Light-activatable molecular beacons with a caged loop sequence

Joshi, Khashti Ballabh; Vlachos, Andreas; Mikat, Vera; Deller, Thomas; Heckel, Alexander

doi:10.1039/c2cc16654b

Cited by 43 publications

(46 citation statements)

References 26 publications

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“…Two approaches exist for this up to now (Figure 7): Tan and co‐workers showed that such an effect can be realized by connecting the two ends of a molecular beacon through a photocleavable linker 180. In our study we demonstrated that the effect can be improved to an almost binary ON/OFF behavior if the nucleobases in the loop region are caged with multiple cages which could still be removed efficiently 181. Abe, Ito, and co‐workers showed that a similar effect is possible when using an oligonucleotide with a caged fluorophore 182.…”

Section: Irreversible Photo(de)activation (Uncaging)mentioning

confidence: 64%

Light‐Controlled Tools

et al. 2012

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Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.

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Section: Irreversible Photo(de)activation (Uncaging)mentioning

confidence: 64%

Light‐Controlled Tools

et al. 2012

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“…A pulse of light, however, cleaved a photosensitive linker, thus forcing the MB probe to report the presence of the analyte. Another example of a light-activatable MB probe was reported by Joshi et al [138]. In their design, the loop sequence was equipped with caged nucleotides that could not form Watson-Crick base pairs.…”

Section: Recent Variations Of Mb Probesmentioning

confidence: 99%

An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Kolpashchikov

2012

Scientifica

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Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

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“…Irradiation of caged compounds, which releases the protected specic functional groups, has been employed to locally control biochemical properties of hydrogels. [49][50][51][52] Hydrogels will be degraded when irradiated with cytocompatible doses of long wavelength UV, visible, or two-photon IR light (365, 405, and 740 nm, respectively), enabling precise control over hydrogel degradation proles in situ. 53 This photodegradation scheme was successfully applied to control the spreading of human mesenchymal stem cell (hMSC) within light-eroded channels.…”

Section: Introductionmentioning

confidence: 99%