Nucleotide Excision Repair And Translesion Synthesis Lab Report

First adenosine monophosphate (AMP), a covalent enzyme, must be formed and linked to a lysine enzyme. Next AMP will transfer to the 5' phosphate end of the missing section between the Okazaki fragments. Last –OH will help remove the AMP sealing the phosphate backbone together producing a continuous DNA strand ("DNA Ligase," n.d.). A visual representation of ligase joining two Okazaki fragments can be viewed in Figure 2.

Then the tRNA molecules link together and transfer the amino acid to the ribosome. An Anticodons pair with a codon takes the

_________ brings DNA gene segments together and cuts at the ends of the heptamers. __________ adds N-nucleotides randomly to the ends of the P-nucleotides.

For example, wings-clipped P-elements that lack the inverted repeats (not able to be mobilized themselves), which are not internally deleted and can produce a transposase source, can be introduced to the internally-deleted P-element to provide transposase and therefore allow transposition to occur. The provided transposase recognizes and binds to inverted repeats on the internally-deleted P-element, which introduces nicks in the DNA beside the inverted repeats. This allows the element to excise and insert into a new location. If it excises neatly out of the DNA, a deletion will not occur. However, if it excises to a homologue towards the right or the left, due to an error in the excision process, a deletion will occur through this pre-meiotic recombination event.

Although this depiction is not a hundred uncovered in bacteria, percent proven through research, it can be said that a cell is more likely to use NHEJ when it has not replicated yet. On the other hand, the cell leans towards homologous recombination after it has replicated. She also entails that yeast is very useful in studies the processes mentioned above. Additionally, she stated that scientists are involved in efforts to study how mutated genes react to breaks in their structure. Equally important, she recounted that double strand breaks can be monitored by inducing a break within cells. Dr. Friedman details that scientists have gone about this by using a specific, regulated protein that recognizes and chews through DNA

ends when the RNA polymerase reaches a triplet of bases then the DNA molecules re-

We know from the induced-fit model that the binding of the substrate (DNA) causes a conformational change in the active site of the enzyme. This model refers to a methylation reaction in which the cysteine needs to interact with cytosine of the DNA. Cytosine-5-methyltransferase transfers a methyl group from S-adenosyl-L-methionine to the C5 of cytosine. Cysteine residue attacks the cytosine causing the

Some mutations serve as a form of natural selection and can help better the life of an organism. The mutation rate of the mitochondrial DNA has been proven to be one hundred fold higher than that of nuclear DNA. A recent study conducted by scientists has suggest the reason for the abundance of mitochondrial DNA mutations. In the study, they suggested that the nucleotide imbalance within mitochondria cause a decrease in polymerase gamma, or POLG, and an increase in mutation rates. The main responsibility POLG is to encode the DNA polymerase that duplicates the mitochondrial genome. This protein also consists of a two domains. The catalytic domain displays polymerase activity, while the anexonuclease domain recognizes and removes DNA base pair mistakes that occur during DNA replication. As a result of the vast population of mitochondrial DNA, mitochondria are considered heteroplasmic. Heteroplasmy surrounds the presence of various types of genomes within a single cell. When considering the severity of mutations and mitochondrial diseases heteroplasmy is a prominent factor. When a single cell divides mitochondrial segregation occurs in a random matter and the mitochondria is divided between daughter cells. This process is not very well organized, which causes the daughter cells to receive similar, but not identical, copies of their mitochondrial DNA. Unlike the segregation of mitochondrial DNA, chromosome

This mutagenesis kit can make point mutations, replace certain amino acids, and delete or insert adjacent amino acids, making it an incredibly powerful tool. First, the mutant strand is synthesized by denaturing the DNA template and anneal the mutagenic primer(s) and then incorporated using DNA polymerase. A mutated plasmid is created and then digested by Dpn I endonuclease and transformed into competent cells for cell nick repair (Agilent, n.d.).

