A selective, inexpensive probe for UV-induced damage in nucleic acids

2013 ◽  
Vol 91 (5) ◽  
pp. 320-325 ◽  
Author(s):  
Amira F. El-Yazbi ◽  
Glen R. Loppnow
Keyword(s):  
Dna Damage ◽  
Nucleic Acids ◽  
Molecular Beacon ◽  
Uv Light ◽  
Lower Sensitivity ◽  
Uv Damage ◽  
Dna Oligonucleotides ◽  
Dna And Rna ◽  
Hairpin Oligonucleotide ◽  
Hypochromic Effect

Absorption of UV light by nucleic acids can result in the formation of molecular lesions in DNA and RNA, leading to mutagenesis, carcinogenesis, and cell death. In this work, hairpin oligonucleotide probes, which have previously been shown to be selective for DNA damage, are used. The hypochromic effect, which arises from the formation of the target–hairpin hybrid when there is no damage, is used to measure the amount of UV damage by measuring the amount of single-stranded DNA oligonucleotides. With accumulated UV exposure, the target–hairpin hybrid concentration decreases and the absorbance increases, enabling detection of UV-induced DNA damage. Our results show that the selectivity for DNA damage of the hypochromism probe is comparable with the molecular beacon probes, detecting between one and three lesions in an oligonucleotide. In addition, this probe is more than 10 times cheaper than molecular beacon probes. However, it shows lower sensitivity to DNA damage. This makes its use recommended for high-throughput, qualitative analysis of DNA damage. This introduces a simple, fast, mix-and-read assay for the detection of DNA damage.

scholarly journals Pulsed Electron Double Resonance in Structural Studies of Spin-Labeled Nucleic Acids

Acta Naturae ◽  
2013 ◽  
Vol 5 (1) ◽  
pp. 9-32 ◽  
Author(s):  
O. S. Fedorova ◽  
Yu. D. Tsvetkov
Keyword(s):  
Dna Damage ◽  
Nucleic Acids ◽  
Double Resonance ◽  
Spatial Structures ◽  
Structural Studies ◽  
Dna And Rna

This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described.

scholarly journals Out in the midday sun: Repair of UV damage in the Archaea

2004 ◽  
Vol 26 (3) ◽  
pp. 26-29
Author(s):  
Shirley McCready ◽  
Lucio Marcello
Keyword(s):  
Dna Damage ◽  
Uv Irradiation ◽  
Uv Light ◽  
Dna Polymerases ◽  
Life Forms ◽  
Uv Damage ◽  
The Earth ◽  
Lethal Damage ◽  
Living Organisms ◽  
Uv Rays

Living organisms have been exposed to the damaging UV rays in sunlight ever since life began on the Earth, a little over 3.5 billion years ago. Indeed, UV levels on the early Earth's surface were significantly higher than they are now. UV light is absorbed by DNA and causes mutagenic and lethal damage, and today's life forms have evolved a range of strategies for surviving UV irradiation. These include protection from UV (e.g. by pigments, such as melanin, that absorb UV), repair of damaged DNA, and ways of surviving when the damage remains unrepaired (e.g. DNA polymerases that bypass DNA damage).

scholarly journals Preferential repair of UV damage in highly transcribed DNA diminishes UV-induced intrachromosomal recombination in mammalian cells

1994 ◽  
Vol 14 (1) ◽  
pp. 391-399
Author(s):  
W P Deng ◽  
J A Nickoloff
Keyword(s):  
Dna Damage ◽  
Mammalian Cells ◽  
Uv Light ◽  
Uv Damage ◽  
Dna Damage And Repair ◽  
Intrachromosomal Recombination ◽  
Dna Damaging Agents ◽  
Mouse Mammary Tumor ◽  
Tumor Virus ◽  
Virus Promoter

The relationships among transcription, recombination, DNA damage, and repair in mammalian cells were investigated. We monitored the effects of transcription on UV-induced intrachromosomal recombination between neomycin repeats including a promoterless allele and an inducible heteroallele regulated by the mouse mammary tumor virus promoter. Although transcription and UV light separately stimulated recombination, increasing transcription levels reduced UV-induced recombination. Preferential repair of UV damage in transcribed strands was shown in highly transcribed DNA, suggesting that recombination is stimulated by unrepaired UV damage and that increased DNA repair in highly transcribed alleles removes recombinogenic lesions. This study indicates that the genetic consequences of DNA damage depend on transcriptional states and provides a basis for understanding tissue- and gene-specific responses to DNA-damaging agents.

