Photoremovable Protecting Groups in Organic Synthesis

Pillai, V. N. Rajasekharan

doi:10.1055/s-1980-28908

Cited by 287 publications

(33 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2, panels 2). Near-UV light absorption by the aromatic 2-nitrobenzyl linker causes reduction of the 2-nitro group to a nitroso group and an oxygen insertion into the carbon-hydrogen bond followed by cleavage and decarboxylation (20). As can be seen from Fig.…”

Section: Resultsmentioning

confidence: 92%

Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides

Seo

Bai

Kim

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

120

View full text Add to dashboard Cite

; R6G, 6-carboxyrhodamine-6G). Each nucleotide analogue consists of a different fluorophore attached to the 5 position of the pyrimidines and the 7 position of the purines through a photocleavable 2-nitrobenzyl linker. After verifying that these nucleotides could be successfully incorporated into a growing DNA strand in a solutionphase polymerase reaction and the fluorophore could be cleaved using laser irradiation (Ϸ355 nm) in 10 sec, we then performed an SBS reaction on a chip that contains a self-priming DNA template covalently immobilized by using 1,3-dipolar azide-alkyne cycloaddition. The DNA template was produced by PCR, using an azidolabeled primer, and the self-priming moiety was attached to the immobilized DNA template by enzymatic ligation. Each cycle of SBS consists of the incorporation of the photocleavable fluorescent nucleotide into the DNA, detection of the fluorescent signal, and photocleavage of the fluorophore. The entire process was repeated to identify 12 continuous bases in the DNA template. These results demonstrate that photocleavable fluorescent nucleotide analogues can be incorporated accurately into a growing DNA strand during a polymerase reaction in solution and on a chip. Moreover, all four fluorophores can be detected and then efficiently cleaved using near-UV irradiation, thereby allowing continuous identification of the DNA template sequence. Optimization of the steps involved in this SBS approach will further increase the read-length. 2-nitrobenzyl linkerNA sequencing is a fundamental tool for biological science. The completion of the Human Genome Project has set the stage for screening genetic mutations to identify disease genes on a genome-wide scale (1). Accurate high-throughput DNA sequencing methods are needed to explore the complete human genome sequence for applications in clinical medicine and health care. Recent studies have indicated that an important route for identifying functional elements in the human genome involves sequencing the genomes of many species representing a wide sampling of the evolutionary tree (2). To overcome the limitations of the current electrophoresis-based sequencing technology (3-5), a variety of new DNA sequencing methods have been investigated. Such approaches include sequencing by hybridization (6), MS-based sequencing (7-9), and sequence-specific detection of single-stranded DNA by using engineered nanopores (10). More recently, DNA sequencing by synthesis (SBS) approaches such as pyrosequencing (11), sequencing of single DNA molecules (12), and polymerase colonies (13) have been widely explored.The concept of DNA SBS was revealed in 1988 (14). This approach involves detection of the identity of each nucleotide immediately after its incorporation into a growing strand of DNA in a polymerase reaction. Thus far, no complete success has been reported in using such a system to sequence DNA unambiguously. We proposed an SBS approach using photocleavable fluorescent nucleotide analogues on a surface in 2000 (15). In this approach, modified nucle...

show abstract

Section: Resultsmentioning

confidence: 92%

Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides

Seo

Bai

Kim

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

120

View full text Add to dashboard Cite

show abstract

“…It has to be considered that the isomerization rates and final conversions of the chromophores obtained by FT‐IR studies do not allow a direct correlation with network degradation and formation of soluble products. Previous work has demonstrated that covalent links are reformed in o ‐NBE networks by the formation of photodimerized byproducts such as azobenzene derivatives …”

Section: Resultsmentioning

confidence: 99%

Dual‐Responsive Polydimethylsiloxane Networks

Giebler

Radl

Ast

et al. 2018

J. Polym. Sci. Part A: Polym. Chem.

View full text Add to dashboard Cite

Exploiting the salient features of o‐nitrobenzyl chemistry, this work aims at the preparation of polydimethylsiloxane networks that undergo well‐defined bond cleavage in response to either UV light or different pH values as external trigger. Polydimethylsiloxane (PDMS) oligomers with terminal anhydride groups are thermally crosslinked in the presence of a bi‐functional epoxy monomer containing a photolabile o‐nitrobenzyl ester (o‐NBE) group. The susceptibility of the ester groups toward hydrolytic cleavage reactions is used for a pH‐triggered network degradation. Sol–gel analysis confirms that the degradation time can be easily controlled by the base concentration over different time scales varying between hours and weeks. Along with classical ester hydrolysis, photoinduced degradation of the elastomeric networks is carried out by photoisomerization and cleavage of the o‐NBE links upon exposure with UV light. Positive‐tone patterns with a structure size of 100 μm are obtained by photolithographic techniques confirming the spatial control of solubility properties. However, by increasing the exposure dose, recrosslinking of the networks is observed due to side reactions of the primary photocleavage products. As the reformed crosslinks are less sensitive to ester hydrolysis, the side reactions are employed to inscribe negative‐tone microstructures in the PDMS network. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2018, 56, 2319–2329

show abstract

“…Photolabile protecting (caging) groups that can be cleaved after light absorption have recently proved attractive in various fields of Chemistry and Biology 1–13. In particular, caged molecules have been already used to study the dynamics of several biological processes with high spatio‐temporal resolution 4–12.…”

Section: Introductionmentioning

confidence: 99%

Coumarinylmethyl Caging Groups with Redshifted Absorption

Fournier

Aujard

Saux

et al. 2013

Chemistry A European J

118

145

View full text Add to dashboard Cite

The small and synthetically easily accessible coumarinylmethyl backbone has been modified to generate a family of photolabile protecting groups with redshifted absorption. We relied on introducing electron‐donating groups in the 7 position and electron‐withdrawing groups in the 2‐, and 2‐ and 3 positions. In particular, we showed that the diethylamino‐thiocoumarylmethyl and the diethylamino‐coumarylidenemalononitrilemethyl are relevant for uncaging with cyan light. They both exhibit a significant action cross section for uncaging in the 470–500 nm wavelength range and a low light absorption between 350 and 400 nm. These attractive features are favorable to perform chromatic orthogonal photoactivation with UV and blue‐cyan light sources, respectively.

show abstract

Photoremovable Protecting Groups in Organic Synthesis

Cited by 287 publications

References 0 publications

Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides

Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides

Dual‐Responsive Polydimethylsiloxane Networks

Coumarinylmethyl Caging Groups with Redshifted Absorption

Contact Info

Product

Resources

About