UV-Visible absorption spectroscopy for the detection of differences in oligonucleotide influenced aggregation of colloidal gold nanoparticles
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abstract
Transposable elements (TEs) or transposons are mobile segments of DNA that are capable of being excised and moved from one chromosomal location to another by a process known as transposition. This process requires an enzyme called the transposase that performs the excision reaction, recognizes specific target site sequences and then promotes insertion of the TE at the target site (transposition). This study provides new clues towards unraveling the causes behind the preferential affinity of the Hermes transposable element for certain insertion sites compared to other sequences which also contain recognizable target sites. The technique consists of a rapid, simple and reproducible assay that can be used to detect differences in the ability of various oligonucleotides to influence the aggregation of colloidal gold nanoparticles. The aggregation of the gold nanoparticles is monitored through UV-Visible absorption spectroscopy. Single isolated colloidal gold particles have a surface plasmon resonance manifested as a single absorbance peak at approximately 520 nm and aggregated gold complexes develop new red-shifted peaks/shoulders depending on the nature and extent of the aggregated complex. A simple ratiometric study of the area under the single and aggregated plasmon resonance peaks gives information about the extent of the aggregation. It is postulated that differences in dynamic flexibility of the oligonucleotides affect their influence on the aggregation state of the gold nanoparticles. Therefore such differences in dynamic flexibility between various insertion sites could directly or indirectly contribute to the observed target site preferences of the Hermes transposable element.
