51
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Fujimoto K, Hashimoto M, Watanabe N, Nakamura S. RNA fluorescence in situ hybridization hybridisation using photo-cross-linkable beacon probes containing pyranocarbazole in living E. coli. Bioorg Med Chem Lett 2019; 29:2173-2177. [DOI: 10.1016/j.bmcl.2019.06.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 12/25/2022]
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52
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Qiu Z, Nakamura S, Fujimoto K. Reversible photo-cross-linking of the GCN4 peptide containing 3-cyanovinylcarbazole amino acid to double-stranded DNA. Org Biomol Chem 2019; 17:6277-6283. [PMID: 31192345 DOI: 10.1039/c9ob00372j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Interaction analysis in vivo greatly promotes the analyses and understanding of biological functions. The interaction between DNA and peptides or proteins is very important in terms of readout and amplifying information from genomic DNA. In this study, we designed and synthesized a photo-cross-linkable amino acid, l-3-cyanovinlycarbazole amino acid (l-CNVA), to double-stranded DNA. Reversible photo-cross-linking between DNA and peptides containing CNVA, having 3-cyanovinylcarbazole moieties capable of photo-cross-linking to nucleic acids, was demonstrated. As a result, it was shown that the GCN4 peptide, containing CNVA, can be photo-cross-linked to DNA, and its adduct was photo-split into the original peptide and DNA with 312 nm-irradiation. This is the first report that reversibly manipulates photo-crosslinking between double stranded DNA and peptides. In addition, this reversible photo-cross-linking, using l-CNVA, is faster and with higher yield than that using diazirine and psoralen.
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Affiliation(s)
- Zhiyong Qiu
- School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology. Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan.
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53
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Tam DY, Zhuang X, Wong SW, Lo PK. Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805481. [PMID: 30861628 DOI: 10.1002/smll.201805481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/30/2019] [Indexed: 05/23/2023]
Abstract
Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xinyu Zhuang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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54
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De Fazio AF, El-Sagheer AH, Kahn JS, Nandhakumar I, Burton MR, Brown T, Muskens OL, Gang O, Kanaras AG. Light-Induced Reversible DNA Ligation of Gold Nanoparticle Superlattices. ACS NANO 2019; 13:5771-5777. [PMID: 30958671 DOI: 10.1021/acsnano.9b01294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA-mediated self-assembly of nanoparticles has been of great interest because it enables access to nanoparticle superstructures that cannot be synthesized otherwise. However, the programmability of higher order nanoparticle structures can be easily lost under DNA denaturing conditions. Here, we demonstrate that light can be employed as an external stimulus to master the stability of nanoparticle superlattices (SLs) via the promotion of a reversible photoligation of DNA in SLs. The oligonucleotides attached to the nanoparticles are encoded to ligate using 365 nm light, effectively locking the SLs and rendering them stable under DNA denaturing conditions. The reversible process of unlocking these structures is possible by irradiation with light at 315 nm, recovering the structures to their natural state. Our work inspires an alternative research direction toward postassembly manipulation of nanoparticle superstructures using external stimuli as a tool to enrich the library of additional material forms and their application in different media and environments.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Jason S Kahn
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
- Department of Chemical Engineering , Columbia University , New York , New York 10027 , United States
| | - Iris Nandhakumar
- School of Chemistry, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
| | - Matthew Richard Burton
- SPECIFIC-IKC, Materials Research Centre, College of Engineering , Swansea University , Bay Campus, Fabian Way , Swansea , SA1 8EN , U.K
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , U.K
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
- Institute for Life Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
| | - Oleg Gang
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
- Department of Chemical Engineering , Columbia University , New York , New York 10027 , United States
- Department of Applied Physics and Applied Mathematics , Columbia University , New York , New York 10027 , United States
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
- Institute for Life Sciences , University of Southampton , Southampton , SO17 1BJ , U.K
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55
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Murayama K, Yamano Y, Asanuma H. 8-Pyrenylvinyl Adenine Controls Reversible Duplex Formation between Serinol Nucleic Acid and RNA by [2 + 2] Photocycloaddition. J Am Chem Soc 2019; 141:9485-9489. [DOI: 10.1021/jacs.9b03267] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuuhei Yamano
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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56
