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Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
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Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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2
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Liang J, Cheng L, Struckhoff JJ, Ravi N. Investigating triazine-based modification of hyaluronan using statistical designs. Carbohydr Polym 2015; 132:472-80. [PMID: 26256372 PMCID: PMC5787032 DOI: 10.1016/j.carbpol.2015.06.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/19/2022]
Abstract
Hyaluronan (HA) and its derivatives have been extensively researched for many biomedical applications. To precisely tailor the property of HA by derivatizing it to a pre-determined extent is challenging, yet critical. In this paper, we used 2-chloro-4,6-dimethoxy-1,3,5-triazine (CDMT) and N-methylmorpholine (NMM) to derivatize HA via a triazine-based coupling reaction. Using a fractional factorial (FF) design, we observed that water content in the solvent, and molar ratios of CDMT and NaHCO3 to the carboxylate were the significant factors controlling the derivatization. We investigated how the effect of each factor changes as reaction conditions change. Moreover, by altering the amount of CDMT and NaHCO3, we developed a cubic regression model for precise control of the extent of derivatization using a response surface methodology (RSM) with a D-optimal design. No spurious peaks were detected by (1)H NMR spectrum and only 10% decrease of molecular weight of the derivatized HA was determined by GPC. The HA with 6% modification was relatively biocompatible up to 15 mg/mL.
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Affiliation(s)
- Jue Liang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, USA
| | - Lulu Cheng
- Statistics Technology Center, Monsanto Company, Saint Louis, Missouri, USA
| | - Jessica J Struckhoff
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, USA
| | - Nathan Ravi
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO, USA; Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO, USA; Research and Development, Veterans Affairs Health Care System, Saint Louis, MO, USA.
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3
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Chen M, Heimer P, Imhof D. Synthetic strategies for polypeptides and proteins by chemical ligation. Amino Acids 2015; 47:1283-99. [DOI: 10.1007/s00726-015-1982-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/02/2015] [Indexed: 11/30/2022]
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ye M, Guillaume J, Liu Y, Sha R, Wang R, Seeman NC, Canary JW. Site-specific inter-strand cross-links of DNA duplexes. Chem Sci 2013; 4:1319-1329. [PMID: 23894693 PMCID: PMC3719409 DOI: 10.1039/c2sc21775a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2'-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.
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Affiliation(s)
- Miao Ye
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Johan Guillaume
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
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Kunishima M, Ujigawa T, Nagaoka Y, Kawachi C, Hioki K, Shiro M. Study on 1,3,5-triazine chemistry in dehydrocondensation: gauche effect on the generation of active triazinylammonium species. Chemistry 2012; 18:15856-67. [PMID: 23059753 DOI: 10.1002/chem.201202236] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Indexed: 01/09/2023]
Abstract
The reaction of 2-chloro-4,6-dimethoxy-1,3,5-triazine (CDMT) with various nitrogen-containing compounds, particularly tertiary amines (tert-amines), has been studied for the preparation of 2-(4,6-dimethoxy-1,3,5-triazinyl)trialkylammonium salts [DMT-Am(s)]. DMT-Ams derived from aliphatic tert-amines exhibited activity for the dehydrocondensation between a carboxylic acid and an amine to form an amide in a model reaction. Based on a conformational analysis of DMT-Ams and tert-amines by NMR and X-ray diffraction methods, we concluded that a β-alkyl group maintained in a gauche relationship with the nitrogen lone pair of tert-amines significantly hinders the approach of CDMT to the nitrogen. Thus, trimethylamine and quinuclidine without such alkyl groups readily react with CDMT whereas triethylamine, possessing two or three such gauche β-alkyl groups in the stable conformations, does not react at all. The theory of "gauche β-alkyl group effect" proposed here provides useful guidelines for the preparation of DMT-Ams possessing various tertiary amine moieties. An investigation of the dehydrocondensation activity of tert-amines in a CDMT/tert-amine system that involves in situ generation of DMT-Am, showed that the gauche effect of the β-alkyl group becomes quite pronounced; the yield of the amide decreases significantly with tert-amines possessing an unavoidable gauche β-alkyl group. Thus, the tert-amine/CDMT systems are useful for judging whether tert-amines can readily react with CDMT without isolation of DMT-Ams.
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Affiliation(s)
- Munetaka Kunishima
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Japan.
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Liu Y, Wang R, Ding L, Sha R, Seeman NC, Canary JW. Templated synthesis of nylon nucleic acids and characterization by nuclease digestion. Chem Sci 2012; 3:1930-1937. [PMID: 23125913 PMCID: PMC3486707 DOI: 10.1039/c2sc20129a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Liang Ding
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Roujie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
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Andersen CS, Knudsen MM, Chhabra R, Liu Y, Yan H, Gothelf KV. Distance dependent interhelical couplings of organic rods incorporated in DNA 4-helix bundles. Bioconjug Chem 2009; 20:1538-46. [PMID: 19572635 PMCID: PMC3412156 DOI: 10.1021/bc900078c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of a conjugated linear organic module containing terminal salicylaldehyde groups and a central activated ester, designed for conjugation to amino-modified oligonucleotides, is presented. The organic module has a phenylene-ethynylene backbone and is highly fluorescent. It is conjugated to oligonucleotide sequences and incorporated into specific locations in a well-defined DNA 4-helix bundle (4-HB). The DNA-nanostructure offers precise location control of the organic modules which allows for selective interhelical coupling reactions. In this study, metal-salen formation as well as dihydrazone formation are used to covalently interlink the organic modules. Both coupling reactions are highly dependent on the distances between the organic modules in the 4-HB. Neighboring modules dimerize easier, whereas more distanced modules are less prone to react, even when the linkers are extended. The dimeric products are characterized by denaturing polyacrylamide gel electrophoresis (PAGE), high performance liquid chromatography (HPLC), and matrix assisted laser desorption/absorption ionization time-of-flight (MALDI TOF) mass spectrometry.
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Affiliation(s)
- Casper S. Andersen
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
| | - Martin M. Knudsen
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
| | - Rahul Chhabra
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Yan Liu
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Hao Yan
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Kurt V. Gothelf
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
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Construction of a DNA nano-object directly demonstrates computation. Biosystems 2009; 98:80-4. [PMID: 19607875 DOI: 10.1016/j.biosystems.2009.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/23/2009] [Accepted: 07/01/2009] [Indexed: 11/22/2022]
Abstract
We demonstrate a computing method in which a DNA nano-object representing the solution of a problem emerges as a result of self-assembly. We report an experiment in which three-vertex colorability for a six-vertex graph with nine edges is solved by constructing a DNA molecule representing the colored graph itself. Our findings show that computation based on "shape processing" is a viable alternative to symbol processing when computing by molecular self-assembly.
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