5-Amidodansyl-U (UD) Peptide Nucleic Acid (PNA) as a Fluorescent Sensor of the Local Dielectric Constant (ε) in PNA Duplexes: Major Grooves in PNA Duplexes Are More Hydrophobic Than Major Grooves in DNA–DNA Duplexes

2018 ◽  
Vol 122 (25) ◽  
pp. 14004-14013
Author(s):  
Vijay N. Kadam ◽  
Kayarat Saikrishnan ◽  
Krishna N. Ganesh
Keyword(s):  
Dielectric Constant ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Fluorescent Sensor ◽  
Dna Duplexes

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

2014 ◽  
Vol 10 ◽  
pp. 2166-2174 ◽  
Author(s):  
Nattawut Yotapan ◽  
Chayan Charoenpakdee ◽  
Pawinee Wathanathavorn ◽  
Boonsong Ditmangklo ◽  
Hans-Achim Wagenknecht ◽  
...  
Keyword(s):  
Optical Properties ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Nile Red ◽  
Fluorescent Label ◽  
Dna Duplexes ◽  
Enhanced Fluorescence ◽  
Structure And Dynamics ◽  
Close Proximity ◽  
Base Insertion

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.

scholarly journals Label-Free Detection of Zeptomol miRNA via Peptide Nucleic Acid Hybridization Using Novel Cyclic Voltammetry Method

Sensors ◽  
2020 ◽  
Vol 20 (3) ◽  
pp. 836
Author(s):  
Shintaro Takase ◽  
Kouta Miyagawa ◽  
Hisafumi Ikeda
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Microelectrode Array ◽  
Pcr Amplification ◽  
Nucleic Acid Hybridization ◽  
Detection Sensitivity ◽  
Cyclic Voltammograms ◽  
Dna Duplexes ◽  
Label Free ◽  
Label Free Detection

To harness the applicability of microribonucleic acid (miRNA) as a cancer biomarker, the detection sensitivity of serum miRNA needs to be improved. This study evaluated the detection sensitivity of miRNA hybridization using cyclic voltammograms (CVs) and microelectrode array chips modified with peptide nucleic acid (PNA) probes and 6-hydroxy-1-hexanethiol. We investigated the PNA probe modification pattern on array chips using fluorescently labeled cDNA. The pattern was not uniformly spread over the working electrode (WE) and had a one-dimensional swirl-like pattern. Accordingly, we established a new ion-channel sensor model wherein the WE is negatively biased through the conductive π–π stacks of the PNA/DNA duplexes. This paper discusses the mechanism underlying the voltage shift in the CV curves based on the electric double-layer capacitance. Additionally, the novel hybridization evaluation parameter ΔE is introduced. Compared to conventional evaluation using oxidation current changes, ΔE was more sensitive. Using ΔE and a new hybridization system for ultrasmall amounts of aqueous solutions (as low as 35 pL), 140 zeptomol label-free miRNA were detected without polymerase chain reaction (PCR) amplification at an adequate sensitivity. Herein, the differences in the target molar amount and molar concentration are elucidated from the viewpoint of hybridization sensitivity.

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

2015 ◽  
Vol 13 (35) ◽  
pp. 9223-9230 ◽  
Author(s):  
Peggy R. Bohländer ◽  
Tirayut Vilaivan ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acid ◽  
Peptide Nucleic Acids ◽  
Dna Duplexes ◽  
Strand Displacement ◽  
Nucleic Acid Probes ◽  
Double Stranded Dna

Strand displacement and duplex invasion of DNA duplexes by pyrrolidinyl peptide nucleic acid are demonstrated using the concept of wavelength-shifting nucleic acid probes.

Single-Molecule, Real-Time Dissecting of Peptide Nucleic Acid–DNA Duplexes with a Protein Nanopore Tweezer

2018 ◽  
Vol 90 (12) ◽  
pp. 7682-7690 ◽  
Author(s):  
Andrei Ciuca ◽  
Alina Asandei ◽  
Irina Schiopu ◽  
Aurelia Apetrei ◽  
Loredana Mereuta ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Single Molecule ◽  
Peptide Nucleic Acid ◽  
Dna Duplexes

Peptide Nucleic Acid-DNA Duplexes Containing the Universal Base 3-Nitropyrrole

Methods ◽  
2001 ◽  
Vol 23 (2) ◽  
pp. 132-140 ◽  
Author(s):  
By Peiming Zhang ◽  
Michael Egholm ◽  
Natasha Paul ◽  
Maneesh Pingle ◽  
Donald E. Bergstrom
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Dna Duplexes

Correction to Peptide Nucleic Acid (PNA)-DNA Duplexes: Comparison of Hybridization Affinity between Vertically and Horizontally Tethered PNA Probes

2013 ◽  
Vol 5 (15) ◽  
pp. 7659-7659 ◽  
Author(s):  
Arpita De ◽  
Serhiy Souchelnytskyi ◽  
Albert van den Berg ◽  
Edwin T. Carlen
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Dna Duplexes

scholarly journals Peptide nucleic acid-DNA duplexes: Long range hole migration from an internally linked anthraquinone

1997 ◽  
Vol 94 (23) ◽  
pp. 12320-12325 ◽  
Author(s):  
B. Armitage ◽  
D. Ly ◽  
T. Koch ◽  
H. Frydenlund ◽  
H. Orum ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Long Range ◽  
Peptide Nucleic Acid ◽  
Dna Duplexes ◽  
Hole Migration

Peptide Nucleic Acid (PNA)–DNA Duplexes: Comparison of Hybridization Affinity between Vertically and Horizontally Tethered PNA Probes

2013 ◽  
Vol 5 (11) ◽  
pp. 4607-4612 ◽  
Author(s):  
Arpita De ◽  
Serhiy Souchelnytskyi ◽  
Albert van den Berg ◽  
Edwin T. Carlen
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Dna Duplexes

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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