The main purpose of primase in DNA replication is to synthesize RNA; it makes RNA oligonucleotides that are used as primers for DNA synthesis. Without this, DNA Polymerase could not start a new chain of DNA, so primase serves as a starting point for replication. After Helicase breaks the strands apart, primase comes in to add short, new RNA nucleotide chains (about 10 nucleotides long) to the template strand. Then the DNA polymerase can add new DNA nucleotides to the strand forming new DNA strands. Without the correct functioning of this enzyme, the Polymerase could not carry out its functions, so the synthesis of a new DNA strand would be interrupted, causing no new DNA to

Mutations are caused by errors in DNA replication or repairs, or chemical or radiation damage

Restriction enzymes cut double stranded DNA into individual fragments. The endonuclease scans the DNA until it locates the recognition sequence. It then makes one cut in each of the sugar-phosphate backbones of the double helix. The fragments are held together weakly by hydrogen bonds, but due to their weak interaction the fragments separate. Although the DNA is cut, its bases are not damaged; therefore the DNA fragments can be

The Cas9 System and a small guide RNA molecule. The Cas9 is an enzyme that “snips through DNA like a pair of molecule scissors”(Zagorulya). The second component is a RNA molecule that acts as a guide to direct the Cas9 to the targeted sequence of DNA in the genome. DNA repair mechanisms in the cell can silence the gene if cut. When adding a new DNA fragment to the Cas9-gRNA complex, repair machinery repair DNA by adding the new DNA where the enzyme cut, through the DNA. With this, a mutation can be introduced into the gene or a new gene can be introduced into the cell DNA. Scientists are able to manipulate DNA in numerous ways using the system and study the function of health and mutated forms of specific genes. The flexibility of this system allows scientists to study any gene despite its location or composition of DNA. Flexibility is due to the RNAs design as it is created to target any site of the

This msDNA is usually small single-stranded cDNA molecule bound covalently to an RNA molecule which can fold into a stable secondary structure. Eventhough still there are no proof to conform retrons as mobile elements, copies of inserted msDNA can be found in bacterial genome (Lampson and rice 1997). In E. coli overexpression of some msDNAs has increased the number of base substitution mutations and frameshift mutations (Maas et al,. 1994). When most cellular mismatch repair proteins bind with mismatches on msDNA molecules it increase the mutagenic level. During matings of E. coli and Salmonella cells when some msDNAs are overexpressed it increase the recombination between donor and recipient DNA sequences, because of the action of mismatch repair usually the interspecific recombination frequency is normally reduced (Maas et al,. 1996). Even though the function of msDNA is still unknown it helps the bacteria to increase their mutations when the mutations are required for their survival. These retrons

Modification of damaged DNA seems to be an understudied subject, there is much to understand on the restoration of DNA damage, repair and DNA methylation. Genomic DNA can be modified by methylation but much of it is affected on a gene when silenced. When epigenetic modification has been implicated with cancer and aging it causes DNA methylation to also have an impact on the double strand of DNA analysis. Modification as such provoke deteriorating changes like aging found in multicellular organisms and DNA damage may magnify biochemical pathways that regulate a cells growth or control DNA replication with DNA repair. In the article “DNA Damage, Homology-Directed Repair, and DNA Methylation” written by Concetta Cuozzo, Antonio Porcellini, Tiziana Angrisano, et al. they hypothesize how DNA damage and gene silencing may induce a DNA double-strand break within a genome as well as when DNA methylation is induced by homologous recombination that it may somewhat mark its reparation through a DNA segment and protect its cells against any unregulated gene expression that may be followed by DNA damage. The experiments used to demonstration how gene conversion can modify methylation pattern of repaired DNA and when that occurs methylation is able to silence the recombined gene. When exploring the molecular mechanisms that link DNA damage and the silencing gene then there is an induced double strand break that can be found at a specific location or DNA sequence in where the