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Onizuka K, Ishida K, Mano E, Nagatsugi F. Alkyne-Alkyne Photo-cross-linking on the Flipping-out Field. Org Lett 2019; 21:2833-2837. [PMID: 30951316 DOI: 10.1021/acs.orglett.9b00817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The base flip-inducing nucleic acids are expected to create a specific field for various chemical reactions. We now report a novel type of base-flip-inducing oligodeoxynucleotide and photo-cross-linking reaction. Two 3-arylethynyl-5-methyl-2-pyridone nucleosides, Ph and An, were synthesized, and their properties were investigated. The alkyne-alkyne photo-cross-linking rapidly proceeded by taking advantage of the base-flipping-out field where two alkynes overlap each other. This photo-cross-linking would be a new candidate to form cross-linked DNAs.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Kei Ishida
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai , Miyagi 980-8577 , Japan.,Department of Chemistry, Graduate School of Science , Tohoku University , Aoba-ku, Sendai 980-8578 , Japan
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57
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Fujimoto K, Yang-Chun H, Nakamura S. Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking. Chem Asian J 2019; 14:1912-1916. [PMID: 30806028 DOI: 10.1002/asia.201801917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/22/2019] [Indexed: 11/06/2022]
Abstract
We have reported the photochemical regulation of the intracellular antisense effect of antisense probes containing a photo-responsive artificial nucleic acid, 3-cyanovinylcarbazole nucleoside (CNV K). Here we focus on the importance of the photocrosslinking rate on the inhibitory effect on gene expression using photocrosslinkable antisense probes (pcASOs). The inhibitory effect of pcASOs on GFP gene expression was dependent on the photocrosslinking rate of 3-cyanovinylcarbazole with d-threoninol (CNV D), CNV K, or psoralen. The ultrafast RNA photocrosslinking induced the formation of a thermally irreversible covalent bond between pcASOs and the target RNA. These ASOs strongly inhibited gene expression only when the photocrosslinking rate was faster than the random walk of branch migration. In addition, pcASOs containing CNV D or CNV K targeted the RNAs with secondary structures. These results indicate the regulatory effect of photocrosslinker and photoirradiation energy using pcASOs on the gene expression level.
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Affiliation(s)
- Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Hung Yang-Chun
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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58
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Yamada K, Abe Y, Nagatsugi F. Synthesis of RNA Crosslinking Oligonucleotides Modified with 2-Amino-7-Deaza-7-Propynyl-6-Vinylpurine. ACTA ACUST UNITED AC 2019; 77:e79. [PMID: 30860656 DOI: 10.1002/cpnc.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article describes procedures to synthesize 2'-OMe-RNA modified with cross-linkable 2-amino-7-deaza-7-propynyl-6-vinylpurine (ADpVP) and preparation of the RNA-crosslinking experiment in vitro. All synthesis steps yield the desired compound in moderate or high yield without expensive chemical reagents or specific devices. The crosslink-active form of modified RNA can also be purified by commonly used reversed-phase HPLC, can be stored at -80°C after lyophilization for a few days, and is ready to use for crosslinking experiments. This crosslink-active RNA can efficiently form covalent bonds with complementary RNA in a sequence-specific manner. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
| | - Yusuke Abe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai-shi, Japan
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59
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Investigation of 8-Aza-7-Deaza Purine Nucleoside Derivatives. Molecules 2019; 24:molecules24050983. [PMID: 30862058 PMCID: PMC6429420 DOI: 10.3390/molecules24050983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/05/2019] [Indexed: 11/16/2022] Open
Abstract
Glycosylation of 6-amino-4-methoxy-1H-pyrazolo[3,4-d]pyrimidine and its iodo- and bromo- analogues with the protected ribofuranose and 2′-deoxyribofuranose under different conditions resulted in the synthesis of N9- and N8-glycosylated purine nucleosides. Five key intermediate nucleosides, having 6-methoxy, 7-iodo, and 2-bromo groups, were further derivatized to 23 final 8-aza-7-deazapurine nucleoside derivatives. The structures of N9- and N8-glycosylated products were assigned based on UV and NMR spectra. HMBC analysis of 2D NMR spectra and X-ray crystallographic studies of the representative compounds unambiguously verified the connection of ribose ring to N9- or N8-position of the purine ring. The anticancer activity of these new compounds was evaluated.
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60
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Gerling T, Dietz H. Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies. Angew Chem Int Ed Engl 2019; 58:2680-2684. [PMID: 30694591 PMCID: PMC6984961 DOI: 10.1002/anie.201812463] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/07/2022]
Abstract
Stacking bonds formed between two blunt-ended DNA double helices can be used to reversibly stabilize higher-order complexes that are assembled from rigid DNA components. Typically, at low cation concentrations, stacking bonds break and thus higher-order complexes disassemble. Herein, we present a site-specific photochemical mechanism for the reversible covalent stabilization of stacking bonds in DNA assemblies. To this end, we modified one blunt end with the 3-cyanovinylcarbazole (cnv K) moiety and positioned a thymine residue (T) at the other blunt end. In the bound state, the two blunt-ended helices are stacked together, resulting in a co-localization of cnv K and T. Such a configuration induces the formation of a covalent bond across the stacking contact upon irradiation with 365 nm light. This bond can also be cleaved upon irradiation with 310 nm light, allowing repeated formation and cleavage of the same covalent bond on the timescale of seconds. Our system will expand the range of conditions under which stacking-bond-stabilized objects may be utilized.
