DNA oxidation
Encyclopedia
DNA oxidation is the process of oxidative damage on Deoxyribonucleic Acid. It occurs most readily at guanine
residues due to the high oxidation potential of this base relative to cytosine
, thymine
, and adenine
. It is widely believed to be linked to certain disease and cancers.
is one of major reasons that cause damage to RNAs. Level of oxidative stress that cell is enduring is reflected by the quantity of Reactive oxidative species (ROS). ROS are generated from normal oxygen metabolism in cells, recognized as a list of active molecules, such as free radicals O2-, 1O2, H2O2 and, •OH . Nucleic acid
can be oxidized by ROS through Fenton reaction. To date, around 20 oxidative lesions have been discovered in DNA. RNAs are likely to be more sensitive to ROS for the following reasons: i) the basically single-stranded structure expose more sites to ROS. ii) compared with nuclear DNA, RNAs are less compartmentalized iii) RNAs distribute broadly in cell not only in nucleus as DNAs do, but also in cytoplasm in large portion. This theory has been supported by a series of discoveries from rat liver, human leukocytes and so on. Actually, monitoring system by applying isotopical label [18O]-H2O2 shows greater oxidation in cellular RNA than in DNA.
Oxidation randomly damages RNAs, each attack would bring problem to the normal cellular metabolism. Although alteration of genetic information on mRNA is relative rare, oxidation on mRNAs in vitro
and in vivo
results in low translation
efficiency and aberrant protein products.
Though the oxidation strikes the nucleic strands randomly, particular residues are more susceptible to ROS and there are such hotspot sites hit by ROS at high rate. Among all the lesions discovered so far, one of the most abundant lesions in DNA and RNA is the 8-hydroxyguanine. Moreover, 8-hydroxyguanine is the only one measurable among all the RNA lesions. Besides its abundance, 8-hydroxydeoxyguanosine (8-oxodG) and 8-hydroxyguanosine
(8-oxoG) are identified as the most detrimental oxidation lesion for its mutagenic effect, which this non-canonical counterpart can faultily pair with both adenine and cytosine at the same efficiency. This mis-pairing brings about the alteration in genetic information through the synthesis of DNA and RNA. In RNA, oxidation levels are mainly estimated through 8-oxoG-based assays. So far, approaches developed for directly measure 8-oxoG level include HPLC-based analysis and assays employing monoclonal anti-8-oxoG antibody. The HPLC-based method measures 8-oxoG by electrochemical detector (ECD) and total G by UV detector. Ratio by comparing the two numbers provides the oxidized extent of total the G .Monoclonal anti-8-oxoG mouse antibody is broadly applied to directly detect this residue either on tissue sections or membrane, offering a more visual way to study its distribution not only in tissues but also in discrete subset of DNA or RNA possible . The established indirect techniques are mainly grounded on this lesion’s mutagenic aftermath. One typical example is lacZ assay. This method was firstly set up and described by Taddei and was potentially a powerful tool to understand the oxidation situation both at RNA sequence level and single nucleotide level.
Another source of oxidized RNAs is mis-incorporation of oxidized counterpart of single nucleotides. Indeed, the RNA precursor pool size is hundreds size bigger than DNA’s.
Some potential facors include ribonucleases, which are suspected to selectively degrade damaged RNAs under stresses. Also enzymes working at RNA precursor pool level,are known to control quality of RNA sequence by changing error precursor to the form that can't be included directly into nascent strand.
Guanine
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine . In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with...
residues due to the high oxidation potential of this base relative to cytosine
Cytosine
Cytosine is one of the four main bases found in DNA and RNA, along with adenine, guanine, and thymine . It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached . The nucleoside of cytosine is cytidine...
, thymine
Thymine
Thymine is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at...
, and adenine
Adenine
Adenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
. It is widely believed to be linked to certain disease and cancers.
