Radiation Quality
K. H. Chadwick in Understanding Radiation Biology, 2019
A series of assumptions have been made in the calculation of DNA single and double strand breaks, namely: The DNA molecule is visualised as a linear array of DNA bases every 0.34 nm, each linked to a second linear array of bases at 1.2 nm distance.Strand breakage occurs via radiolysis products (radicals) produced in the water surrounding the DNA molecule.The radicals have a limited lifetime and thus a limited diffusion range.A water molecule is ionised or excited when one of its 10 electrons is scattered by the charged particle.Ionisation involves energy transfers of more than 20 eV, excitation involves energy transfers between 5 and 20 eV and energy transfers of less than 5 eV are not effective.Fion is the number of effective radiolysis products per water molecule created by ionisation events and Fexc is the number of radiolysis products created by excitation events.To be effective, the radiolysis products have to be created within their diffusion range (ρ) of the DNA.
The Fight Against Cancer
Nathan Keighley in Miraculous Medicines and the Chemistry of Drug Design, 2020
Mustard gases were used in the First World War to devastating effect. It was later realised, however, that nitrogen mustards had potential as anti-cancer agents. They are classified as alkylating agents, referring to their mechanism of action. These compounds are highly electrophilic and readily react with nucleophiles to form strong covalent bonds. Alkylating molecules will react with the nucleophilic nitrogen groups of DNA bases, particularly N-7 of guanine. Symmetrical molecules are used, with electrophilic groups on either side, which will react with guanine bases on each strand of DNA and therefore cross-link them, which causes transcription and translation to be disrupted and therefore impede the progress of cancer. Conversely, the drug may link to two guanine bases on the same strand of DNA and cover that portion of the DNA from the actions of enzymes involved in replication. Predictably, there are limitations to alkylating drugs. Such reactive compounds will attack other nucleophilic groups on proteins also, so have poor selectivity, and themselves are mutagenic due to their action on DNA.
B Cells and Humoral Immunity
Constantin A. Bona, Francisco A. Bonilla in Textbook of Immunology, 2019
Somatic mutation in memory cells is restricted to the functionally rearranged VH and VL genes, and approximately one kb of DNA on either side. The ratio of replacement to silent mutations varies between the framework (3:1) and hypervariable regions (CDRs, 6.2:1). Although the vast majority of mutations are simple DNA base changes, small insertions or deletions are also occasionally observed. Mutations accumulate in a step-wise fashion with higher-affinity mutants deriving selective advantage and being preserved, mutations destroying specificity or decreasing affinity are effectively lost. The rate of mutation is estimated to be 10−3–10−4 per base pair per generation, or roughly one mutation per cell division. Mutations are extremely rare in unrearranged or non-functional genes or in the C regions. Whether or not mutation occurs in the absence of activation remains open to question, however, it is greatly increased in dividing cells. T cell cytokines may have some influence on the rate of mutation.
Is subretinal AAV gene replacement still the only viable treatment option for choroideremia?
Published in Expert Opinion on Orphan Drugs, 2021
Ruofan Connie Han, Lewis E. Fry, Ariel Kantor, Michelle E. McClements, Kanmin Xue, Robert E. MacLaren
To address the limitations of HDR-mediated gene editing, CRISPR-Cas-mediated single-base pair editing systems (or ‘base editing’ systems) have been devised which allow for targeted restoration of single-base mutations. Two classes of DNA base editors have been described to date: cytosine base editors and adenine base editors [58,59]. DNA base editors encompass two key components. The first is an inactivated Cas enzyme (or Cas nickase, nCas9) which retains its programmable DNA binding ability, but which has lost its ability to generate DSBs. The second is a single-stranded DNA-modifying enzyme (cytidine or adenine deaminase) fused to nCas9 for targeted nucleotide alteration. Collectively, all four transition mutations (A > G, C > T, G > A and T > C) can be installed with the available CRISPR/Cas base editor systems. Recently, Kurt et al. described the engineering of two novel base editor architectures that can efficiently induce targeted C-to-G base transversions [60]. In addition, recent studies report dual-base editor systems for combinatorial editing in human cells. Together, these new base editors expand the range of DNA base editors to transversion mutations and may allow for targeting of more complex compound edits than are currently achievable by a single DNA base editor.
Development of computational model for cell dose and DNA damage quantification of multicellular system
Published in International Journal of Radiation Biology, 2019
Ruirui Liu, Tianyu Zhao, Maciej H. Swat, Francisco J. Reynoso, Kathryn A. Higley
In this work, for applying DBSCAN in DNA damage quantification, the homogenous water containment was used to approximate the cell nucleus containing DNA and the complex DNA structure is not considered. Considering that the chromatin formed by DNA in a cell is randomly distributed inside the nucleus, a term named SpointsProb was introduced to quantify the probability of the direct and indirect interactions induced by radiation energy deposition in the nucleus of cell (Francis et al. 2011). The SpointsProb defines the probability that an interaction point is in a sensitive position where it can directly or indirectly reach the DNA. The SpointsProb is determined according to the DNA volume. The diameter of general mammalian cell nucleus is about 10 μm, so the volume of nucleus is as 523.33 3. Roughly, a DNA base pair has a volume about 1 nm3. For mammalian cells, the total number of base pairs is on the order of 3. The fractional DNA volume with respect to the cell nucleus is therefore calculated as fDNA = 1.146%. We can approximately take fDNA as the sensitive fractional volume of cell nucleus to quantify the DNA damage due to radiation interactions within the cell nucleus.
Combining cell and gene therapy to advance cardiac regeneration
Published in Expert Opinion on Biological Therapy, 2018
Pina Marotta, Eleonora Cianflone, Iolanda Aquila, Carla Vicinanza, Mariangela Scalise, Fabiola Marino, Teresa Mancuso, Michele Torella, Ciro Indolfi, Daniele Torella
Like ZFNs, TALENs are also engineered restriction enzymes consisting of a DNA-binding domain fused to FokI. The DNA-binding domain is a transcription activator-like effector domain adapted from proteins secreted by the plant pathogen Xanthomonas bacteria, consisting of 10–30 repeats of 33–35 amino acids [123]. The amino acid sequences are highly conserved with the exception of two amino acids, named as the repeat variable di-residue, which recognize distinct DNA base pairs and thus confer DNA sequence specificity. Each repeat recognizes and binds to a single DNA base pair and, therefore, the number of repeats and their alternation in the DNA-binding domain determines the overall length and specificity of the bound sequence. As with ZFNs, TALENs function after dimerization of two independent TALENs on opposite strands (Figure 2).