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Affiliation(s)
- Thomas Gerling
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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61
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Gerling T, Dietz H. Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas Gerling
- Physik DepartmentWalter Schottky InstituteTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Hendrik Dietz
- Physik DepartmentWalter Schottky InstituteTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
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62
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Abstract
Self-replication and exponential growth are ubiquitous in nature but until recently there were few examples of artificial self-replication. Often replication is a templated process where a parent produces a single offspring, doubling the population in each generation. Many species however produce more than one offspring at a time, enabling faster population growth and higher probability of species perpetuation. We have made a system of cross-shaped origami tiles that yields a number of offspring, four to eight or more, depending on the concentration of monomer units to be assembled. The parent dimer template serves as a seed to crystallize a one-dimensional crystal, a ladder. The ladder rungs are then UV-cross-linked and the offspring are then released by heating, to yield a litter of autonomous daughters. In the complement study, we also optimize the growth conditions to speed up the process and yield a 103 increase in the growth rate for the single-offspring replication system. Self-replication and exponential growth of autonomous motifs is useful for fundamental studies of selection and evolution as well as for materials design, fabrication, and directed evolution. Methods that increase the growth rate, the primary evolutionary drive, not only speed up experiments but provide additional mechanisms for evolving materials toward desired functionalities.
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63
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Reuther JF, Dahlhauser SD, Anslyn EV. Tunable Orthogonal Reversible Covalent (TORC) Bonds: Dynamic Chemical Control over Molecular Assembly. Angew Chem Int Ed Engl 2019; 58:74-85. [PMID: 30098086 PMCID: PMC10851707 DOI: 10.1002/anie.201808371] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 11/08/2022]
Abstract
Dynamic assembly of macromolecules in biological systems is one of the fundamental processes that facilitates life. Although such assembly most commonly uses noncovalent interactions, a set of dynamic reactions involving reversible covalent bonding is actively being exploited for the design of functional materials, bottom-up assembly, and molecular machines. This Minireview highlights recent implementations and advancements in the area of tunable orthogonal reversible covalent (TORC) bonds for these purposes, and provides an outlook for their expansion, including the development of synthetically encoded polynucleotide mimics.
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Affiliation(s)
- James F. Reuther
- Department of Chemistry, University of Texas at Austin Austin, TX (USA)
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA (USA)
| | | | - Eric V. Anslyn
- Department of Chemistry, University of Texas at Austin Austin, TX (USA)
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64
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Reuther JF, Dahlhauser SD, Anslyn EV. Einstellbare orthogonale reversible kovalente Bindungen: dynamische Kontrolle über die molekulare Selbstorganisation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808371] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James F. Reuther
- Department of Chemistry University of Texas at Austin Austin TX USA
- Department of Chemistry University of Massachusetts Lowell Lowell MA USA
| | | | - Eric V. Anslyn
- Department of Chemistry University of Texas at Austin Austin TX USA
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65
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Masubuchi T, Endo M, Iizuka R, Iguchi A, Yoon DH, Sekiguchi T, Qi H, Iinuma R, Miyazono Y, Shoji S, Funatsu T, Sugiyama H, Harada Y, Ueda T, Tadakuma H. Construction of integrated gene logic-chip. NATURE NANOTECHNOLOGY 2018; 13:933-940. [PMID: 30038365 DOI: 10.1038/s41565-018-0202-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
In synthetic biology, the control of gene expression requires a multistep processing of biological signals. The key steps are sensing the environment, computing information and outputting products1. To achieve such functions, the laborious, combinational networking of enzymes and substrate-genes is required, and to resolve problems, sophisticated design automation tools have been introduced2. However, the complexity of genetic circuits remains low because it is difficult to completely avoid crosstalk between the circuits. Here, we have made an orthogonal self-contained device by integrating an actuator and sensors onto a DNA origami-based nanochip that contains an enzyme, T7 RNA polymerase (RNAP) and multiple target-gene substrates. This gene nanochip orthogonally transcribes its own genes, and the nano-layout ability of DNA origami allows us to rationally design gene expression levels by controlling the intermolecular distances between the enzyme and the target genes. We further integrated reprogrammable logic gates so that the nanochip responds to water-in-oil droplets and computes their small RNA (miRNA) profiles, which demonstrates that the nanochip can function as a gene logic-chip. Our approach to component integration on a nanochip may provide a basis for large-scale, integrated genetic circuits.
