Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

Charoenpakdee, Chayan; Vilaivan, Tirayut

doi:10.1039/d0ob01299h

Cited by 6 publications

(6 citation statements)

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“…The fluorescence change was induced by the hybridization between the PNA probe and the DNA target that alters the environment of the dye. 134,276,277 Alternatively, a simple fluorophore-labeled PNA probe was used in combination with a quencher which can be present on the same PNA strand 166 or as a separate entity such as another quencher labeled PNA or DNA strand, 278 oligo(dG), 279 graphene oxide (GO), 280 and metal nanoparticles. 281 In all cases, the fluorescence of the free probe could be restored after hybridization with the correct DNA/RNA target which resulted in the separation of the probe and the quencher.…”

Section: Modified Pna For Nucleic Acid Biosensing and Bioimagingmentioning

confidence: 99%

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Suparpprom

Vilaivan

2022

RSC Chem. Biol.

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Section: Modified Pna For Nucleic Acid Biosensing and Bioimagingmentioning

confidence: 99%

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Suparpprom

Vilaivan

2022

RSC Chem. Biol.

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“…Since electrostatic effects play a vital role in the association of DNA/PNA and GO, we postulated that additional stabilizing interaction might be achieved by engineering the number of positive charges on the PNA probe to provide further attractive forces. 51 We began by investigating the ability of GO nanocolloids to quench various charge-modified 10mer FAM-labeled acpcPNA strands in comparison with FAM-labeled DNA. The data in Figure 1A show that the quenching efficiency depends on the number of positive charges on the PNA probes.…”

Section: Effect Of Charge Modification On the Acpcpnamentioning

confidence: 99%

Enhancing Peptide Nucleic Acid–Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Faikhruea

Choopara

Somboonna

et al. 2022

ACS Appl. Bio Mater.

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Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dyelabeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO-and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA−nanomaterial interactions, which paves the way toward improving the performance of PNA−nanomaterial based assays of nucleic acids.

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“…Recently, a fabrication of paper-based colorimetric DNA biosensors to detect MERS-CoV, mycobacterium tuberculosis (MTB), and human papillomavirus (HPV) DNA [ 99 ] was developed using pyrrolidinyl peptide nucleic acid (acpcPNA) as a probe. The acpcPNA probe has a single positive charge from the lysine at the C-terminus to induce the aggregation of nanoparticles [ 100 ]. The citrate anion-stabilized AgNPs were used as a colorimetric agent in this study.…”

Section: The Development Of Optical and Electrochemical Metal Nanoparticles-based Biosensors For The Detection Of Viral Rnamentioning

confidence: 99%

A Review on the Development of Gold and Silver Nanoparticles-Based Biosensor as a Detection Strategy of Emerging and Pathogenic RNA Virus

Ibrahim

Jamaluddin

Tan

et al. 2021

Sensors

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The emergence of highly pathogenic and deadly human coronaviruses, namely SARS-CoV and MERS-CoV within the past two decades and currently SARS-CoV-2, have resulted in millions of human death across the world. In addition, other human viral diseases, such as mosquito borne-viral diseases and blood-borne viruses, also contribute to a higher risk of death in severe cases. To date, there is no specific drug or medicine available to cure these human viral diseases. Therefore, the early and rapid detection without compromising the test accuracy is required in order to provide a suitable treatment for the containment of the diseases. Recently, nanomaterials-based biosensors have attracted enormous interest due to their biological activities and unique sensing properties, which enable the detection of analytes such as nucleic acid (DNA or RNA), aptamers, and proteins in clinical samples. In addition, the advances of nanotechnologies also enable the development of miniaturized detection systems for point-of-care (POC) biosensors, which could be a new strategy for detecting human viral diseases. The detection of virus-specific genes by using single-stranded DNA (ssDNA) probes has become a particular interest due to their higher sensitivity and specificity compared to immunological methods based on antibody or antigen for early diagnosis of viral infection. Hence, this review has been developed to provide an overview of the current development of nanoparticles-based biosensors that target pathogenic RNA viruses, toward a robust and effective detection strategy of the existing or newly emerging human viral diseases such as SARS-CoV-2. This review emphasizes the nanoparticles-based biosensors developed using noble metals such as gold (Au) and silver (Ag) by virtue of their powerful characteristics as a signal amplifier or enhancer in the detection of nucleic acid. In addition, this review provides a broad knowledge with respect to several analytical methods involved in the development of nanoparticles-based biosensors for the detection of viral nucleic acid using both optical and electrochemical techniques.

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Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

Abstract: Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we...

Cited by 6 publications

References 64 publications

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Enhancing Peptide Nucleic Acid–Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

A Review on the Development of Gold and Silver Nanoparticles-Based Biosensor as a Detection Strategy of Emerging and Pathogenic RNA Virus

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