scholarly journals Electrochemical Capacitance DNA Sensing at Hairpin-Modified Au Electrodes

2011 ◽  
Vol 2011 ◽  
pp. 1-6 ◽  
Author(s):  
Joel Rivera-Gandía ◽  
Maria del Mar Maldonado ◽  
Yarimar De La Torre-Meléndez ◽  
Edwin O. Ortiz-Quiles ◽  
Nella M. Vargas-Barbosa ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Surface Coverage ◽  
Large Change ◽  
Electrochemical Technique ◽  
Capacitance Measurement ◽  
Dna Hairpin ◽  
Electrochemical Capacitance ◽  
Dna Hairpins ◽  
Hairpin Probes ◽  
Interfacial Capacitance

An interfacial capacitance measurement electrochemical technique has been used for the sensing of self-assembled DNA hairpin probes (M. tuberculosisandB. anthracis) attached to Au electrodes. The double-layer capacitance (Cdl) was determined with electrochemical perturbations from 0.2 V to 0.5 V versus Ag/AgCl at a Au/M. tuberculosisDNA hairpin probe at surface coverage Au electrodes. The capacitance study was done at pH 7, which was necessary to maintain theM. tuberculosis and B. anthracisDNA probes closed during the electrochemical perturbation. Detailed experimental analysis carried out by repetitively switching the electrochemical potential between 0.2 and 0.5 V (versus Ag/AgCl) strongly supports the use of capacitance measurements as a tool to detect the hybridization of DNA targets. A large change in the capacitance deference between 0.2 and 0.5 V was observed in the DNA hybridization process. Therefore, no fluorophores or secondary transducers were necessary to sense a DNA target for both DNA hairpins.

Monitoring DNA hybridization on alkyl modified silicon surface through capacitance measurement

2003 ◽  
Vol 18 (9) ◽  
pp. 1157-1163 ◽  
Author(s):  
Fang Wei ◽  
Bin Sun ◽  
Yuan Guo ◽  
Xin Sheng Zhao
Keyword(s):  
Dna Hybridization ◽  
Silicon Surface ◽  
Capacitance Measurement

scholarly journals The Role of DNA-PKcs and Artemis in Opening Viral DNA Hairpin Termini in Various Tissues in Mice

2007 ◽  
Vol 81 (20) ◽  
pp. 11304-11321 ◽  
Author(s):  
Katsuya Inagaki ◽  
Congrong Ma ◽  
Theresa A. Storm ◽  
Mark A. Kay ◽  
Hiroyuki Nakai
Keyword(s):  
Dna Repair ◽  
Inverted Terminal Repeat ◽  
Dependent Manner ◽  
Dna Hairpin ◽  
Dna Hairpins ◽  
Alternative Pathways ◽  
Hairpin Loops ◽  
Dependent Protein ◽  
Significant Pathway ◽  
Cellular Dna

ABSTRACT A subset of cellular DNA hairpins at double-strand breaks is processed by DNA-dependent protein kinase catalytic subunit (DNA-PKcs)- and Artemis-associated endonuclease. DNA hairpin termini of adeno-associated virus (AAV) are processed by DNA repair machinery; however, how and what cellular factors are involved in the process remain elusive. Here, we show that DNA-PKcs and Artemis open AAV inverted terminal repeat (ITR) hairpin loops in a tissue-dependent manner. We investigated recombinant AAV (rAAV) genome metabolism in various tissues of DNA-PKcs- or Artemis-proficient or -deficient mice. In the absence of either factor, ITR hairpin opening was impaired, resulting in accumulation of double-stranded linear rAAV genomes capped with covalently closed hairpins at termini. The 5′ end of 3-base hairpin loops of the ITR was the primary target for DNA-PKcs- and Artemis-mediated cleavage. In the muscle, heart, and kidney, DNA-PKcs- and Artemis-dependent hairpin opening constituted a significant pathway, while in the liver, undefined alternative pathways effectively processed hairpins. In addition, our study revealed a Holliday junction resolvase-like activity in the liver that cleaved T-shaped ITR hairpin shoulders by making nicks at diametrically opposed sites. Thus, our approach furthers our understanding of not only rAAV biology but also fundamental DNA repair systems in various tissues of living animals.

scholarly journals Disturbance of the Conformation of DNA Hairpin Containing the 5′-GT-3′ Binding Site Caused by Zn(II)bleomycin-A5 Studied through NMR Spectroscopy

2019 ◽  
Vol 5 (3) ◽  
pp. 52
Author(s):  
Covington ◽  
Lehmann
Keyword(s):  
Binding Site ◽  
Dna Cleavage ◽  
Chemical Structure ◽  
Structural Changes ◽  
Wide Spectrum ◽  
Undesirable Side Effect ◽  
Dna Hairpin ◽  
Site Specific ◽  
Dna Hairpins ◽  
Biochemical Studies