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Affiliation(s)
- Takeya Masubuchi
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Masayuki Endo
- Graduate School of Science, Department of Chemistry, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.
| | - Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ayaka Iguchi
- Department of Nanoscience and Nanoengineering (ASE Graduate School), Waseda University, Tokyo, Japan
| | - Dong Hyun Yoon
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Tetsushi Sekiguchi
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Hao Qi
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
- Department of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ryosuke Iinuma
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
| | - Yuya Miyazono
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan
| | - Shuichi Shoji
- Department of Nanoscience and Nanoengineering (ASE Graduate School), Waseda University, Tokyo, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Sugiyama
- Graduate School of Science, Department of Chemistry, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.
| | - Yoshie Harada
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Takuya Ueda
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan.
| | - Hisashi Tadakuma
- Graduate School of Frontier Science, The University of Tokyo, Chiba, Japan.
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.
- Institute for Protein Research, Osaka University, Osaka, Japan.
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66
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Yamada K, Abe Y, Murase H, Ida Y, Hagihara S, Nagatsugi F. Synthesis and Properties of 2′-OMe-RNAs Modified with Cross-Linkable 7-Deazaguanosine Derivatives. J Org Chem 2018; 83:8851-8862. [DOI: 10.1021/acs.joc.8b01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yusuke Abe
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Hirotaka Murase
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yuta Ida
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
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67
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Nakamura S, Nakajima R, Fujimoto K. DNA Photocrosslinking Using 3-Vinylcarbazole Derivatives in Two-color Detection of Methylcytosine. CHEM LETT 2018. [DOI: 10.1246/cl.180205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Ryo Nakajima
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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68
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Marschner DE, Frisch H, Offenloch JT, Tuten BT, Becer CR, Walther A, Goldmann AS, Tzvetkova P, Barner-Kowollik C. Visible Light [2 + 2] Cycloadditions for Reversible Polymer Ligation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00613] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Janin T. Offenloch
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Bryan T. Tuten
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - C. Remzi Becer
- Polymer Chemistry Laboratory, School of Engineering and Materials Science, Queen Mary University of London (QMUL), E1 4NS London, United Kingdom
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Straße 31, University of Freiburg, 79104 Freiburg, Germany
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 − Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
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69
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Suzuki Y, Sugiyama H, Endo M. Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801983] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences; Tohoku University; 6-3 Aramaki aza Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences; Kyoto University; Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences; Kyoto University; Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
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70
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Suzuki Y, Sugiyama H, Endo M. Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking. Angew Chem Int Ed Engl 2018; 57:7061-7065. [PMID: 29644771 DOI: 10.1002/anie.201801983] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/01/2018] [Indexed: 01/08/2023]
Abstract
Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Herein, we used the cavities of a preassembled 2D DNA origami framework to incorporate square-shaped DNA origami structures (SQ-origamis). The framework was self-assembled on a lipid bilayer membrane from cross-shaped DNA origami structures (CR-origamis) and subsequently exposed to the SQ-origamis. High-speed AFM revealed the dynamic adsorption/desorption behavior of the SQ-origamis, which resulted in continuous changing of their arrangements in the framework. These dynamic SQ-origamis were trapped in the cavities by increasing the Mg2+ concentration or by introducing sticky-ended cohesions between extended staples, both from the SQ- and CR-origamis, which enabled the directed docking of the SQ-origamis. Our study offers a platform to create supramolecular structures or systems consisting of multiple DNA origami components.
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
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71
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Fujimoto K, Sasago S, Mihara J, Nakamura S. DNA Photo-cross-linking Using Pyranocarbazole and Visible Light. Org Lett 2018; 20:2802-2805. [DOI: 10.1021/acs.orglett.8b00593] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shinobu Sasago
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Junichi Mihara
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, Asahidai 1-1, Nomi, Ishikawa, 923-1292, Japan
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72
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Sethi S, Nakamura S, Fujimoto K. Study of Photochemical Cytosine to Uracil Transition via Ultrafast Photo-Cross-Linking Using Vinylcarbazole Derivatives in Duplex DNA. Molecules 2018; 23:molecules23040828. [PMID: 29617316 PMCID: PMC6017022 DOI: 10.3390/molecules23040828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022] Open
Abstract
Gene therapies, including genome editing, RNAi, anti-sense technology and chemical DNA editing are becoming major methods for the treatment of genetic disorders. Techniques like CRISPR-Cas9, zinc finger nuclease (ZFN) and transcription activator-like effector-based nuclease (TALEN) are a few such enzymatic techniques. Most enzymatic genome editing techniques have their disadvantages. Thus, non-enzymatic and non-invasive technologies for nucleic acid editing has been reported in this study which might possess some advantages over the older methods of DNA manipulation. 3-cyanovinyl carbazole (CNVK) based nucleic acid editing takes advantage of photo-cross-linking between a target pyrimidine and the CNVK to afford deamination of cytosine and convert it to uracil. This method previously required the use of high temperatures but, in this study, it has been optimized to take place at physiological conditions. Different counter bases (inosine, guanine and cytosine) complementary to the target cytosine were used, along with derivatives of CNVK (NH2VK and OHVK) to afford the deamination at physiological conditions.
