I have a dsDNA sequence that contains 14 nucleotides which inserted into cell through nanoparticle and shows good cytotoxicity. Also 6 sequences repeats at two end but in reverse order and two sequence in between. I have found no similarity with human genes or any protein in BLAST search. Further it was found to be identical to some microbes genomic part and their putative proteins. Is it possible that it has 3D str i.e. aptamer that have some binding function, or it may recombine or got inserted like transposons.
Interesting finding but you need to demonstrate that the cytotoxicity is induced by this DNA sequence and is not a non specific action. You may have already done this. Have you controlled your experiment with another known sequence? What was the reason for using this particular sequence and did you expect this result or was it a serendipitous finding? I think you may have a potentially useful molecule in your hand. Good luck with your work
I agree, you should control for the DNA sequence to show if the cytotoxicity is indeed caused by the dsDNA, and not by, say, the nanoparticle. There are several reviews that have investigated several types of nanoparticles and their effects on cellular toxicity. Perhaps the nanoparticle itself is to blame?
Typcically, dsDNA has a very hard time forming interesting "aptamer-like" 3D structures simply because its persistence length (when duplexed) does not allow for that < 50bp.
I agree with Eric that dsDNA can have difficulty in acting as an "Aptamer" due to the long sequence. My suggestion would be to use your nanoparticle alone as one control and the dsDNA alone as another control and then to compare the cell killing rate.
Certainly, the nanoparticle shape, size and chemistry can have toxic effect on the cells. I am just curious to know if your nanoparticle is organic or inorganic?
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