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Mitochondrial Genome Damage, Dysfunction and Repair
Published in Shamim I. Ahmad, Handbook of Mitochondrial Dysfunction, 2019
Kalyan Mahapatra, Sayanti De, Sujit Roy
Mitochondrial genome of many eukaryotes had been considered to exist in the form of super-coiled circular DNA. However, there is now strong evidence that many of these circular mapped mtDNA consists primarily of linear, multimeric head-to-tail concatemers (Bendich, 1993, 1996). These, for example, have been found in few unrelated organisms such as ciliates, Apicomplexa (Plasmodium and its relatives), fungi, Chlorophycean green algae (Chlamydomonas and relatives) and several Cnidarian animals. These linear molecules contain various specialized end structures, such as covalently closed single-stranded DNA termini and terminally attached proteins. They also tend to have telomere-like repeats of differing lengths. In fact, the difference in size of mitochondrial genomes is mostly caused by the variations in the length and organization of intergenic regions which, in some cases are consisting of extensive tandem-repeats or stem-loop motifs.
Human Bocavirus
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
José Luiz Proença-Módena, Guilherme Paier Milanez, Eurico Arruda
In the “rolling-hairpin” model, hairpin structures flanking the viral genome are used as primers for the initiation of DNA replication, generating DNA concatemers, which may be present in two possible intermediate structures: head-to-head and tail-to-tail. In studies assessing primary airway epithelial cells, it was possible to verify the formation of head-to-head structures. However, to date, these structures have not been observed in vivo, supporting the hypothesis that HBoV replicates using an alternative mechanism, supposedly by helper virus-dependent initiation in a rolling-circle replication model.
Herpes Simplex Virus and Human CNS Infections
Published in Sunit K. Singh, Daniel Růžek, Neuroviral Infections, 2013
Marcela Kúdelová, Július Rajčáni
In 1997, a model for HSV DNA replication was formulated (Boehmer and Lehman 1997). Once the β proteins are expressed, a number of proteins localize into the nucleus and assemble in DNA replication complexes at prereplicative sites, where viral DNA synthesis initiates on the circular molecule. Then, the UL9 (the origin binding) protein binds to specific elements—origin of replication (either OriL or Oris)—thus beginning to unwind the DNA. Then, it recruits ICP8 (the ssDNA binding protein) to the unwound ssDNA and they both recruit the five other viral replication proteins (helicase–primase complex of three proteins UL5, UL8, and UL52, viral DNA polymerase catalytic subunit UL30, and its processivity factor UL42) to begin the initial round of θ (theta) form replication (Wu et al. 1988). Leading strand synthesis involves the unwinding of the DNA and synthesis of a primer by the HSV helicase–primase complex. Then, replication switches from θ form to rolling circle mode, producing long head-to-tail concatemers of viral DNA by an unknown mechanism (Jacob et al. 1979). Concatemers are cleaved into monomeric molecules during packaging.
Cytogenetic and molecular genetic methods for chromosomal translocations detection with reference to the KMT2A/MLL gene
Published in Critical Reviews in Clinical Laboratory Sciences, 2021
Nikolai Lomov, Elena Zerkalenkova, Svetlana Lebedeva, Vladimir Viushkov, Mikhail A. Rubtsov
Illumina and Ion Torrent compete in the field of short-read sequencing with the sequencing platform produced by MGI (Shenzhen, China) that utilizes the technology developed by Complete Genomics (San Jose, California). During template preparation, the fragments are amplified using the rolling circle amplification, instead of PCR. The resulting concatemers form DNA nanoballs (DNBs), which are placed into the flow cell. Each DNB rests in a separate section of the patterned flow cell [90]. The MGI instrument performs sequencing using the combinatorial probe-anchor synthesis (cPAS) technology. The sequencing process consists of three steps: the addition of a labeled terminated nucleotide, the detection of the added nucleotide by fluorescently labeled monoclonal antibodies, and the cleavage of a terminator [91]. The sequencing reads produced by the MGI platform can reach up to 400 nt in length (or 150 nt in the paired-end sequencing). However, 400 nt reads come at the cost of sequencing time; for example, sequencing the entire human genome can take several days. The MGI platform covers the range of applications that other short-read sequencing platforms have, but with a lower sequencing cost [92–97].
Targeted cancer drug delivery with aptamer-functionalized polymeric nanoparticles
Published in Journal of Drug Targeting, 2019
Sepideh Zununi Vahed, Nazanin Fathi, Mohammad Samiei, Solmaz Maleki Dizaj, Simin Sharifi
SELEX technology was developed by Ellington and Gold (1990) as an effective technology for the identification and screening of aptamers [31]. After decades of improvement, this technique has undertaken dramatic alterations and developments since conventional technology had interfaced with some significant challenges, including incidence of non-specific binding of oligonucleotides, time of the selection process, concatamers formation from PCR artefacts as well as a low molar ratio of ribonucleic library (DNA/RNA) to the target [32]. At the present time, for rapid and easy aptamer selection, various SELEX-based methods have been developed for different purposes [33,34]. The improved versions are cell-SELEX [35–37], capillary electrophoresis [38,39], magnetic [40,41], automated [42,43] and complex-target SELEX [44,45]. It is obvious that high-throughput selection of aptamers can fulfil the role of applicable antibodies in clinic. Despite the traditional SELEX method, improved affinity and selectivity along with rapid aptamer selection can be achieved with microfluidic and capillary electrophoresis SELEX. Moreover, by a post-SELEX modification or applying modified oligonucleotides during SELEX one can overcome the unstable natural oligonucleotides body fluids. It should be taken into account that post-SELEX modifications may affect the aptamer properties (e.g. binding affinity and function) [34,46].
Voretigene neparvovec-rzyl for the treatment of biallelic RPE65 mutation–associated retinal dystrophy
Published in Expert Opinion on Orphan Drugs, 2018
Stephen Russell, Jean Bennett, Albert M. Maguire, Katherine A. High
VN is an adeno-associated virus vector-based gene therapy (AAV2-hRPE65v2) administered via subretinal injection. It is designed to deliver a normal single-stranded copy of the complementary DNA encoding the human RPE 65 kDa protein (hRPE65) to cells of the retina in persons lacking a functional version of RPE65. The AAV2 capsid components of VN facilitate cell surface binding, entry, and delivery of the vector genome packaged within the capsid to the nucleus of the cell. Once in the nucleus, the genome is uncoated and replicated by cellular DNA polymerases into a double-stranded genome, which subsequently forms extrachromosomal concatemers (multiple copies of the same DNA sequence arranged end to end in tandem, which may be circular or linear) of the expression cassette. Following delivery and formation of concatemers, VN achieves efficient and durable expression of the hRPE65 enzyme in cells of the retina.