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

ABSTRACT: DNA 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.

SUBMITTER: Yotapan N

PROVIDER: S-EPMC4168962 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Yotapan Nattawut N Charoenpakdee Chayan C Wathanathavorn Pawinee P Ditmangklo Boonsong B Wagenknecht Hans-Achim HA Vilaivan Tirayut T

Beilstein journal of organic chemistry 20140911

DNA 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 ...[more]

PMID: 25246975

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Project description:The development of simple fluorescent and colorimetric assays that enable point-of-care DNA and RNA detection has been a topic of significant research because of the utility of such assays in resource limited settings. The most common motifs utilize hybridization to a complementary detection strand coupled with a sensitive reporter molecule. Here, a paper-based colorimetric assay for DNA detection based on pyrrolidinyl peptide nucleic acid (acpcPNA)-induced nanoparticle aggregation is reported as an alternative to traditional colorimetric approaches. PNA probes are an attractive alternative to DNA and RNA probes because they are chemically and biologically stable, easily synthesized, and hybridize efficiently with the complementary DNA strands. The acpcPNA probe contains a single positive charge from the lysine at C-terminus and causes aggregation of citrate anion-stabilized silver nanoparticles (AgNPs) in the absence of complementary DNA. In the presence of target DNA, formation of the anionic DNA-acpcPNA duplex results in dispersion of the AgNPs as a result of electrostatic repulsion, giving rise to a detectable color change. Factors affecting the sensitivity and selectivity of this assay were investigated, including ionic strength, AgNP concentration, PNA concentration, and DNA strand mismatches. The method was used for screening of synthetic Middle East respiratory syndrome coronavirus (MERS-CoV), Mycobacterium tuberculosis (MTB), and human papillomavirus (HPV) DNA based on a colorimetric paper-based analytical device developed using the aforementioned principle. The oligonucleotide targets were detected by measuring the color change of AgNPs, giving detection limits of 1.53 (MERS-CoV), 1.27 (MTB), and 1.03 nM (HPV). The acpcPNA probe exhibited high selectivity for the complementary oligonucleotides over single-base-mismatch, two-base-mismatch, and noncomplementary DNA targets. The proposed paper-based colorimetric DNA sensor has potential to be an alternative approach for simple, rapid, sensitive, and selective DNA detection.

Project description:The impact of optical berry sorting was investigated using Grenache, Barbera, and Cabernet Sauvignon grapes from Yolo County, California in 2016. Optical sorting parameters were adjusted to remove underripe berries and material other than grapes using color parameters. Wines were made from three treatments, control (no sorting), sort (accepted material), and reject (material rejected by the optical sorter). The rate of rejection was approximately 14.9%, 3.9%, and 1.5% (w/w) for Grenache, Barbera, and Cabernet Sauvignon, respectively. Chemical composition in the finished wines was analyzed by the Adams-Harbertson assay and reversed-phase high-performance liquid chromatography for phenolics, and head-space solid-phase microextraction gas chromatography mass spectrometry for aroma profiling. In general, optical sorting was successful in removing underripe berries and material other than grapes as evidenced by lower ethanol levels and higher concentrations of total phenolics and tannin (due to the inclusion of material other than grapes) in wine made from rejected material. Despite this, no difference in final ethanol content and minimal differences in phenolic composition were observed between control and sort treatment wines for the three varieties studied. Differences were observed in the aroma profiles of the reject treatments for all three varieties compared to sort and control; however, few compounds differed significantly between the sort and control treatments. Descriptive sensory analysis revealed that panelists had difficulty distinguishing aroma, taste, mouthfeel, and color parameters among wines made from different treatments for all three varieties. Thus, optical sorting had minimal impact on wine sensory properties using the varieties and vineyards studied. Optical sorting may be used to differentiate and sort for different ripeness levels using color as a primary criterion; however, the impact on the resulting wine is likely dependent on the initial variability in grape ripeness.

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

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

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