Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo‐crosslinking

Nakamura, Shigetaka; Hashimoto, Hirokazu; Kobayashi, Satoshi; Fujimoto, Kenzo

doi:10.1002/cbic.201700430

Cited by 18 publications

(9 citation statements)

References 36 publications

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“…The process of hybridizing ASOs to RNAs with secondary structures at target regions is similar to strand displacement. We have reported the acceleration of DNA strand displacement using ultrafast photocrosslinking, wherein high photocrosslinking rate increased the acceleration in previous report . Therefore, the inhibitory effect on gene expression was increased with CNV D, while no inhibitory effects were observed following photocrosslinking with psoralen that requires photoirradiation for several minutes.…”

Section: Figurementioning

confidence: 75%

“…Psoralen requires light irradiation for several minutes to activate the process of photocrosslinking . As the photocrosslinking reaction of nucleic acid probes toward RNAs forming higher order structures requires peeling of the chain and hybridization of the probe, the same discussion as the already reported DNA strand exchange reaction is possible. Therefore, photocrosslinking rate is considered as an important property for photocrosslinking of RNAs forming higher order structures.…”

Section: Figurementioning

confidence: 95%

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Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking

Fujimoto

Yang‐Chun

Nakamura

2019

Chemistry An Asian Journal

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We have reported the photochemical regulation of the intracellular antisense effect of antisense probes containing ap hoto-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 dependento nt he photocrosslinking rate of 3-cyanovinylcarbazole with d-threoninol ( CNV D), CNV K, or psoralen. The ultrafast RNA photocrosslinking induced the formation of at hermally irreversible covalent bond between pcASOs andt he 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 Do r CNV Kt argeted the RNAs with secondary structures.T hese results indicatet he regulatory effect of photocrosslinker and photoirradiation energy using pcASOs on the gene expression level.[a] Prof.

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Section: Figurementioning

confidence: 75%

Section: Figurementioning

confidence: 95%

Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking

Fujimoto

Yang‐Chun

Nakamura

2019

Chemistry An Asian Journal

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“… 109 C NVK also was shown to accelerate in vitro DNA strand displacement reactions, which may be employed for rapid-response DNA nano device technology using higher-order DNA structures. 117 …”

Section: Photochemical Modifications For Dna/rna Oligonucleotidesmentioning

confidence: 99%

Photochemical modifications for DNA/RNA oligonucleotides

Tavakoli

Min

2022

RSC Adv.

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“…This group recently utilized the CNV K modification to achieve accelerated strand displacement. [ 41 ] A fluorophore‐labeled template strand featuring a toehold was hybridized to a quencher‐labeled “passenger” strand. In the presence of an invader strand that is complementary to the toehold region, the passenger strand was released and fluorescence was restored.…”

Section: Photoinduced Aptamer Switchingmentioning

confidence: 99%

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

et al. 2020

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specific and strong recognition of molecular targets (i.e., aptamers), catalyze biochemical reactions (i.e., ribozymes), or form sophisticated and dynamic "smart materials" or even 3D constructs (i.e., DNA origami). [2] There is particular interest in the use of nucleic acids for the construction of molecular switches, which undergo a function-altering structural change in response to an external stimulus. [3] Many such examples exist in nature, where switches enable organisms to sense physiological changes and selectively control biological functions in response. For example, riboswitches exist naturally as domains within messenger RNA (mRNA) transcripts that can bind to specific metabolites with high specificity in order to stabilize a secondary structure that prevents subsequent translation. [4] Synthetic, engineered molecular switches based on nucleic acids can achieve even greater diversity of function. Such designs make use of aptamersnucleic acid-based affinity reagents isolated via an in vitro process of systematic evolution by exponential enrichment (SELEX), in which DNA or RNA sequences with specific ligand binding are isolated from a large pool of random sequences. [5] Aptamers have proven to be robust recognition elements due to their thermal stability, ease of synthesis, and capacity to undergo ready modification with a broad array of functional groups. Importantly, traditional selection methods can be expanded upon by innovative engineering techniques to enable the incorporation of additional functions that further extend the utility of aptamers. Aptamers can adopt various 2-and 3-D structures such as duplexes, hairpins, and G-quadruplexes, and the inducible formation and disruption of these configurations can be exploited to enable complex functions besides simple biosensing. Consequently, aptamers have been incorporated into many intricate configurations, such as logic gates and dynamic nanomachines. Various research groups have also described aptamer-based switches that undergo conformational changes in response to triggers such as shifts in pH, stimulation with light, or the presence of a specific ligand. [6] Although still a relatively young area of research, these efforts could prove highly useful for materials research-conferring even greater and more selective control over devices based on functionalized nucleic acids. Aptamers are becoming increasingly integrated with various organic and inorganic molecules in order to control the assembly and operation of novel functional Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" ...

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Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo‐crosslinking

Cited by 18 publications

References 36 publications

Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking

Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking

Photochemical modifications for DNA/RNA oligonucleotides

Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

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