RNA Oxidation
RNAs in native milieu are exposed to various insults. Among those threats, oxidative stressOxidative stress
Oxidative stress represents an imbalance between the production and manifestation of reactive oxygen species and a biological system's ability to readily detoxify the reactive intermediates or to repair the resulting damage...
is one of major reasons that cause damage to RNAs. Level of oxidative stress that cell is enduring is reflected by the quantity of Reactive oxidative species (ROS). ROS are generated from normal oxygen metabolism in cells, recognized as a list of active molecules, such as free radicals O2-, 1O2, H2O2 and, •OH . Nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
can be oxidized by ROS through Fenton reaction. To date, around 20 oxidative lesions have been discovered in DNA. RNAs are likely to be more sensitive to ROS for the following reasons: i) the basically single-stranded structure expose more sites to ROS. ii) compared with nuclear DNA, RNAs are less compartmentalized iii) RNAs distribute broadly in cell not only in nucleus as DNAs do, but also in cytoplasm in large portion. This theory has been supported by a series of discoveries from rat liver, human leukocytes and so on. Actually, monitoring system by applying isotopical label [18O]-H2O2 shows greater oxidation in cellular RNA than in DNA.
Oxidation randomly damages RNAs, each attack would bring problem to the normal cellular metabolism. Although alteration of genetic information on mRNA is relative rare, oxidation on mRNAs in vitro
In vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
and in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...
results in low translation
Translation
Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. Whereas interpreting undoubtedly antedates writing, translation began only after the appearance of written literature; there exist partial translations of the Sumerian Epic of...
efficiency and aberrant protein products.
Though the oxidation strikes the nucleic strands randomly, particular residues are more susceptible to ROS and there are such hotspot sites hit by ROS at high rate. Among all the lesions discovered so far, one of the most abundant lesions in DNA and RNA is the 8-hydroxyguanine. Moreover, 8-hydroxyguanine is the only one measurable among all the RNA lesions. Besides its abundance, 8-hydroxydeoxyguanosine (8-oxodG) and 8-hydroxyguanosine
8-Hydroxyguanosine
8-Hydroxyguanosine is a nucleoside which is an oxidative derivative of guanosine. Measurement of the levels of 8-hydroxyguanosine is used as a biomarker of oxidative stress....
(8-oxoG) are identified as the most detrimental oxidation lesion for its mutagenic effect, which this non-canonical counterpart can faultily pair with both adenine and cytosine at the same efficiency. This mis-pairing brings about the alteration in genetic information through the synthesis of DNA and RNA. In RNA, oxidation levels are mainly estimated through 8-oxoG-based assays. So far, approaches developed for directly measure 8-oxoG level include HPLC-based analysis and assays employing monoclonal anti-8-oxoG antibody. The HPLC-based method measures 8-oxoG by electrochemical detector (ECD) and total G by UV detector. Ratio by comparing the two numbers provides the oxidized extent of total the G .Monoclonal anti-8-oxoG mouse antibody is broadly applied to directly detect this residue either on tissue sections or membrane, offering a more visual way to study its distribution not only in tissues but also in discrete subset of DNA or RNA possible . The established indirect techniques are mainly grounded on this lesion’s mutagenic aftermath. One typical example is lacZ assay. This method was firstly set up and described by Taddei and was potentially a powerful tool to understand the oxidation situation both at RNA sequence level and single nucleotide level.
Another source of oxidized RNAs is mis-incorporation of oxidized counterpart of single nucleotides. Indeed, the RNA precursor pool size is hundreds size bigger than DNA’s.
Potential factors for RNA quality control
There have been furious debates on whether the issue of RNA quality control does exist. However, with the concern of various length of half life of diverse RNA species ranging from several minutes to hours, degradation of defective RNA can not easily be attributed to its transient character anymore. Indeed, reaction with ROS takes only few minutes, which is even shorter than average life-span of the most unstable RNAs. Adding the fact that stable RNA take the lion’s share of total RNA, RNA error deleting become hypercritical and should not be neglected anymore .This theory is upheld by the fact that level of oxidized RNA decreases after removal the oxidative challenge .Some potential facors include ribonucleases, which are suspected to selectively degrade damaged RNAs under stresses. Also enzymes working at RNA precursor pool level,are known to control quality of RNA sequence by changing error precursor to the form that can't be included directly into nascent strand.