From DC polarographic presodium wave of proteins to electrochemistry of biomacromolecules

2009 ◽  
Vol 74 (11-12) ◽  
pp. 1739-1755 ◽  
Author(s):  
Emil Paleček ◽  
Michael Heyrovský ◽  
Bořivoj Janík ◽  
Dušan Kaláb ◽  
Zdeněk Pechan
Keyword(s):  
Dna Damage ◽  
Nucleic Acids ◽  
Dna Hybridization ◽  
Protein Structures ◽  
Constant Current ◽  
Redox States ◽  
Dna And Rna ◽  
History Of ◽  
Protein Research ◽  
Potential Use

History of electrochemistry of proteins and nucleic acids is briefly reviewed. The ability of proteins to catalyze hydrogen evolution at Hg electrodes was discovered almost 80 years ago in J. Heyrovský’s laboratory. This phenomenon was not sufficiently appreciated for several decades. Recently it has been shown that using constant current chronopotentiometric stripping (CPS) with hanging mercury drop, solid amalgam or Hg-film electrodes the CPS peak H is obtained with nanomolar concentrations of peptides and proteins. This peak is derived from the presodium wave but it has some new properties useful in protein research. It is sensitive to changes in protein structures and to protein redox states, representing a new tool for protein analysis applicable in biomedicine. Electroactivity of nucleic acids was discovered about 50 years ago. Electrochemistry of DNA and RNA is now a booming field because of its potential use in sensors for DNA hybridization and DNA damage. Quite recently it has been shown that electrochemistry can be applied also in polysaccharide analysis. A review with 99 references.

scholarly journals Preferential repair of UV damage in highly transcribed DNA diminishes UV-induced intrachromosomal recombination in mammalian cells.

1994 ◽  
Vol 14 (1) ◽  
pp. 391-399 ◽  
Author(s):  
W P Deng ◽  
J A Nickoloff
Keyword(s):  
Dna Damage ◽  
Mammalian Cells ◽  
Uv Light ◽  
Uv Damage ◽  
Dna Damage And Repair ◽  
Intrachromosomal Recombination ◽  
Dna Damaging Agents ◽  
Mouse Mammary Tumor ◽  
Tumor Virus ◽  
Virus Promoter

The relationships among transcription, recombination, DNA damage, and repair in mammalian cells were investigated. We monitored the effects of transcription on UV-induced intrachromosomal recombination between neomycin repeats including a promoterless allele and an inducible heteroallele regulated by the mouse mammary tumor virus promoter. Although transcription and UV light separately stimulated recombination, increasing transcription levels reduced UV-induced recombination. Preferential repair of UV damage in transcribed strands was shown in highly transcribed DNA, suggesting that recombination is stimulated by unrepaired UV damage and that increased DNA repair in highly transcribed alleles removes recombinogenic lesions. This study indicates that the genetic consequences of DNA damage depend on transcriptional states and provides a basis for understanding tissue- and gene-specific responses to DNA-damaging agents.

scholarly journals An Improved 4’-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNA

2020 ◽  
Author(s):  
Kevin Wielenberg ◽  
Miao Wang ◽  
Min Yang ◽  
Abdullah Ozer ◽  
John T. Lis ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Uv Light ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Long Wave ◽  
Genome Wide ◽  
In Cells

AbstractNucleic acid crosslinkers that covalently join commentary strands have applications as both pharmaceuticals and biochemical probes. Psoralen is a popular crosslinker moiety that reacts with double stranded DNA and RNA upon irradiation with long wave UV light. A commercially available compound EZ-Link Psoralen-PEG3-Biotin has been used in many studies to crosslink DNA and double strand RNA for genome-wide investigations. Here we present a novel probe, AP3B, which uses a psoralen derivative, 4’-aminomethyltrioxsalen, to biotinylate nucleic acids. We show that this compound is 8-fold more effective at labeling DNA in cells and several hundred-fold more effective at crosslinking two strands of DNA in vitro than the commercially available compound EZ-Link Psoralen-PEG3-Biotin.

Riboflavin and UV-Light Based Pathogen Reduction: Extent and Consequence of DNA Damage at the Molecular Level

2004 ◽  
Vol 80 (1) ◽  
pp. 15 ◽  
Author(s):  
Vijay Kumar ◽  
Owen Lockerbie ◽  
Shawn D. Keil ◽  
Patrick H. Ruane ◽  
Matthew S. Platz ◽  
...  
Keyword(s):  
Dna Damage ◽  
Molecular Level ◽  
Uv Light ◽  
Pathogen Reduction

scholarly journals Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4247 ◽  
Author(s):  
Rita Petrucci ◽  
Isabella Chiarotto ◽  
Leonardo Mattiello ◽  
Daniele Passeri ◽  
Marco Rossi ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Graphene Oxide ◽  
Nucleic Acids ◽  
Reduced Graphene Oxide ◽  
Electrochemical Sensors ◽  
Enzymatic Digestion ◽  
Biologically Active ◽  
Polar Solvents ◽  
Dna And Rna ◽  
Reduced Graphene

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Geneviève Bart ◽  
Daniel Fischer ◽  
Anatoliy Samoylenko ◽  
Artem Zhyvolozhnyi ◽  
Pavlo Stehantsev ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Body Fluids ◽  
Lower Percentage ◽  
Rna Seq ◽  
Protein Coding ◽  
Human Sweat ◽  
Dna And Rna ◽  
Ribonucleoprotein Complexes ◽  
Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

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