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Mathis K, Gaddam S, Koneru R, Sunkavalli N, Wang C, Patel M, Kohon AI, Meckes B. Multifunctional hydrogels with spatially controlled light activation with photocaged oligonucleotides. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101922. [PMID: 38911357 PMCID: PMC11192495 DOI: 10.1016/j.xcrp.2024.101922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Recreating tissue environments with precise control over mechanical, biochemical, and cellular organization is essential for next-generation tissue models for drug discovery, development studies, and the replication of disease environments. However, controlling these properties at cell-scale lengths remains challenging. Here, we report the development of printing approaches that leverage polyethylene glycol diacrylate (PEGDA) hydrogels containing photocaged oligonucleotides to spatially program material characteristics with non-destructive, non-ultraviolet light. We further integrate this system with a perfusion chamber to allow us to alter the composition of PEGDA hydrogels while retaining common light-activatable photocaged DNAs. We demonstrate that the hydrogels can capture DNA functionalized materials, including cells coated with complementary oligonucleotides with spatial control using biocompatible wavelengths. Overall, these materials open pathways to orthogonal capture of any DNA functionalized materials while not changing the sequences of the DNA.
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Affiliation(s)
- Katelyn Mathis
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Saanvi Gaddam
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Rishi Koneru
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Nikhil Sunkavalli
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Catherine Wang
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Manan Patel
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Afia Ibnat Kohon
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Brian Meckes
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
- Lead contact
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Yang L, Trentini D, Kim H, Sul J, Eberwine JH, Dmochowski IJ. Photoactivatable Circular Caged Oligonucleotides for Transcriptome In Vivo Analysis (TIVA). CHEMPHOTOCHEM 2021; 5:940-946. [DOI: 10.1002/cptc.202100098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Linlin Yang
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Dora Trentini
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - HyunBum Kim
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Jai‐Yoon Sul
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - James H. Eberwine
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Ivan J. Dmochowski
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
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3
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Yang L, Dmochowski IJ. Conditionally Activated ("Caged") Oligonucleotides. Molecules 2021; 26:1481. [PMID: 33803234 PMCID: PMC7963183 DOI: 10.3390/molecules26051481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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4
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Jakubovska J, Tauraitė D, Meškys R. Transient N 4 -Acyl-DNA Protection against Cleavage by Restriction Endonucleases. Chembiochem 2019; 20:2504-2512. [PMID: 31090133 DOI: 10.1002/cbic.201900280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Indexed: 01/06/2023]
Abstract
A set of five N4 -acyl-modified 2'-deoxycytidine 5'-triphosphates were incorporated into modified DNA by using phi29 DNA polymerase, and cleavage by selected restriction endonucleases was studied. Modified DNA containing N4 -acyl functional groups in either one or both strands of a DNA molecule was resistant to the majority of restriction enzymes tested, whereas modifications outside of the recognition sequences were well tolerated. The N4 -acylated cytidine derivatives were subjected to competitive nucleotide incorporation by using phi29 DNA polymerase, showing that a high-fidelity phi29 DNA polymerase efficiently used the modified analogues in the presence of its natural counterpart. These N4 modifications were also demonstrated to be easily removed in an aqueous ethanolamine solution, in which all steps, including primer extension, demodification, and cleavage by restriction endonuclease, could be performed in a one-pot procedure that eliminated additional purification stages. It is suggested that N4 -modified nucleotides are promising building blocks for a programmable; transient; and, most importantly, straightforward DNA protection against specific endonucleases.
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Affiliation(s)
- Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257, Vilnius, Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, 10257, Vilnius, Lithuania
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5
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Abstract
A 23-mer DNA “caged” at its 3′-terminus with a 9-anthracenyl moiety was prepared.