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Affiliation(s)
- Siddhant Sethi
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
| | - Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1211, Japan.
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73
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Choudhary A, Vanichkina DP, Ender C, Crawford J, Baillie GJ, Calcino AD, Ru K, Taft RJ. Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics. RNA (NEW YORK, N.Y.) 2018; 24:597-608. [PMID: 29246928 PMCID: PMC5855958 DOI: 10.1261/rna.064923.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel method to identify microRNA targets using miR-29b mimics containing 3-cyanovinylcarbazole (CNVK), a photolabile nucleoside analog. We demonstrate that biotin-tagged, CNVK-containing miR-29b (CNVK-miR-29b) mimics are nontoxic in cell culture, associate with endogenous mammalian Argonaute2, are sensitive for known targets and recapitulate endogenous transcript destabilization. Partnering CNVK-miR-29b with ultra-low-input RNA sequencing, we recover ∼40% of known miR-29b targets and find conservation of the focal adhesion and apoptotic target pathways in mouse and human. We also identify hundreds of novel targets, including NRAS, HOXA10, and KLF11, with a validation rate of 71% for a subset of 73 novel target transcripts interrogated using a high-throughput luciferase assay. Consistent with previous reports, we show that both endogenous miR-29b and CNVK-miR-29b are trafficked to the nucleus, but find no evidence of nuclear-specific miR-29b transcript binding. This may indicate that miR-29b nuclear sequestration is a regulatory mechanism in itself. We suggest that CNVK-containing small RNA mimics may find applicability in other experimental models.
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Affiliation(s)
- Anupma Choudhary
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Newcomb 3220, Australia
| | - Darya P Vanichkina
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Sydney 2050, Australia
| | - Christine Ender
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gregory J Baillie
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew D Calcino
- Department of Integrative Zoology, University of Vienna, Vienna 1090, Austria
| | - Kelin Ru
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Medicine and Health Services, Departments of Integrated Systems Biology and of Pediatrics, George Washington University, Washington DC 20052, USA
- Illumina, Inc., San Diego, California 92122, USA
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74
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De Laet N, Llamas EM, Madder A. Templated DNA Cross-Linking: Towards a Non-Invasive Singlet-Oxygen-Based Triggering Method. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201700175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nathalie De Laet
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Eva M. Llamas
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group Krijgslaan 281, S4; B-9000 Ghent Belgium
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75
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Nakamura S, Takashima Y, Fujimoto K. Multiplexed detection of nucleic acids using 19F NMR chemical shift changes based on DNA photo-cross-linking of 3-vinylcarbazole derivatives. Org Biomol Chem 2018; 16:891-894. [PMID: 29340411 DOI: 10.1039/c7ob03008h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detection methodology for nucleic acids is a useful tool for the analysis of biological systems and diagnosis of diseases. We demonstrated the feasibility of the detection of any nucleic acids based on large chemical shifts via ultrafast DNA photo-cross-linking and the effects of substitution by 3-vinylcarbazole derivatives. These chemical shifts enable the sequence-specific detection of any strand using hybridization chain reaction.
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Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology, Japan Advanced Institute Science and Technology, Asahi-dai, Nomi, Ishikawa 923-1292, Japan.
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76
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Frisch H, Marschner DE, Goldmann AS, Barner‐Kowollik C. Wellenlängengesteuerte dynamische kovalente Chemie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709991] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
| | - David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
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77
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Frisch H, Marschner DE, Goldmann AS, Barner‐Kowollik C. Wavelength‐Gated Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2018; 57:2036-2045. [DOI: 10.1002/anie.201709991] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
| | - David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
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78
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Nakamura S, Kano C, Fujimoto K. Wash-free RNA FISH Using a Photoresponsive Beacon Probe via Photochemical Crosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.170738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Chinami Kano
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
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79
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Nakamura S, Uehara H, Hasegawa T, Fujimoto K. Phototriggered Sequence-specific DNA Transportation into Liposomes Using Ultrafast DNA Photocrosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.170835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Harunobu Uehara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Takashi Hasegawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292
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80
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He X, Sha R, Zhuo R, Mi Y, Chaikin PM, Seeman NC. Exponential growth and selection in self-replicating materials from DNA origami rafts. NATURE MATERIALS 2017; 16:993-997. [PMID: 28920942 DOI: 10.1038/nmat4986] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.
