A Lucifer‐Based Environment‐Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. (13th March 2018)

• Record Type: Journal Article
• Authors: Sabale, Pramod M.; Ambi, Uddhav B.; Srivatsan, Seergazhi G.
• Is Part Of: Chembiochem. Volume 19:Number 8(2018)
• Page Start: 826
• Page End: 835
• Publication Date: 2018-03-13
• Subjects: fluorescent probes -- imaging agents -- peptide nucleic acids -- poly(A) RNA -- RNA; Biochemistry -- Periodicals; Molecular biology -- Periodicals; Pharmaceutical chemistry -- Periodicals; 572
• DOI: 10.1002/cbic.201700661
• Languages: English
• ISSNs: 1439-4227

Abstract

Abstract: Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore( 1, 8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them. Abstract : Chasing tails : A PNA oligomer containing a new microenvironment‐sensitive fluorescent PNA base analogue, obtained by attaching the Lucifer chromophore (1, 8‐naphthalimide) at the 5‐position of uracil, serves as a robust imaging tool for cellular poly(A) RNAs.