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Affiliation(s)
- A. Meyer
- Friedrich-Alexander-University of Erlangen-Nürnberg
- Department of Chemistry and Pharmacy
- Organic Chemistry Chair II
- 91054 Erlangen
- Germany
| | - Margot Schikora
- Friedrich-Alexander-University of Erlangen-Nürnberg
- Department of Chemistry and Pharmacy
- Organic Chemistry Chair II
- 91054 Erlangen
- Germany
| | - A. Mokhir
- Friedrich-Alexander-University of Erlangen-Nürnberg
- Department of Chemistry and Pharmacy
- Organic Chemistry Chair II
- 91054 Erlangen
- Germany
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6
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Sun F, Zhang L, Yan J, Xu L, Fang D, Luo SZ. The synthesis and photolysis mechanisms of 8-nitroquinoline-based photolabile caging groups for carboxylic acid. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Lei Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Jianhua Yan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
| | - Decai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry; Beijing Normal University; Beijing 100875 China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology; Beijing University of Chemical Technology; Beijing 100029 China
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7
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Marcélis L, Van Overstraeten-Schlögel N, Lambermont J, Bontems S, Spinelli N, Defrancq E, Moucheron C, Kirsch-De Mesmaeker A, Raes M. Light-Triggered Green Fluorescent Protein Silencing in Human Keratinocytes in Culture Using Antisense Oligonucleotides Coupled to a Photoreactive Ruthenium(II) Complex. Chempluschem 2014. [DOI: 10.1002/cplu.201402212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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8
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Liu Q, Deiters A. Optochemical control of deoxyoligonucleotide function via a nucleobase-caging approach. Acc Chem Res 2014; 47:45-55. [PMID: 23981235 PMCID: PMC3946944 DOI: 10.1021/ar400036a] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic oligonucleotides have been extensively applied tocontrol a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson-Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanisms of biological processes, researchers need tools that allow for the perturbation of these processes with Nature's precision. Light represents an excellent external regulatory element since irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photolabile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photoregulation of DNA function. Using this approach, we have both activated and deactivated gene expression optochemically at the transcriptional and translational level with spatial and temporal control. Specifically, we have used caged triplex-forming oligomers and DNA decoys to regulate transcription, and we have regulated translation with light-activated antisense agents. Moreover, we also discuss strategies that can trigger DNA enzymatic activity, DNA amplification, and DNA mutagenesis by light illumination. More recently, we have developed light-activated DNA logic operations, an advance that may lay the foundation for the optochemical control of complex DNA calculations.
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Affiliation(s)
- Qingyang Liu
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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9
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1235] [Impact Index Per Article: 112.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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10
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Wang Y, Wu L, Wang P, Lv C, Yang Z, Tang X. Manipulation of gene expression in zebrafish using caged circular morpholino oligomers. Nucleic Acids Res 2012; 40:11155-62. [PMID: 23002141 PMCID: PMC3505977 DOI: 10.1093/nar/gks840] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Morpholino oligomers (MOs) have been widely used to knock down specific genes in zebrafish, but their constitutive activities limit their experimental applications for studying a gene with multiple functions or within a gene network. We report herein a new design and synthesis of caged circular MOs (caged cMOs) with two ends linked by a photocleavable moiety. These caged cMOs were successfully used to photomodulate β-catenin-2 and no tail expression in zebrafish embryos.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing 100191, China
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11
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Ruble BK, Richards JL, Cheung-Lau JC, Dmochowski IJ. Mismatch Discrimination and Efficient Photomodulation with Split 10-23 DNAzymes. Inorganica Chim Acta 2012; 380:386-391. [PMID: 22544974 PMCID: PMC3337724 DOI: 10.1016/j.ica.2011.10.068] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA enzymes (DNAzymes) that catalyze the degradation of complementary RNA molecules have been investigated for many biochemical and sensing applications. Here, we investigated a 10-23 DNAzyme that has been shown previously to possess cellular activity. We determined that it has very low Mg(2+) ion dependence, with DNAzyme activity observed at [Mg(2+)] = 0.01 mM. This metal ion dependence is much lower than is typical for DNAzymes studied to date, and suggests that DNAzymes may be engineered for many additional biological applications. Recently, we demonstrated that this 10-23 DNAzyme can be divided into two parts, which assemble into an active oligonucleotide complex. We investigated in more detail the functionality of the split 10-23 DNAzyme and found that dividing the 15-nucleotide catalytic loop after the 7(th) or 8(th) base maximized its activity. The split DNAzymes required higher metal ion concentrations ([Mg(2+)] = 5 mM), and as we anticipated due to their lower hybridization activity, the split enzymes had the advantage of being more sensitive to single base mismatches in the DNAzyme-RNA duplex. Finally, we demonstrated facile photomodulation of split DNAzyme activity by incorporating a photocleavable biotin moiety bound to streptavidin.
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Affiliation(s)
- Brittani K Ruble
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104
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12
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Li YM, Shi J, Cai R, Chen X, Luo ZF, Guo QX. New quinoline-based caging groups synthesized for photo-regulation of aptamer activity. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2010.02.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Development of new quinoline-based photo-labile groups for photo-regulation of bioactive molecules. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.01.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Li Y, Shi J, Luo Z, Jiang H, Chen X, Wang F, Wu X, Guo Q. Photoregulation of thrombin aptamer activity using Bhc caging strategy. Bioorg Med Chem Lett 2009; 19:5368-71. [PMID: 19682894 DOI: 10.1016/j.bmcl.2009.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/26/2009] [Accepted: 07/28/2009] [Indexed: 11/28/2022]
Abstract
Thrombin aptamer was attempted to cage with Bhc (6-bromo-7-hydroxycoumarin-4-ylmethyl) group for controlling its specific affinity to target molecular through photolysis. By multiple-caging strategy, aptamer could be rendered biologically inert and partially restored with subsequently illumination. This provides a convenient method for photoregulating aptamer activity with exact spatiotemporal resolution.
