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Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
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Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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2
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Kaufmann J, Müller P, Andreadou E, Heckel A. Green‐Light Activatable BODIPY and Coumarin 5’‐Caps for Oligonucleotide Photocaging. Chemistry 2022; 28:e202200477. [PMID: 35420231 PMCID: PMC9322594 DOI: 10.1002/chem.202200477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 12/02/2022]
Abstract
We synthesized two green‐light activatable 5’‐caps for oligonucleotides based on the BODIPY and coumarin scaffold. Both bear an alkyne functionality allowing their use in numerous biological applications. They were successfully incorporated in oligonucleotides via solid‐phase synthesis. Copper‐catalyzed alkyne‐azide cycloaddition (CuAAC) using a bisazide photo‐tether gave cyclic oligonucleotides that could be relinearized by activation with green light and were shown to exhibit high stability against exonucleases. Chemical ligation as another example for bioconjugation yielded oligonucleotides with an internal strand break site. Irradiation at 530 nm or 565 nm resulted in complete photolysis of both caging groups.
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Affiliation(s)
- Janik Kaufmann
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Patricia Müller
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Eleni Andreadou
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
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3
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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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4
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Wang Q, Fan X, Jing N, Zhao H, Yu L, Tang X. Photoregulation of Gene Expression with Ligand-Modified Caged siRNAs through Host/Guest Interaction. Chembiochem 2021; 22:1901-1907. [PMID: 33432703 DOI: 10.1002/cbic.202000763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/22/2020] [Indexed: 02/05/2023]
Abstract
Small interfering RNA (siRNA) can effectively silence target genes through Argonate 2 (Ago2)-induced RNA interference (RNAi). It is very important to control siRNA activity in both spatial and temporal modes. Among different masking strategies, photocaging can be used to regulate gene expression through light irradiation with spatiotemporal and dose-dependent resolution. Many different caging strategies and caging groups have been reported for light-activated siRNA gene silencing. Herein, we describe a novel caging strategy that increases the blocking effect of RISC complex formation/process through host/guest (including ligand/receptor) interactions, thereby enhancing the inhibition of caged siRNA activity until light activation. This strategy can be used as a general approach to design caged siRNAs for the photomodulation of gene silencing of exogenous and endogenous genes.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, P. R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, P. R. China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, P. R. China
| | - Han Zhao
- National Center for Occupational Safety and Health, NHC, No. 27 Shilong Road, Beijing, P. R. China
| | - Lijia Yu
- National Center for Occupational Safety and Health, NHC, No. 27 Shilong Road, Beijing, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, P. R. China
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5
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Chen C, Wang Z, Jing N, Chen W, Tang X. Photomodulation of Caged RNA Oligonucleotide Functions in Living Systems. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Changmai Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Wei Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
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6
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Zhang J, Jing N, Fan X, Tang X. Photoregulation of Gene Expression with Amantadine‐Modified Caged siRNAs through Host–Guest Interactions. Chemistry 2020; 26:14002-14010. [DOI: 10.1002/chem.202003084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/16/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Jinhao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
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Seyfried P, Heinz M, Pintér G, Klötzner DP, Becker Y, Bolte M, Jonker HRA, Stelzl LS, Hummer G, Schwalbe H, Heckel A. Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging. Chemistry 2018; 24:17568-17576. [DOI: 10.1002/chem.201804040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Patrick Seyfried
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Marcel Heinz
- Department of Theoretical Biophysics; Max Planck Institute of Biophysics; Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - György Pintér
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt/, Centre for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Dean-Paulos Klötzner
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Yvonne Becker
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Michael Bolte
- Institute for Inorganic Chemistry; Goethe University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt/, Centre for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics; Max Planck Institute of Biophysics; Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics; Max Planck Institute of Biophysics; Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute of Biophysics; Max-von-Laue-Str. 1 60438 Frankfurt am Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt/, Centre for Biomolecular Magnetic Resonance (BMRZ); Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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8
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Yang L, Kim HB, Sul JY, Yeldell SB, Eberwine JH, Dmochowski IJ. Efficient Synthesis of Light-Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression. Chembiochem 2018; 19:1250-1254. [PMID: 29479781 PMCID: PMC6248878 DOI: 10.1002/cbic.201800012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 02/06/2023]
Abstract
Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at submicron spatial resolution through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures because of their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here, we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yields through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Caging stability and light activation were characterized by FRET efficiency, denaturing gel assay, and melting temperature measurements. Finally, a cyclized caged oligo was designed to target gfap, and it gave a tenfold reduction in glial fibrillary acidic protein upon photoactivation in astrocytes.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Hyun Bum 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
| | - Sean B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, 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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9
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Yang J, Chen C, Tang X. Cholesterol-Modified Caged siRNAs for Photoregulating Exogenous and Endogenous Gene Expression. Bioconjug Chem 2018. [DOI: 10.1021/acs.bioconjchem.8b00080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiali Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, the School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University Health Center, Peking University, Beijing 100191, China
| | - Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, the School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University Health Center, Peking University, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, the School of Pharmaceutical Sciences and Center for Noncoding RNA Medicine, Peking University Health Center, Peking University, Beijing 100191, China
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10
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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11
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Zhang L, Chen C, Fan X, Tang X. Photomodulating Gene Expression by Using Caged siRNAs with Single-Aptamer Modification. Chembiochem 2018; 19:1259-1263. [PMID: 29488297 DOI: 10.1002/cbic.201700623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Indexed: 12/21/2022]
Abstract
Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer-modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future.
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Affiliation(s)
- Liangliang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
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12
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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13
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Seyfried P, Eiden L, Grebenovsky N, Mayer G, Heckel A. Photo‐Tethers for the (Multi‐)Cyclic, Conformational Caging of Long Oligonucleotides. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Patrick Seyfried
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Laura Eiden
- Life and Medical Science Institute University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Nikolai Grebenovsky
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Günter Mayer
- Life and Medical Science Institute University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Alexander Heckel
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
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Seyfried P, Eiden L, Grebenovsky N, Mayer G, Heckel A. Photo-Tethers for the (Multi-)Cyclic, Conformational Caging of Long Oligonucleotides. Angew Chem Int Ed Engl 2016; 56:359-363. [PMID: 27897376 DOI: 10.1002/anie.201610025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Indexed: 12/28/2022]
Abstract
Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne-modified photolabile nucleosides into DNA sequences, followed by a CuI -catalyzed alkyne-azide cycloaddition with bis-azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full-length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo-tether strategy presented here provides a robust and versatile tool for the light-activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.
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Affiliation(s)
- Patrick Seyfried
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Laura Eiden
- Life and Medical Science Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Nikolai Grebenovsky
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Günter Mayer
- Life and Medical Science Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Alexander Heckel
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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