Genetically encoded RNA photoswitches as tools for the control of gene expression

The artificial control of DNA structure and function is an attractive field in chemical and synthetic biology, [1] and light is a powerful and convenient trigger: it is non-invasive, provides high spatio-temporal resolution, and offers the option of orthogonality. DNA is reactive to light: the UVlight-induced cyclodimerization of pyrimidine nucleosides is an important type of DNA damage and has been studied intensively. [2] Interestingly, this chemical property has never been exploited for the construction of DNA-based reversible photoswitches, and all published work in this field is based on the covalent functionalization of DNA with small autonomous photoactive molecules. [3] Different classes of such photoactive molecules have been studied for DNA photoregulation; [4] azobenzenes have been used most frequently and were, for example, employed for modulating oligonucleotide duplex and triplex formation and DNA transcription. [5] Other substance classes studied in this context include arylvinyl derivatives, [6] spiropyranes, [3a] and recently also diarylethenes. [3a, 7] While a certain influence of photoisomerization on the properties of the nucleic acid was always observed, these approaches share one common limitation: because an autonomous photoswitch was attached to the DNA, either as an appendage or substituting for nucleosides, the rearrangement of chemical bonds upon encountering a photon (i.e., the photochemical reaction) was strictly confined to this non-nucleosidic moiety.Recently, our lab reported a new type of diarylethene photoswitches in which one of the two aryl moieties was replaced by a nucleoside, namely 7-deaza-8-methyldeoxyadenosine (Scheme 1). [8] These photoswitches were synthesized in a convergent multi-step approach in which a substi-tuted cyclopentenyl boronic ester was reacted with protected 7-iodo-8-methyl-7-deazadeoxyadenosine by Suzuki crosscoupling, followed by deprotection. Upon irradiation with light, these compounds were found to undergo a highly efficient, reversible, electrocyclic rearrangement and the switching wavelength could be tuned by the chemical nature of substituents. Switching was found to be near-quantitative in aprotic solvents, and the compounds retained the key properties of nucleotides, such as their capability to form Watson-Crick base-pairs. Unfortunately, the photoisomerization was found to proceed with low efficiency in aqueous solvents, and the demanding synthesis involved limited the application of these photoswitches to oligonucleotides.To develop straight-forward access to truly photoswitchable DNA, we reconsidered our design approach; in contrast to 7-iodo-8-methyl-7-deazadeoxyadenosine, the 5-iodo-substituted pyrimidine nucleosides 5I-dU and 5I-dC represent oligonucleotide modifications readily available from commercial suppliers, and offer the desired reactivity for different cross-coupling reactions. [9] This could allow for the postsynthetic conversion of an iodo-modified oligonucleotide into a photoswitch, leading to the target compounds shown i...

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mentioning

confidence: 99%

Nucleoside‐Based Diarylethene Photoswitches and Their Facile Incorporation into Photoswitchable DNA

2013

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“…This introduces several new structural and property elements, including electronics, flexibility, and bond hybridization of the nucleotide. In a previous work, they investigated the effects of incorporation of deoxyadenosine and guanosine into diarylethenes [19,102]. The photochromic species were attached to several different oligonucleotide sequences, ranging from 15 to 19 residues long using a palladium-catalyzed cross-coupling reaction between an iodinated base pair and boronic acid-derived dithienylethene.…”

Section: Diarylethene-modified Oligonucleotidesmentioning

confidence: 99%

“…Instead, our intent is to present a general overview of recent progress made in the field of light-controlled biomolecules in a variety of contexts. These individual topics have been reviewed in detail elsewhere, and the reader is referred to the following references for earlier examples [1,[3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Photochromic Materials in Biochemistry

Wilson

Branda

2016

Photochromic Materials: Preparation, Properties and Applications

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“…Indeed, recent studies have begun to utilize this type of approach to create light‐regulated RNA‐based switches . For instance, RNA aptamers that only bind the trans form of an arginine‐substituted azobenzene were generated .…”

Section: Realizing Light‐regulated Rnas Using Photoswitchable Small Mmentioning

confidence: 99%

Designing optogenetically controlled RNA for regulating biological systems

Meng

Jaffrey

2015

Annals of the New York Academy of Sciences

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Light-responsive proteins have been used in the field of optogenetics to control cellular functions. However, surprisingly, analogous approaches to regulate and alter the functions of RNA molecules by light remain underdeveloped. RNA aptamers and RNA devices can perform diverse intracellular functions and are important tools in synthetic biology. This report explores the challenges of and potential strategies for engineering light regulation into functional RNAs in cells. We discuss approaches for using existing light-regulated proteins and small molecules to control RNA function in living cells. Additionally, applications of light-regulated RNAs for synthetic biology and for studying functions of endogenously expressed RNAs are discussed.

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Genetically encoded RNA photoswitches as tools for the control of gene expression

Cited by 29 publications

References 44 publications

Nucleoside‐Based Diarylethene Photoswitches and Their Facile Incorporation into Photoswitchable DNA

Nucleoside‐Based Diarylethene Photoswitches and Their Facile Incorporation into Photoswitchable DNA

Photochromic Materials in Biochemistry

Designing optogenetically controlled RNA for regulating biological systems

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