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Affiliation(s)
- Yiming Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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15
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Shah S, Jain PK, Kala A, Karunakaran D, Friedman SH. Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups. Nucleic Acids Res 2009; 37:4508-17. [PMID: 19477960 PMCID: PMC2715251 DOI: 10.1093/nar/gkp415] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diazo-based precursors of photolabile groups have been used extensively for modifying nucleic acids, with the intention of toggling biological processes with light. These processes include transcription, translation and RNA interference. In these cases, the photolabile groups have been typically depicted as modifying the phosphate backbone of RNA and DNA. In this work we find that these diazo-based reagents in fact react very poorly with backbone phosphates. Instead, they show a remarkable specificity for terminal phosphates and very modest modification of the nucleobases. Furthermore, the photo deprotection of these terminal modifications is shown to be much more facile than nucleobase modified sites. In this study we have characterized this regiospecificity using RNA duplexes and model nucleotides, analyzed using LC/MS/MS. We have also applied this understanding of the regio-specificity to our technique of light activated RNA interference (LARI). We examined 27-mer double-stranded precursors of siRNA (‘dsRNA’), and have modified them using the photo-cleavable di-methoxy nitro phenyl ethyl group (DMNPE) group. By incorporating terminal phosphates in the dsRNA, we are able to guide DMNPE to react at these terminal locations. These modified dsRNA duplexes show superior performance to our previously described DMNPE-modified siRNA, with the range of expression that can be toggled by light increasing by a factor of two.
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Affiliation(s)
- Samit Shah
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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16
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Young DD, Lusic H, Lively MO, Deiters A. Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization. Nucleic Acids Res 2009; 37:e58. [PMID: 19293272 PMCID: PMC2677887 DOI: 10.1093/nar/gkp150] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The effects of photocaged nucleosides on the DNA polymerization reaction was investigated, finding that most polymerases are unable to recognize and read through the presence of a single caging group on the DNA template. Based on this discovery, a new method of introducing mutations into plasmid DNA via a light-mediated mutagenesis protocol was developed. This methodology is advantageous over several common approaches in that it requires the use of only two polymerase chain reaction primers, and does not require any restriction sites or use of restriction enzymes. Additionally, this approach enables not only site-directed mutations, but also the insertion of DNA strands of any length into plasmids and the deletion of entire genes from plasmids.
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Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607-8204, USA
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17
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FRET-based assay of the processing reaction kinetics of stimulus-responsive peptides: influence of amino acid sequence on reaction kinetics. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.01.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Tanaka K, Katada H, Shigi N, Kuzuya A, Komiyama M. Site-selective blocking of PCR by a caged nucleotide leading to direct creation of desired sticky ends in the products. Chembiochem 2009; 9:2120-6. [PMID: 18688827 DOI: 10.1002/cbic.200800285] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In order to terminate the polymerase reaction at a desired position, a caged thymine derivative--4-O-[2-(2-nitrophenyl)propyl]thymine--was incorporated into PCR primers. In the PCR cycles, the elongation of the nascent strand (5'-->3' direction) by polymerase was site-selectively terminated at the 3'-side of T(NPP). Accordingly, predetermined protruding ends were obtained after the removal of the protecting group by short UVA irradiation. Recombinant vectors coding the GFP gene were successfully prepared by direct ligation of these light-assisted cohesive-ending PCR (LACE-PCR) products with scission fragments obtained by use either of restriction enzymes or of artificial restriction DNA cutters and were used for transformation of E. coli.
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Affiliation(s)
- Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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19
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Richards JL, Tang X, Turetsky A, Dmochowski IJ. RNA bandages for photoregulating in vitro protein synthesis. Bioorg Med Chem Lett 2008; 18:6255-8. [PMID: 18926697 PMCID: PMC2593108 DOI: 10.1016/j.bmcl.2008.09.093] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/24/2022]
Abstract
'RNA bandages' are composed of two 6-12-mer 2'-OMe RNA strands complementary to a mRNA target that are joined by a photocleavable linker. These tandem oligonucleotides typically exhibit much higher affinity for the mRNA than the individual strands. An RNA bandage with binding arms of different lengths and a 4-base gap blocked translation in vitro of GFP mRNA; subsequent near-UV irradiation restored translation. This provides a general method of photomodulating hybridization for a variety of oligonucleotide-based technologies.
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Affiliation(s)
- Julia L. Richards
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - XinJing Tang
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Anna Turetsky
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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20
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Lusic H, Lively MO, Deiters A. Light-activated deoxyguanosine: photochemical regulation of peroxidase activity. MOLECULAR BIOSYSTEMS 2008; 4:508-11. [PMID: 18493645 DOI: 10.1039/b800166a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical activation of a deoxyribozyme with peroxidase activity was achieved by the synthesis and incorporation of a caged deoxyguanosine.
