Nucleic Acid Lab Report

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Detection of the target nucleic acids can be done using the reactions in which reacting parts are chemically attached to the oligonucleotides which are complementary to the target. In diluted solutions in the absence of a target (template) nucleic acid these reagents do not interact with each other. However, in the presence of the template the reaction occurs due to the increase of an effective substrate concentration. Products of the reaction can be detected using the standard methods and therefore the specific target can be recognized. Practically it is possible to distinguish three types of the nucleic acid template-supported reactions. The template interstrand crosslinking (Figure 1.19A) occurs when two complementary strands have reacting sites close to each other. It can be achieved via chemical modification of nucleobases in the complementary nucleic acids. Upon the hybridization these two modifications can react with each other forming product. Peng and Greenberg reported a few examples of interstrand crosslinking reactions using DNA strands with phenylselenyl substituted…show more content…
Using the SN2 reaction Kool and co-workers were able to ligate two nucleic acid strands in the presence of a template. The investigated phosphorothioate nucleophile act as the part of resulting nulceic acid substrate whereas the second conjugate contained a good leaving group. It was also possible to improve the reaction by using phosphorodithioate and phosphorotrithioate as nucleophilic moieties [41], [42]. Recently a valuable example of ligation based on Diels-Alder reaction was demostrated by Brown and co-workers [43]. Using the conjugates labelled with diene and dienophil they were able to achieve rapid reaction within 1 minute in the presence of template DNA strand (Figure 1.24). However, authors noticed pH limitations for chosen
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