scholarly journals Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes

2020 ◽  
Vol 10 (12) ◽  
pp. 4133
Author(s):  
Chun-xia Wang ◽  
Yusuke Sato ◽  
Takashi Sugimoto ◽  
Norio Teramae ◽  
Seiichi Nishizawa
Keyword(s):  
Nucleic Acid ◽  
Sequence Analysis ◽  
Fluorescent Probes ◽  
Dna Duplexes ◽  
Thiazole Orange ◽  
Fluorescence Sensing ◽  
Binding Selectivity ◽  
Target Dna ◽  
Fluorescence Signaling ◽  
Ap Site

Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.

scholarly journals Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification

BIOspektrum ◽  
2020 ◽  
Vol 26 (6) ◽  
pp. 624-627
Author(s):  
Ole Behrmann ◽  
Iris Bachmann ◽  
Frank Hufert ◽  
Gregory Dame
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Dna Polymerase ◽  
Fluorescent Probes ◽  
Reverse Transcription ◽  
Nucleic Acid Detection ◽  
Detection Scheme ◽  
Recombination Proteins ◽  
Target Dna ◽  
Rapid Amplification

Abstract The COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.

Synthetic fluorescent probes capable of selective recognition of 3′-overhanging nucleotides for siRNA delivery imaging

2015 ◽  
Vol 51 (8) ◽  
pp. 1421-1424 ◽  
Author(s):  
Takaya Sato ◽  
Yusuke Sato ◽  
Kenta Iwai ◽  
Shusuke Kuge ◽  
Seiichi Nishizawa ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Fluorescent Probes ◽  
Peptide Nucleic Acid ◽  
Sirna Delivery ◽  
Selective Recognition ◽  
Thiazole Orange ◽  
Accurate Analysis

Peptide nucleic acid (PNA)–thiazole orange (TO) conjugates are developed as fluorescent probes capable of selective recognition of 3′-overhanging nucleotides of siRNAs for an accurate analysis of the siRNA delivery process.

Nucleic acid & protein electrophoresis v1

2021 ◽  
Author(s):  
Shuning Guo
Keyword(s):  
Nucleic Acid ◽  
Protein Electrophoresis ◽  
Target Dna

This protocol concludes two types of the electrophoresis used to detect target DNA or protein.

scholarly journals Metal-mediated base pairs in parallel-stranded DNA

2017 ◽  
Vol 13 ◽  
pp. 2671-2681 ◽  
Author(s):  
Jens Müller
Keyword(s):  
Nucleic Acid ◽  
Complex Formation ◽  
Transition Metal Ions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Experimental Conditions ◽  
Site Specific ◽  
Glycosidic Bonds ◽  
Double Helices ◽  
Significant Extension

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

scholarly journals Effect of an alkyl amino group on the binding of 1,8-naphthyridines to AP site-containing DNA duplexes

2008 ◽  
Vol 52 (1) ◽  
pp. 117-118 ◽  
Author(s):  
T. Ichihashi ◽  
Y. Sato ◽  
T. Seino ◽  
S. Nishizawa ◽  
N. Teramae
Keyword(s):  
Amino Group ◽  
Dna Duplexes ◽  
Ap Site

scholarly journals Low Molecular Weight Fluorescent Probes (LMFPs) to Detect the Group 12 Metal Triad

Chemosensors ◽  
2019 ◽  
Vol 7 (2) ◽  
pp. 22 ◽  
Author(s):  
Ashley D. Johnson ◽  
Rose M. Curtis ◽  
Karl J. Wallace
Keyword(s):  
Molecular Weight ◽  
Metal Ions ◽  
21St Century ◽  
Fluorescent Probes ◽  
Environmental Applications ◽  
Chemical Characteristics ◽  
Low Molecular Weight ◽  
Fluorescence Sensing ◽  
Similar Chemical ◽  
Group 12

Fluorescence sensing, of d-block elements such as Cu2+, Fe3+, Fe2+, Cd2+, Hg2+, and Zn2+ has significantly increased since the beginning of the 21st century. These particular metal ions play essential roles in biological, industrial, and environmental applications, therefore, there has been a drive to measure, detect, and remediate these metal ions. We have chosen to highlight the low molecular weight fluorescent probes (LMFPs) that undergo an optical response upon coordination with the group 12 triad (Zn2+, Cd2+, and Hg2+), as these metals have similar chemical characteristics but behave differently in the environment.

Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA

2020 ◽  
Vol 3 (5) ◽  
pp. 2643-2650 ◽  
Author(s):  
Lingling Zhang ◽  
Xiangjun Liu ◽  
Shanshan Lu ◽  
Jing Liu ◽  
Shilong Zhong ◽  
...  
Keyword(s):  
Fluorescent Probes ◽  
Thiazole Orange ◽  
Quadruplex Dna ◽  
G Quadruplex
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