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Affiliation(s)
- Hrvoje Lusic
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, USA
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21
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Dmochowski IJ, Tang X. Taking control of gene expression with light-activated oligonucleotides. Biotechniques 2007; 43:161, 163, 165 passim. [PMID: 17824383 DOI: 10.2144/000112519] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The recent development of caged oligonucletides that are efficiently activated by ultraviolet (UV) light creates opportunities for regulating gene expression with very high spatial and temporal resolution. By selectively modulating gene activity, these photochemical tools will facilitate efforts to elucidate gene function and may eventually serve therapeutic aims. We demonstrate how the incorporation of a photocleavable blocking group within a DNA duplex can transiently arrest DNA polymerase activity. Indeed, caged oligonucleotides make it possible to control many different protein-oligonucleotide interactions. In related experiments, hybridization of a reverse complementary (antisense) oligodeoxynucleotide to target mRNA can inhibit translation by recruiting endogenous RNases or sterically blocking the ribosome. Our laboratory recently synthesized caged antisense oligonucleotides composed of phosphorothioated DNA or peptide nucleic acid (PNA). The antisense oligonucleotide, which was attached to a complementary blocking oligonucleotide strand by a photocleavable linker, was blocked from binding target mRNA. This provided a useful method for photomodulating hybridization of the antisense strand to target mRNA. Caged DNA and PNA oligonucleotides have proven effective at photoregulating gene expression in cells and zebrafish embryos.
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Affiliation(s)
- Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
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22
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Smith EE, McClean JN, Cooke LA, Duprey JL, McCourt M, Fabani MM, Tucker JH, Vyle JS. A novel structural class of photoswitchable oligonucleotide. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Tang X, Maegawa S, Weinberg ES, Dmochowski IJ. Regulating gene expression in zebrafish embryos using light-activated, negatively charged peptide nucleic acids. J Am Chem Soc 2007; 129:11000-1. [PMID: 17711280 DOI: 10.1021/ja073723s] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- XinJing Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Tang X, Dmochowski IJ. Controlling RNA digestion by RNase H with a light-activated DNA hairpin. Angew Chem Int Ed Engl 2007; 45:3523-6. [PMID: 16634105 DOI: 10.1002/anie.200600954] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xinjing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Abstract
This protocol describes a general method for the preparation of RNAs in which the reactivity or hydrogen-bonding properties of the molecule are modified in a photoreversible fashion by use of a caging strategy. A single caged adenosine, modified at the 2' position as a nitro-benzyl ether, can be incorporated into short RNAs by chemical synthesis or into long RNAs by a combination of chemical and enzymatic synthesis. The modified RNAs can be uncaged by photolysis under a variety of conditions including the use of a laser or xenon lamp, and the course of this uncaging reaction may be readily followed by HPLC or thin-layer chromatography.
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Affiliation(s)
- Steven G Chaulk
- Department of Biochemistry, University of Alberta Edmonton, Alberta, Canada T6G 2H7
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Tanabe K, Zhang Z, Ito T, Hatta H, Nishimoto SI. Current molecular design of intelligent drugs and imaging probes targeting tumor-specific microenvironments. Org Biomol Chem 2007; 5:3745-57. [DOI: 10.1039/b711244k] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Tang X, Dmochowski IJ. Regulating gene expression with light-activated oligonucleotides. MOLECULAR BIOSYSTEMS 2006; 3:100-10. [PMID: 17245489 DOI: 10.1039/b614349k] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the development of light-responsive amino acids, the activity of numerous biomolecules has been photomodulated in biochemical, biophysical, and cellular assays. Biological problems of even greater complexity motivate the development of quantitative methods for controlling gene activity with high spatial and temporal resolution, using light as an external trigger. Photoresponsive DNA and RNA oligonucleotides would optimally serve this purpose, but have proven difficult to expand from proofs-of-concept to in vivo experiments. Until recently, the development of this technology was limited by the synthesis of oligonucleotides whose function could be significantly modulated with near-UV light. New synthetic protocols and strategies for both up- and down-regulating gene activity finally make it possible to address biological considerations. In the near future, we can expect photoresponsive DNA and RNA molecules that are relatively non-toxic, nuclease-resistant, and maintain their specificity and activity in vivo. Quantitative, laser-initiated methods for controlling DNA and RNA function will illuminate new areas in cell and developmental biology.
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Affiliation(s)
- XinJing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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Tang X, Dmochowski IJ. Controlling RNA Digestion by RNase H with a Light-Activated DNA Hairpin. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600954] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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