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Nicole M Nichols
Current protocols in molecular biology, Chapter 3, Unit3-Unit3 (2011-01-13)
Reaction conditions for a variety of endonucleases are detailed in this unit along with discussions of potential applications. Enzymes covered include BAL 31 nuclease, S1 nuclease, mung bean nuclease, micrococcal nuclease, and DNase I. A general discussion regarding the use
Stephen R Doyle et al.
BMC biotechnology, 11, 83-83 (2011-08-31)
Many SNP discrimination strategies employ natural restriction endonucleases to discriminate between allelic states. However, SNPs are often not associated with a restriction site and therefore, a number of attempts have been made to generate sequence-adaptable restriction endonucleases. In this study
Larissa A Balabanova et al.
Marine biotechnology (New York, N.Y.), 14(1), 87-95 (2011-06-08)
An extracellular nuclease was purified 165-fold with a specific activity of 41,250 U/mg poly(U) by chromatography with modified chitosan from the culture of marine fungus Penicillium melinii isolated from colonial ascidium collected near Shikotan Island, Sea of Okhotsk, at a
Joachim Kloehn et al.
Methods in molecular biology (Clifton, N.J.), 2116, 587-609 (2020-03-30)
This protocol describes the use of heavy water (2H2O) labeling to determine the growth rate and metabolic state of Leishmania parasites in culture and in infected animals. In vitro labeling studies are undertaken by cultivating defined parasite developmental stages in
Gerard Mazón et al.
Nature structural & molecular biology, 19(9), 964-971 (2012-08-14)
Holliday junctions can be formed during homology-dependent repair of DNA double-strand breaks, and their resolution is essential for chromosome segregation and generation of crossover products. The Mus81-Mms4 and Yen1 nucleases are required for mitotic crossovers between chromosome homologs in Saccharomyces
Dai Kato et al.
Analytical chemistry, 83(20), 7595-7599 (2011-09-13)
We describe the electrochemical detection of DNA methylation through the direct oxidation of both 5-methylcytosine (mC) and cytosine (C) in 5'-CG-3' sequence (CpG) oligonucleotides using a sputtered nanocarbon film electrode after digesting a longer CpG oligonucleotide with endonuclease P1. Direct
T E Shenk et al.
Proceedings of the National Academy of Sciences of the United States of America, 72(3), 989-993 (1975-03-01)
S1 nuclease (EC 3.1.4.X), a single-strand-specific nuclease, can be used to accurately map the location of mutational alterations in simian virus 40 (SV40) DNA. Deletions of between 32 and 190 base pairs, which are at or below the limit of
Tiziana Cervelli et al.
PloS one, 6(8), e23474-e23474 (2011-08-20)
Adeno-associated virus (AAV)-based vectors are promising tools for targeted transfer in gene therapy studies. Many efforts have been accomplished to improve production and purification methods. We thought to develop a simple eukaryotic system allowing AAV replication which could provide an
Rong-Zhen Liao et al.
Inorganic chemistry, 49(15), 6883-6888 (2010-07-08)
Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis
Meiying Liu et al.
Biosensors & bioelectronics, 26(11), 4294-4300 (2011-05-25)
We report here an optical approach that enables highly selective and colorimetric single-base mismatch detection without the need of target modification, precise temperature control or stringent washes. The method is based on the finding that nucleoside monophosphates (dNMPs), which are
Shao-Yi Hou et al.
Talanta, 99, 375-379 (2012-09-13)
In this study, the tested microRNA and the detection probe perfectly match with the capture probe instead of the traditional sandwich methods in which the tested oligonucleotide matches with the detection and capture probes. To avoid non-specific signals, mung-bean nuclease
S1 nuclease from Aspergillus oryzae for the detection of DNA damage and repair in the gamma-irradiated intracerebral rat gliosarcoma 9L.
P H Gutin et al.
Radiation research, 72(1), 100-106 (1977-10-01)
Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae.
V M Vogt
European journal of biochemistry, 33(1), 192-200 (1973-02-15)
Ning Tsao et al.
Molecular cell, 81(20), 4228-4242 (2021-10-24)
Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the
Hitesh S Chaouhan et al.
Journal of biochemical and molecular toxicology, 35(8), e22819-e22819 (2021-06-01)
Hexavalent chromium [Cr(VI)] is a genotoxic chemical, and in the chemical-exposed organism, oxidative stress is one of the leading causative mechanisms of genotoxicity. Heat shock protein-70 (Hsp70) is reported to be modulated in environmental chemical exposed organisms. Inadequate information on
Gary Rowley et al.
Microbiology (Reading, England), 157(Pt 3), 848-858 (2010-12-15)
The alternative sigma factor σ(E) (rpoE) is essential for survival in vivo of Salmonella Typhimurium but is dispensable during growth in the laboratory. We have been identifying σ(E)-regulated genes and studying their regulation and function to elucidate their potential role
A crude nuclease preparation suitable for use in DNA reassociation experiments.