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Affiliation(s)
- Xiaojin He
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Rebecca Zhuo
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Yongli Mi
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Paul M Chaikin
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, USA
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81
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Nakamura S, Hashimoto H, Kobayashi S, Fujimoto K. Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking. Chembiochem 2017; 18:1984-1989. [DOI: 10.1002/cbic.201700430] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science; Japan Advanced Institute Science and Technology; 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
| | - Hirokazu Hashimoto
- School of Materials Science; Japan Advanced Institute Science and Technology; 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
| | - Satoshi Kobayashi
- Department of Computer Science; University of Electro-Communications; 1-1-1 Chofugaoka Chofu Tokyo 182-8585 Japan
| | - Kenzo Fujimoto
- School of Materials Science; Japan Advanced Institute Science and Technology; 1-1 Asahidai Nomi Ishikawa 923-1292 Japan
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82
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Sugihara Y, Nakata Y, Yamayoshi A, Murakami A, Kobori A. Inhibition Effect of Photoresponsive α-Haloaldehyde-conjugated Oligonucleotides on the Gene Expression in HeLa Cells Stably Expressing GFP. CHEM LETT 2017. [DOI: 10.1246/cl.170298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yuta Sugihara
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Yuki Nakata
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
| | - Asako Yamayoshi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502
- The Hakubi Center for Advanced Research, Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501
| | - Akira Murakami
- Kyoto Pharmaceutical University, 1 Misasagi-Shichonocho, Yamashina-ku, Kyoto 607-8412
| | - Akio Kobori
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585
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83
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Sethi S, Takashima Y, Nakamura S, Fujimoto K. Effect of substitution of photo-cross-linker in photochemical cytosine to uracil transition in DNA. Bioorg Med Chem Lett 2017; 27:3905-3908. [DOI: 10.1016/j.bmcl.2017.06.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 11/25/2022]
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84
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193
| | - Marina Kabumoto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
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85
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Sethi S, Ooe M, Sakamoto T, Fujimoto K. Effect of nucleobase change on cytosine deamination through DNA photo-cross-linking reaction via 3-cyanovinylcarbazole nucleoside. MOLECULAR BIOSYSTEMS 2017; 13:1152-1156. [PMID: 28453010 DOI: 10.1039/c7mb00082k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photo-chemical deamination of cytosine using 3-cyanovinylcarbazole nucleoside (CNVK) mediated photo-cross-linking is a technique for site-directed mutagenesis. Using this technique in vivo requires the elimination of a high-temperature incubation step; instead, incubation should be carried out under physiological conditions. To improve the reactivity of CNVK mediated photo-cross-link induced deamination of cytosine under physiological conditions, an evaluation of base pairing in cytosine was carried out with respect to its deamination. Guanine was replaced with 4 different counter bases (inosine, 2-aminopurine, 5-nitroindole, and nebularine), showing distinct hydrogen bonding patterns with target cytosine, which was incorporated at the -1 position with respect to CNVK in the CNVK-modified photo-responsive oligodeoxyribonucleotides to ascertain the role of hydrogen bonding in deamination under physiological conditions. Among the counter bases, inosine showed the highest acceleration towards the photo-induced deamination reaction.
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Affiliation(s)
- Siddhant Sethi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Minako Ooe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
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86
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Yamada K, Ishiyama S, Onizuka K, Nagatsugi F. Synthesis and properties of cross-linkable DNA duplex using 4-amino-2-oxo-6-vinyl-1,3,5-triazine. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.01.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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87
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Sato Y, Hiratsuka Y, Kawamata I, Murata S, Nomura SIM. Micrometer-sized molecular robot changes its shape in response to signal molecules. Sci Robot 2017; 2:2/4/eaal3735. [DOI: 10.1126/scirobotics.aal3735] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/03/2017] [Indexed: 11/02/2022]
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88
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Sugihara Y, Tatsumi S, Kobori A. Development of Novel Photoresponsive Oligodeoxyribonucleotides with a 2′-O-Diazirine-conjugated Adenosine for DNA Interstrand Crosslinking. CHEM LETT 2017. [DOI: 10.1246/cl.160998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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89
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Nakamura S, Kawabata H, Fujimoto K. Double duplex invasion of DNA induced by ultrafast photo-cross-linking using 3-cyanovinylcarbazole for antigene methods. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc01746d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
New photoresponsive antigene probes containingCNVK andCNU have a high double-duplex invasion capability upon photoirradiation because of the inhibition of photo-cross-linking between the probes.
