Molecular Biology


    Protocols in Current Issue
    Evaluation of the Efficiency of Genome Editing Tools by a Frameshift Fluorescence Protein Reporter
    Authors:  Balaji T. Moorthy, Akhilesh Kumar, Lauren X. Lotenfoe and Fangliang Zhang, date: 05/20/2020, view: 755, Q&A: 0
    [Abstract] In the last decade, genome editing has been the center of attention as a novel tool for mechanistic investigations and for potential clinical applications. Various genome editing tools like meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector-based nucleases (TALEN), and the clustered regularly interspaced short ...
    Ex vivo Analysis of DNA Repair Capacity of Human Peripheral Blood Mononuclear Cells by a Modified Host Cell Reactivation Assay
    Authors:  Katja Matt and Jörg Bergemann, date: 08/05/2019, view: 1133, Q&A: 0
    [Abstract] The ability of humans to repair DNA damages decreases with increasing age. In order to be able to repair daily occurring DNA damages, it becomes more and more important to preserve repair capability of cells with aging. The preservation of DNA repair processes contributes to preventing DNA mutations and subsequently the onset of age-related ...
    Viral Chromosome Conformation Capture (V3C) Assays for Identifying Trans-interaction Sites between Lytic Viruses and the Cellular Genome
    Authors:  Kinjal Majumder, Maria Boftsi and David J Pintel, date: 03/20/2019, view: 1850, Q&A: 0
    [Abstract] The folding mechanisms of the mammalian genome package our genetic material into the nucleus, and in doing so, dictate its appropriate replication and expression. Chromosome conformation capture technology has enabled the dissection of the folding principles of the cellular genome. This has led to a better understanding of the role played by ...
    Microbial Mutagenicity Assay: Ames Test
    Authors:  Urvashi Vijay, Sonal Gupta, Priyanka Mathur, Prashanth Suravajhala and Pradeep Bhatnagar, date: 03/20/2018, view: 19782, Q&A: 2
    [Abstract] The Microbial mutagenicity Ames test is a bacterial bioassay accomplished in vitro to evaluate the mutagenicity of various environmental carcinogens and toxins. While Ames test is used to identify the revert mutations which are present in strains, it can also be used to detect the mutagenicity of environmental samples such as drugs, dyes, ...
    Determination of DNA Damage in the Retina Photoreceptors of Drosophila
    Authors:  Damulewicz Milena and Pyza Elzbieta, date: 02/05/2018, view: 3633, Q&A: 0
    [Abstract] The retina is sensitive for light damages, because of direct light exposure, especially intense blue and UV light, which increase level of ROS and other toxic phototransduction products in photoreceptor cells. In our previous work (Damulewicz et al., 2017a and 2017b), we used 8-oxo-deoxyguanosine (8-OHdG) as a marker for oxidative stress ...
    In vitro Assay to Measure DNA Polymerase β Nucleotide Insertion Coupled with the DNA Ligation Reaction during Base Excision Repair
    Authors:  Melike Çağlayan and Samuel H. Wilson, date: 06/20/2017, view: 5166, Q&A: 0
    [Abstract] We previously reported that oxidized nucleotide insertion by DNA polymerase β (pol β) can confound the DNA ligation step during base excision repair (BER) (Çağlayan et al., 2017). Here, we describe a method to investigate pol β nucleotide insertion coupled with DNA ligation, in the same reaction mixture including dGTP or 8-oxo-dGTP, pol β ...
    Targeted Nucleotide Substitution in Mammalian Cell by Target-AID
    Authors:  Takayuki Arazoe, Keiji Nishida and Akihiko Kondo, date: 06/05/2017, view: 8613, Q&A: 0
    [Abstract] Programmable RNA-guided nucleases based on CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) systems have been applied to various type of cells as powerful genome editing tools. By using activation-induced cytidine deaminase (AID) in place of the nuclease activity of the CRISPR/Cas9 system, we have ...
    PCR-based Assay for Genome Integrity after Methyl Methanesulfonate Damage in Physcomitrella patens
    Authors:  Masaki Odahara, Takayuki Inouye, Yoshiki Nishimura and Yasuhiko Sekine, date: 10/05/2016, view: 5142, Q&A: 0
    [Abstract] In plant cells, genomic DNA exists in three organelles: the nucleus, chloroplast, and mitochondrion. Genomic DNA can be damaged by endogenous and exogenous factors, but the damaged DNA can be repaired by DNA repair systems. To quantify the extent of their repair activity of on individual genomic DNA, a PCR-based assay utilizing long amplicons is ...
    Laser Microirradiation and Temporal Analysis of XRCC1 Recruitment to Single-strand DNA Breaks
    Authors:  Anna Campalans and J. Pablo Radicella, date: 03/05/2016, view: 6043, Q&A: 0
    [Abstract] The DNA molecule is exposed to a multitude of damaging agents that can compromise its integrity: single (SSB) and double strand breaks (DSB), intra- or inter-strand crosslinks, base loss or modification, etc. Many different DNA repair pathways coexist in the cell to ensure the stability of the DNA molecule. The nature of the DNA lesion ...
    In vitro DNA Protection Assay Using Oxidative Stress
    Authors:  Yuri Ushijima, Ryosuke L. Ohniwa and Kazuya Morikawa, date: 07/20/2015, view: 6874, Q&A: 0
    [Abstract] A wide range of stresses such as oxidative stress, acid, alkaline, UV, and metal can damage DNA. Here, we describe a protocol to measure the DNA nicking damage by Fenton reaction-mediated oxidative stress. Fenton reaction (Fe2+ + H2O2 → Fe3+ + OH- + ∙OH) produces the highly deleterious ...

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