W D Sutton
Biochimica et biophysica acta, 240(4), 522-531 (1971-07-29)
Yong Feng et al.
RNA (New York, N.Y.), 18(11), 2083-2092 (2012-09-18)
Dicer cleaves double-stranded RNAs (dsRNAs) or precursor microRNAs (pre-miRNAs) to yield ≈ 22-nt RNA duplexes. The pre-miRNA structure requirement for human Dicer activity is incompletely understood. By large-scale in vitro dicing assays and mutagenesis studies, we showed that human Dicer
Siu-Hong Chan et al.
Nucleic acids research, 39(1), 1-18 (2010-09-02)
Restriction endonucleases (REases) are highly specific DNA scissors that have facilitated the development of modern molecular biology. Intensive studies of double strand (ds) cleavage activity of Type IIP REases, which recognize 4-8 bp palindromic sequences, have revealed a variety of mechanisms
Marwan Hassani et al.
iScience, 24(8), 102913-102913 (2021-08-20)
Mepolizumab (anti-IL-5) is a successful biological for treatment of T2/eosinophilic asthma by blocking the IL-5-eosinophil axis. The kinetics of human eosinophils in blood and sputum was determined to better understand the underlying mechanism(s). Pulse-chase labeling was performed with 6,6-2H2-glucose in
Scott A Jones et al.
Journal of virology, 86(9), 5134-5150 (2012-03-02)
Hepatitis B virus (HBV) replicates its DNA genome through reverse transcription of a pregenomic RNA (pgRNA) by using a multifunctional polymerase (HP). A critical function of HP is its specific recognition of a viral RNA signal termed ε (Hε) located
F Harada et al.
Nucleic acids research, 2(6), 865-871 (1975-06-01)
Nuclease S1 specifically hydrolizes tRNAs in their anticodon loops, forming new 5' phosphate and 3' OH ends. Some single-stranded regions are not cut by nuclease S1. The strong preference of nuclease S1 for the anticodon region can be used for
Zhong De Liu et al.
Analytica chimica acta, 706(1), 171-175 (2011-10-15)
Carbon nanotubes (CNTs) can efficiently quench the fluorescence of the adsorbed fluorophores and nonconvalently interact with soft single-stranded DNA (ssDNA). Upon disruption of CNTs-fluorescent oligonucleotides hybrid by nuclease S1, fluorescence turn-on was observed. Using this strategy, a platform based on
Robert Buscaglia et al.
Nucleic acids research, 40(9), 4203-4215 (2012-01-14)
The use of time-resolved fluorescence measurements in studies of telomeric G-quadruplex folding and stability has been hampered by the complexity of fluorescence lifetime distributions in solution. The application of phasor diagrams to the analysis of time-resolved fluorescence measurements, collected from
Fuyang Li et al.
The EMBO journal, 32(3), 461-472 (2013-01-10)
The Saccharomyces cerevisiae Rad1/Rad10 complex is a multifunctional, structure-specific endonuclease that processes UV-induced DNA lesions, recombination intermediates, and inter-strand DNA crosslinks. However, we do not know how Rad1/Rad10 recognizes these structurally distinct target molecules or how it is incorporated into
Purification and properties of S1 nuclease from Aspergillus.
V M Vogt
Methods in enzymology, 65(1), 248-255 (1980-01-01)
Ning Tsao et al.
STAR protocols, 3(2), 101268-101268 (2022-04-09)
Cellular RNAs are modified by both physiological factors and exogenous agents, such as methyl methanesulfonate (MMS). However, techniques for analyzing how proteins may interact with these modified RNAs are limited. Here, we provide a protocol combining RNA immunoprecipitation (RIP) with
A nuclease specific for heat-denatured DNA in isolated from a product of Aspergillus oryzae.
T Ando
Biochimica et biophysica acta, 114(1), 158-168 (1966-01-18)
Michele Menotta et al.
The Journal of biological chemistry, 287(49), 41352-41363 (2012-10-12)
Ataxia telangiectasia (AT) is a rare genetic disease, still incurable, resulting from biallelic mutations in the ataxia telangiectasia-mutated (ATM) gene. Recently, short term treatment with glucocorticoid analogues improved neurological symptoms characteristic of this syndrome. Nevertheless, the molecular mechanism involved in
Rebecca Rodell et al.
Methods in molecular biology (Clifton, N.J.), 2444, 125-140 (2022-03-16)
Physiological and chemically induced modifications to nucleosides are common in both DNA and RNA. Physiological forms of these modifications play critical roles in gene expression, yet aberrant marks, if left unrepaired, may be associated with increased genome instability. Due to
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