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Affiliation(s)
- Shigetaka Nakamura
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Hayato Kawabata
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
| | - Kenzo Fujimoto
- Department of Advanced Science and Technology
- Japan Advanced Institute Science and Technology
- Nomi
- Japan
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90
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Sun H, Fan H, Eom H, Peng X. Coumarin-Induced DNA Ligation, Rearrangement to DNA Interstrand Crosslinks, and Photorelease of Coumarin Moiety. Chembiochem 2016; 17:2046-2053. [DOI: 10.1002/cbic.201600240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Huabing Sun
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Heli Fan
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Hyeyoung Eom
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry; University of Wisconsin-Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
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91
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Fujimoto K, Toyosato K, Nakamura S, Sakamoto T. RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes. Bioorg Med Chem Lett 2016; 26:5312-5314. [PMID: 27680586 DOI: 10.1016/j.bmcl.2016.09.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/29/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022]
Abstract
Photo-cross-linkable fluorescent oligodeoxyribonucleotides having 3-cyanovinylcarbazole nucleoside were applied to fluorescence in situ hybridization (FISH) based 16S rRNA detection in Escherichia coli cells. As the photo-cross-linked probe/rRNA hybrid was stable under the denaturing condition, decrease of the fluorescence signal through the washing process was prevented. The thermally irreversible hybridization property also enabled stable hybridization with the structured region on the target RNA, and facilitated design of the sequence for the FISH probe. Further development of the method might contribute to quantitative and stable FISH staining.
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Affiliation(s)
- Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kei Toyosato
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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92
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Rezzoug F, Thomas SD, Rouchka EC, Miller DM. Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression. PLoS One 2016; 11:e0161588. [PMID: 27551915 PMCID: PMC4995011 DOI: 10.1371/journal.pone.0161588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/08/2016] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex forming sequences are particularly enriched in the promoter regions of eukaryotic genes, especially of oncogenes. One of the most well studied G-quadruplex forming sequences is located in the nuclease hypersensitive element (NHE) III1 of the c-MYC promoter region. The oncoprotein c-MYC regulates a large array of genes which play important roles in growth regulation and metabolism. It is dysregulated in >70% of human cancers. The silencer NHEIII1 located upstream of the P1 promoter regulates up-to 80% of c-MYC transcription and includes a G-quadruplex structure (Pu27) that is required for promoter inhibition. We have identified, for the first time, a family of seventeen G-quadruplex-forming motifs with >90% identity with Pu27, located on different chromosomes throughout the human genome, some found near or within genes involved in stem cell maintenance or neural cell development. Notably, all members of the Pu27 family interact specifically with NHEIII1 sequence, in vitro. Crosslinking studies demonstrate that Pu27 oligonucleotide binds specifically to the C-rich strand of the NHEIII1 resulting in the G-quadruplex structure stabilization. Pu27 homologous sequences (Pu27-HS) significantly inhibit leukemic cell lines proliferation in culture. Exposure of U937 cells to the Pu27-HS induces cell growth inhibition associated with cell cycle arrest that is most likely due to downregulation of c-MYC expression at the RNA and/or protein levels. Expression of SOX2, another gene containing a Pu27-HS, was affected by Pu27-HS treatment as well. Our data suggest that the oligonucleotides encoding the Pu27 family target complementary DNA sequences in the genome, including those of the c-MYC and SOX2 promoters. This effect is most likely cell type and cell growth condition dependent. The presence of genomic G-quadruplex-forming sequences homologous to Pu27 of c-MYC silencer and the fact that they interact specifically with the parent sequence suggest a common regulatory mechanism for genes whose promoters contain these sequences.
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Affiliation(s)
- Francine Rezzoug
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
| | - Shelia D. Thomas
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Kentucky, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
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93
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Nakamura S, Kawabata H, Fujimoto K. Sequence-Specific DNA Photosplitting of Crosslinked DNAs Containing the 3-Cyanovinylcarbazole Nucleoside by Using DNA Strand Displacement. Chembiochem 2016; 17:1499-503. [PMID: 27357523 DOI: 10.1002/cbic.201600236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/30/2022]
Abstract
An oligodeoxynucleotide (ODN) containing the ultrafast reversible 3-cyanovinylcarbazole ((CNV) K) photo-crosslinker was photo-crosslinked to a complementary strand upon exposure to 366 nm irradiation and photosplit by use of 312 nm irradiation. In this paper we report that the photoreaction of (CNV) K on irradiation at 366 nm involves a photostationary state and that its reaction can be controlled by temperature. Guided by this new insight, we proposed and have now demonstrated previously unknown photosplitting of (CNV) K aided by DNA strand displacement as an alternative to heating. The photo-crosslinked double-stranded DNA (dsDNA) underwent >80 % photosplitting aided by DNA strand displacement on irradiation at 366 nm without heating. In this photosplitting based on DNA strand displacement, the relative thermal stability of the invader strand with respect to the template strands plays an important role, and an invader strand/template strand system that is more stable than the passenger strand/template strand system induces photosplitting without heating. This new strand-displacement-aided photosplitting occurred in a sequence-specific manner through irradiation at 366 nm in the presence of an invader strand.
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Affiliation(s)
- Shigetaka Nakamura
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Hayato Kawabata
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa, Japan.
