene expression or as basic tools for chemical biology studies. The 6-vinylpurine (2) newly designed in the current study serves well as a new purine-base moiety for increasing cross-link reactivity to target cytosine. Thus, oligonucleotides containing 6-vinylpurine exhibit a more selective and much smoother DNA cross-linking ability to cytosine than the oligonucleotide analogs derived from 2-amino-6-vinylpurine (1) previously explored.
Collapse
Affiliation(s)
- Shuhei Imoto
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto-city, Kumamoto, Japan.
| | | | | | | | | |
Collapse
|
113
|
Fujimo K, Konishi-Hiratsuka K, Sakamoto T. Quick, Selective and Reversible Photocrosslinking Reaction between 5-Methylcytosine and 3-Cyanovinylcarbazole in DNA Double Strand. Int J Mol Sci 2013; 14:5765-74. [PMID: 23481638 PMCID: PMC3634424 DOI: 10.3390/ijms14035765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/12/2013] [Accepted: 02/26/2013] [Indexed: 02/02/2023] Open
Abstract
Selective photocrosslinking reaction between 3-cyanovinylcarbazole nucleoside (CNVK) and 5-methylcytosine (mC), which is known as epigenetic modification in genomic DNA, was developed. The reaction was completely finished within 5 s of 366 nm irradiation, and the rate of this photocrosslinking reaction was ca. 30-fold higher than that in the case of unmodified normal cytosine. There were no significant differences in the thermodynamic parameters and the kinetics of hybrid formation of oligonucleotide (ODN) containing CNVK and its complementary ODN containing C or mC at the photocrosslinking site, and suggesting that the quick and selective photoreaction has potential for the selective detection of mC in the DNA strand via the photocrosslinking reaction.
Collapse
Affiliation(s)
- Kenzo Fujimo
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-761-51-1671
| | - Kaoru Konishi-Hiratsuka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan; E-Mails: (K.K.-H.); (T.S.)
| |
Collapse
|
114
|
Fujimoto K, Futamura D, Sakamoto T. Diamine Derivatives Accelerate Photochemical C → U Transition in DNA Double Strand. CHEM LETT 2013. [DOI: 10.1246/cl.2013.289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
- Research Center for Bio-Architecture, Japan Advanced Institute of Science and Technology
| | - Daiki Futamura
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology
| |
Collapse
|
115
|
Fujimoto K, Yoshinaga H, Yoshio Y, Sakamoto T. Quick and reversible photocrosslinking reaction of 3-cyanovinylcarbazole nucleoside in a DNA triplex. Org Biomol Chem 2013; 11:5065-8. [DOI: 10.1039/c3ob40915e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
116
|
Mie Y, Kowata K, Kojima N, Komatsu Y. Electrochemical properties of interstrand cross-linked DNA duplexes labeled with Nile blue. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:17211-17216. [PMID: 23153070 DOI: 10.1021/la3036538] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA molecules have attracted considerable attention as functional materials in various fields such as electrochemical sensors with redox-labeled DNA. However, the recently developed interstrand cross-link (ICL) technique for double-stranded DNA can adequately modify the electronic properties inside the duplex. Hence, the electrochemical investigation of ICL-DNA helps us to understand the electron transfer of redox-labeled DNA at an electrode surface, which would develop useful sensors. In this study, the first insight into this matter is presented. We prepared 17-mer DNA duplexes incorporating Nile blue (NB-DNA) at one end as a redox marker and a disulfide tether at the other end for immobilization onto an electrode. The duplexes were covalently cross-linked by bifunctional cross-linkers that utilize either a propyl or naphthalene residue to replace a base pair. Their electrochemical responses at the electrode surface were compared to evaluate the effect of the ICL on the electron-transfer reactions of the redox-labeled DNA duplexes. A direct transfer of electrons between NB and the electrode was observed for a standard DNA, as previously reported, whereas interstrand cross-linked DNA (CL-DNA) strands showed a decrease in the direct electron-transfer pathway. This is expected to result from constraining the elastic bending/flexibility of the duplex caused by the covalent cross-links. Interestingly, the CL-DNA incorporating naphthalene residues exhibited additional voltammetric peaks derived from DNA-mediated electron transfer (through base π stacking), which was not observed in the mismatched CL-DNA. The present results indicate that the ICL significantly affects electron transfer in the redox-labeled DNA at the electrode and can be an important determinant for electrochemical signaling in addition to its role in stabilizing the duplex structure.
