Hello, I am doing whole cell-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) process to look for DNA aptamers for the detection of bacteria.
I have purchased my DNA oligonucleotide library (81 bases, single-stranded) with 45 randomized bases in the central region. When I checked it on 3% agarose gel electrophoresis (without PCR amplification), it showed multiple bands instead of a single band.
Could I get an explanation for this result? 1uL of DNA library was inserted into each lane, and the electrophoresis was run at 90V, 40min.
Thank you.
What about some potential secondary structures? Try to denature it before the run on agarose gel or even better use denaturing (urea) 8-15% AA gel.
There is a probability of aptamer degradation. Try running a pcr and then performing another gel seperation to confirm the degradation and contact the seller about the same.
Please read my PhD thesis at: https://scholarworks.uark.edu/cgi/viewcontent.cgi?article=4985&context=etd
I have full chapter discussing this issue
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