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94
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Nakamura S, Kawabata H, Muramatsu H, Fujimoto K. Effect of 5-Substitution of Uracil Base in DNA Photocrosslinking Using 3-Cyanovinylcarbazole. CHEM LETT 2016. [DOI: 10.1246/cl.160382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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95
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Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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96
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Kandatsu D, Cervantes-Salguero K, Kawamata I, Hamada S, Nomura SIM, Fujimoto K, Murata S. Reversible Gel-Sol Transition of a Photo-Responsive DNA Gel. Chembiochem 2016; 17:1118-21. [PMID: 27123549 DOI: 10.1002/cbic.201600088] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 12/13/2022]
Abstract
Stimuli-responsive DNA gels that can undergo a sol-gel transition in response to photo-irradiation provide a way to engineer functional gel material with fully designed DNA base sequences. We propose an X-shaped DNA motif that turns into a gel by hybridization of self-complementary sticky ends. By embedding a photo-crosslinking artificial base in the sticky-end sequence, repetitive gel-sol transitions are achieved through UV irradiation at different wavelengths. The concentration of the DNA motif necessary for gelation is as low as 40 μm after modification of the geometrical properties of the motif. The physical properties, such as swelling degree and diffusion coefficient, were assessed experimentally.
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Affiliation(s)
- Daisuke Kandatsu
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | | | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | - Shogo Hamada
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
| | - Shin-Ichiro M Nomura
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, 923-1292, Japan
| | - Satoshi Murata
- Department of Robotics, Tohoku University, Aoba, Sendai, Miyagi, 980-8579, Japan.
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97
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Nakamura S, Fujimoto K. Photo-cross-linking using trifluorothymidine and 3-cyanovinylcarbazole induced a large shifted (19)F MR signal. Chem Commun (Camb) 2016; 51:11765-8. [PMID: 26027537 DOI: 10.1039/c5cc02972d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Photo-cross-linking of trifluorothymidine ((TF)T) using 3-cyanovinylcarbazole ((CNV)K) clearly shifted its (19)F nuclear magnetic resonance (NMR) signal 8 ppm. This (CNV)K mediated ultrafast photo-cross-linking-induced shift can be utilized for miRNA detection by hybridization chain reaction (HCR) to detect 10 nM of a target in a sequence-specific manner.
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Affiliation(s)
- Shigetaka Nakamura
- Materials Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan.
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98
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Ohayon YP, Sha R, Flint O, Liu W, Chakraborty B, Subramanian HKK, Zheng J, Chandrasekaran AR, Abdallah HO, Wang X, Zhang X, Seeman NC. Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion. ACS NANO 2015; 9:10304-10312. [PMID: 26343906 DOI: 10.1021/acsnano.5b04335] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The construction of DNA nanostructures from branched DNA motifs, or tiles, typically relies on the use of sticky-ended cohesion, owing to the specificity and programmability of DNA sequences. The stability of such constructs when unligated is restricted to a specific range of temperatures, owing to the disruption of base pairing at elevated temperatures. Paranemic (PX) cohesion was developed as an alternative to sticky ends for the cohesion of large topologically closed species that could be purified reliably on denaturing gels. However, PX cohesion is also of limited stability. In this work, we added sticky-ended interactions to PX-cohesive complexes to create interlocked complexes by functionalizing the sticky ends with psoralen, which can form cross-links between the two strands of a double helix. We were able to reinforce the stability of the constructs by creating covalent linkages between the 3'-ends and 5'-ends of the sticky ends; the sticky ends were added to double crossover domains via 3'-3' and 5'-5' linkages. Catenated arrays were obtained either by enzymatic ligation or by UV cross-linking. We have constructed finite-length one-dimensional arrays linked by interlocking loops and have positioned streptavidin-gold particles on these constructs.
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Affiliation(s)
- Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ortho Flint
- Department of Mathematics, University of Western Ontario , London, ON N6A 5B7, Canada
| | - Wenyan Liu
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Banani Chakraborty
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Hari K K Subramanian
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Jianping Zheng
- Department of Chemistry, New York University , New York, New York 10003, United States
| | | | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xing Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xiaoping Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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99
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Mochizuki Y, Suzuki T, Fujimoto K, Nemoto N. A versatile puromycin-linker using cnvK for high-throughput in vitro selection by cDNA display. J Biotechnol 2015; 212:174-80. [DOI: 10.1016/j.jbiotec.2015.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/04/2023]
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100
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Sakamoto T, Ooe M, Fujimoto K. Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside. Bioconjug Chem 2015; 26:1475-8. [PMID: 26190032 DOI: 10.1021/acs.bioconjchem.5b00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.
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Affiliation(s)
- Takashi Sakamoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Minako Ooe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahi-dai, Nomi, Ishikawa 923-1292, Japan
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