Collapse
Affiliation(s)
- Yasuhiro Mie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo 062-8517, Japan
| | | | | | | |
Collapse
|
117
|
Gerrard SR, Hardiman C, Shelbourne M, Nandhakumar I, Nordén B, Brown T. A new modular approach to nanoassembly: stable and addressable DNA nanoconstructs via orthogonal click chemistries. ACS NANO 2012; 6:9221-9228. [PMID: 22989197 DOI: 10.1021/nn3035759] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Thermodynamic instability is a problem when assembling and purifying complex DNA nanostructures formed by hybridization alone. To address this issue, we have used photochemical fixation and orthogonal copper-free, ring-strain-promoted, click chemistry for the synthesis of dimeric, trimeric, and oligomeric modular DNA scaffolds from cyclic, double-stranded, 80-mer DNA nanoconstructs. This particular combination of orthogonal click reactions was more effective for nanoassembly than others explored. The complex nanostructures are stable to heat and denaturation agents and can therefore be purified and characterized. They are addressable in a sequence-specific manner by triplex formation, and they can be reversibly and selectively deconstructed. Nanostructures utilizing this orthogonal, chemical fixation methodology can be used as building blocks for nanomachines and functional DNA nanoarchitectures.
Collapse
Affiliation(s)
- Simon R Gerrard
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ. UK
| | | | | | | | | | | |
Collapse
|
118
|
Efficient synthesis of 3-cyanovinylcarbazole-1′-β-deoxyriboside-5′-triphosphate: a reversible photo-cross-linking probe. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.05.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
119
|
Hagihara S, Kusano S, Lin WC, Chao XG, Hori T, Imoto S, Nagatsugi F. Production of truncated protein by the crosslink formation of mRNA with 2'-OMe oligoribonucleotide containing 2-amino-6-vinylpurine. Bioorg Med Chem Lett 2012; 22:3870-2. [PMID: 22613261 DOI: 10.1016/j.bmcl.2012.04.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/28/2012] [Indexed: 12/29/2022]
Abstract
The development of convenient methods for controlling the protein expression is an important challenge in the postgenomic era. We applied the crosslink forming oligonucleotide (CFO) as a terminator of the ribosomal translation. In this study, we demonstrated that the improved reactivity of our CFO under physiological conditions enabled the sequence-specific introduction of a steric block for a ribosome on mRNAs. In vitro and in cell translation experiments revealed that the crosslinked mRNA can produce the truncated proteins in which the translation terminates at the desired position.
Collapse
Affiliation(s)
- Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Miyagi 980-8577, Japan
| | | | | | | | | | | | | |
Collapse
|
120
|
Ichikawa K, Kojima N, Hirano Y, Takebayashi T, Kowata K, Komatsu Y. Interstrand cross-link of DNA by covalently linking a pair of abasic sites. Chem Commun (Camb) 2012; 48:2143-5. [DOI: 10.1039/c2cc16785a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
121
|
Fujimoto K, Hiratsuka-Konishi K, Sakamoto T, Ohtake T, Shinohara KI, Yoshimura Y. Specific and reversible photochemical labeling of plasmid DNA using photoresponsive oligonucleotides containing 3-cyanovinylcarbazole. MOLECULAR BIOSYSTEMS 2011; 8:491-4. [PMID: 22183016 DOI: 10.1039/c2mb05422a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To develop a covalent and specific labeling method for single- and double-stranded plasmid DNA, photoresponsive oligonucleotide containing 3-cyanovinylcarbazole nucleoside was adopted. Single- and double-stranded plasmid DNA was successfully labeled/de-labeled with Cy3 and/or biotin by photoirradiation.
