Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

Abstract

SummaryDNA or its analogues with an environment-sensitive fluorescent label are potentially useful as a probe for studying the structure and dynamics of nucleic acids. In this work, pyrrolidinyl peptide nucleic acid (acpcPNA) was labeled at its backbone with Nile red, a solvatochromic benzophenoxazine dye, by means of click chemistry. The optical properties of the Nile red-labeled acpcPNA were investigated by UV–vis and fluorescence spectroscopy in the absence and in the presence of DNA. In contrast to the usual quenching observed in Nile red-labeled DNA, the hybridization with DNA resulted in blue shifting and an enhanced fluorescence regardless of the neighboring bases. More pronounced blue shifts and fluorescence enhancements were observed when the DNA target carried a base insertion in close proximity to the Nile red label. The results indicate that the Nile red label is located in a more hydrophobic environment in acpcPNA–DNA duplexes than in the single-stranded acpcPNA. The different fluorescence properties of the acpcPNA hybrids of complementary DNA and DNA carrying a base insertion are suggestive of different interactions between the Nile red label and the duplexes.

Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids

“…(i) The first strand displacements of 7mer DNA1 by 10mer DNA2 or DNA4 take place relatively fast (within 5 minutes). 17 Especially the dye attachment in the hybrid PNA1-DNA4 causes less destabilizing effects and gives a T m of >90°C. This can be explained by the increasing affinity of acpcPNA to longer DNA pieces during the strand displacements and the exceptionally high stability of acpcPNA-DNA hybrids in general.…”

“…5,6 Among several of those PNA architectures reported to date, and especially among those with cyclic structures as part of the backbone, 7-9 the so-called acpcPNA system ( Fig. The sequence selectivity can be visualized by fluorescent dyes such as pyrene, 14,15 thiazole orange 16 and nile red, 17 that were synthetically incorporated into acpcPNA. The peptide backbone consists of 4′-substituted proline units with (2′R,4′R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)carboxylic acids.…”

Nile Red and Nile Blue: Applications and Syntheses of Structural Analogues

“…Vilaivan et al. used click chemistry to conjugate a Nile red label to pyrrolidinyl peptide nucleic acid (PNA) . This was done in order to probe the local environment of PNA–DNA duplexes by utilizing Nile red's solvatochromic properties.…”

Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology

“…The specificity has been increased by enzymatic digestion with S1 nuclease resulting in a strong fluorescence enhancement (9-60-fold) with complementary DNA and resulting in a less fluorescence enhancement nearly 3.5-fold with mismatched DNA (Ditmangklo et al, 2013). In addition to thiazole orange, the other labels, like fluorine (Englund & Appella, 2005), pyrene (Boonlua et al, 2014), diaminocarbazole label (Dangsopon et al, 2016), and the Nile red (Yotapan et al, 2014), have been used as a potential candidate in the discovery of single-labeled fluorogenic…”