The antibiotics known as bleomycins constitute a family of natural products clinically employed for the treatment of a wide spectrum of cancers. These antibiotics have the ability to chelate a metal center, most commonly Fe(II), and cause site-specific DNA cleavage upon oxidation. Bleomycin therapy is a successful course of treatment for some types of cancers. However, the risk of pulmonary fibrosis as an undesirable side effect, limits the use of the antibiotics in cancer chemotherapy. Bleomycins are differentiated by their C-terminal, or tail, regions, which have been shown to closely interact with DNA. Pulmonary toxicity has been correlated to the chemical structure of the bleomycin C-termini through biochemical studies performed in mice. In the present study, we examined the binding of Zn(II)Bleomycin-A5 to a DNA hairpin of sequence 5′-CCAGTATTTTTACTGG-3′, containing the 5′-GT-3′ binding site. The results were compared to those from a previous study that examined the binding of Zn(II)Bleomycin-A2 and Zn(II)Peplomycin to the same DNA hairpin. We provide evidence that, as shown for DNA hairpins containing the 5′-GC-3′ binding site, Zn(II)BLM-A5 causes the most significant structural changes to the oligonucleotide.

scholarly journals An Exonuclease I-Based Quencher-Free Fluorescent Method Using DNA Hairpin Probes for Rapid Detection of MicroRNA

Sensors ◽  
2017 ◽  
Vol 17 (4) ◽  
pp. 760 ◽  
Author(s):  
Changbei Ma ◽  
Haisheng Liu ◽  
Kefeng Wu ◽  
Mingjian Chen ◽  
Liyang Zheng ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Dna Hairpin ◽  
Exonuclease I ◽  
Fluorescent Method ◽  
Hairpin Probes

scholarly journals Quantifying Tensile Forces at Cell–Cell Junctions with a DNA-based Fluorescent Probe

2020 ◽  
Author(s):  
Bin Zhao ◽  
Ningwei Li ◽  
Tianfa Xie ◽  
Chungwen Liang ◽  
Yousef Bagheri ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Cell Junctions ◽  
Fluorescence Signal ◽  
Dna Hairpin ◽  
Dna Hairpins ◽  
Cell Behaviors ◽  
Tensile Forces ◽  
Precise Quantification ◽  
E Cadherin ◽  
Cell Cell

SUMMARYCells are physically contacting with each other. Direct and precise quantification of forces at cell–cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces. These lipid-modified DNAMeters can spontaneously anchor onto live cell membranes. The DNAMeter consists of two self-assembled DNA hairpins of different force tolerance. Once the intercellular tension exceeds the force tolerance to unfold a DNA hairpin, a specific fluorescence signal will be activated, which enables the real-time imaging and quantification of tensile forces. Using E-cadherin-modified DNAMeter as an example, we have demonstrated an approach to quantify, at the molecular level, the magnitude and distribution of E-cadherin tension among epithelial cells. Compatible with readily accessible fluorescence microscopes, these easy-to-use DNA tension probes can be broadly used to quantify mechanotransduction in collective cell behaviors.

Identification of high-stringency DNA hairpin probes by partial gene folding

2007 ◽  
Vol 23 (2) ◽  
pp. 233-240 ◽  
Author(s):  
Christopher M. Strohsahl ◽  
Todd D. Krauss ◽  
Benjamin L. Miller
Keyword(s):  
Dna Hairpin ◽  
Hairpin Probes ◽  
High Stringency

scholarly journals Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins

2017 ◽  
Vol 19 (1) ◽  
pp. 015006 ◽  
Author(s):  
Hieu Bui ◽  
Sudhanshu Garg ◽  
Vincent Miao ◽  
Tianqi Song ◽  
Reem Mokhtar ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Dna Hairpins ◽  
Linear Cascade ◽  
Chain Reactions

Single-molecule kinetic studies of DNA hybridization under extreme pressures

2020 ◽  
Vol 22 (41) ◽  
pp. 23491-23501
Author(s):  
Hsuan-Lei Sung ◽  
David J. Nesbitt
Keyword(s):  
Single Molecule ◽  
Dna Hybridization ◽  
Kinetic Studies ◽  
Dna Hairpin ◽  
Single Molecule Level

Pressure-responsive dynamics of DNA hairpin hybridization/dehybridization is directly visualized at the single molecule level.

scholarly journals SOME THERMODYNAMIC PROPERTIES OF HYDROCARBONS ADSORBED ON RUTILE

1954 ◽  
Vol 32 (9) ◽  
pp. 842-857 ◽  
Author(s):  
H. P. Schreiber ◽  
R. McIntosh
Keyword(s):  
Phase Transition ◽  
Low Temperature ◽  
Thermodynamic Properties ◽  
Surface Coverage ◽  
Large Change ◽  
Maximum Error ◽  
Reliable Data ◽  
Experimental Techniques ◽  
Heats Of Adsorption ◽  
Temperature Ranges

Differential thermodynamic properties of methane, ethane, propane, and n-butane adsorbed on rutile have been determined from isotherms over appreciable temperature ranges. Ordinary experimental techniques failed to yield reliable data in low temperature and surface coverage regions, but essentially simple modifications of these resulted in accurate thermodynamic values. For methane, the results compared well with similar ones computed by Pace, Heric, and Dennis from data obtained by means of calorimetry. Maximum error in isosteric heats of adsorption was 60 cal. mole−1; in differential molar entropies 0.8 cal. mole−1 degree−1. The thermodynamic properties of methane and ethane are similar but there is a departure in the set pattern for propane. A large change was observed in the heat of adsorption of propane, near 185° K. and surface coverages lower than 0.6 of the monolayer. A phase transition is suggested to account for this occurrence.

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