Collapse
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced institute of Science and Technology, Nomi, Ishikawa, Japan.
| | | | | | | | | | | |
Collapse
|
122
|
Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
123
|
Hong C, Hagihara M, Nakatani K. Ligand-Assisted Complex Formation of Two DNA Hairpin Loops. Angew Chem Int Ed Engl 2011; 50:4390-3. [DOI: 10.1002/anie.201100075] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/11/2022]
|
124
|
Nagatsugi F. Development of the Highly Selective Reactions to Target Gene for the Control of the Gene Expression in Cells. J SYN ORG CHEM JPN 2011. [DOI: 10.5059/yukigoseikyokaishi.69.108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
125
|
Ono T, Yoshida K, Saotome Y, Sakabe R, Okamoto I, Ono A. Synthesis of covalently linked parallel and antiparallel DNA duplexes containing the metal-mediated base pairs T–Hg(ii)–T and C–Ag(i)–C. Chem Commun (Camb) 2011; 47:1542-4. [DOI: 10.1039/c0cc02028a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
126
|
Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y. Site-specific cytosine to uracil transition by using reversible DNA photo-crosslinking. Chembiochem 2010; 11:1661-4. [PMID: 20632434 DOI: 10.1002/cbic.201000274] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | | | | | | |
Collapse
|
127
|
Op de Beeck M, Madder A. Unprecedented C-selective interstrand cross-linking through in situ oxidation of furan-modified oligodeoxynucleotides. J Am Chem Soc 2010; 133:796-807. [PMID: 21162525 DOI: 10.1021/ja1048169] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical reagents that form interstrand cross-links have been used for a long time in cancer therapy. They covalently link two strands of DNA, thereby blocking transcription. Cross-link repair enzymes, however, can restore the transcription processes, causing resistance to certain anti-cancer drugs. The mechanism of these cross-link repair processes has not yet been fully revealed. One of the obstacles in this study is the lack of sufficient amounts of well-defined, stable, cross-linked duplexes to study the pathways of cross-link repair enzymes. Our group has developed a cross-link strategy where a furan moiety is incorporated into oligodeoxynucleotides (ODNs). These furan-modified nucleic acids can form interstrand cross-links upon selective furan oxidation with N-bromosuccinimide. We here report on the incorporation of the furan moiety at the 2'-position of a uridine through an amido or ureido linker. The resulting modified ODNs display an unprecedented selectivity for cross-linking toward a cytidine opposite the modified residue, forming one specific cross-linked duplex, which could be isolated in good yield. Furthermore, the structure of the formed cross-linked duplexes could be unambiguously characterized.
Collapse
Affiliation(s)
- Marieke Op de Beeck
- Laboratory for Organic and Biomimetic Chemistry, University of Ghent, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | | |
Collapse
|
128
|
Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y. Site-specific photochemical RNA editing. Chem Commun (Camb) 2010; 46:7545-7. [PMID: 20848024 DOI: 10.1039/c0cc03151h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Photo-induced artificial RNA editing was demonstrated using photo-reactive oligonucleotides containing 3-cyanovinylcarbazole nucleoside. This non-enzymatic and sequence-specific methodology will make a major contribution to the elucidation of RNA functions including non-coding RNAs and to the development of drugs based on sequence-specific RNA editing.
Collapse
Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, 923-1292, Japan.
| | | | | | | |
Collapse
|
129
|
Nagatsugi F, Sasaki S. Synthesis of Reactive Oligonucleotides for Gene Targeting and Their Application to Gene Expression Regulation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20100010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
130
|
Yoshimura Y, Okada H, Fujimoto K. Photoreversible DNA end capping for the formation of hairpin structures. Org Biomol Chem 2010; 8:1523-6. [PMID: 20237661 DOI: 10.1039/b924989c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a photoreversible DNA end capping via 3-cyanovinylcarbazole nucleoside. Doubly end-capped oligodeoxynucleotide (ODN) exhibits increased stability against snake venom phosphodiesterase and shows high thermal stability.
Collapse
Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | | | | |
Collapse
|
131
|
Yoshimura Y, Ohtake T, Okada H, Fujimoto K. A new approach for reversible RNA photocrosslinking reaction: application to sequence-specific RNA selection. Chembiochem 2009; 10:1473-6. [PMID: 19437470 DOI: 10.1002/cbic.200900057] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yoshinaga Yoshimura
- School of Materials Science (Japan) Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | | | | | | |
Collapse
|
132
|
Hattori K, Hirohama T, Imoto S, Kusano S, Nagatsugi F. Formation of highly selective and efficient interstrand cross-linking to thymine without photo-irradiation. Chem Commun (Camb) 2009:6463-5. [DOI: 10.1039/b915381k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|