Characterization of Novel Nucleic Acid Inhibitors (Aptamers) of Human Immunodeficiency Virus Reverse Transcriptase Selected Using a Primer-Free SELEX Approach

TL;DRAbstract

Aptamers are synthetic, single stranded nucleic acids that bind specifically to the target protein. Aptamers have many potential uses including therapeutic and diagnostic applications. Most aptamers are identified through standard SELEX (<bold>S</bold>ystematic <bold>E</bold>volution of <bold>L</bold>igands by <bold>EX</bold>ponential enrichment) procedures that include a starting pool of nucleic acids with a region of random nucleotides flanked by fixed sequences. A main disadvantage of the traditional SELEX is the potential for the fixed sequences to "bias" the selection by interacting with nucleotides in the random region of the oligonucleotide. I developed a novel primer-free SELEX method for isolating single strand 30 nt DNA aptamers from a random sequence pool for HIV reverse transcriptase (HIV-RT), in which selection occurs in the absence of any flanking, fixed nucleotides. Selected aptamers bound ~10-20 fold tighter than starting material to HIV-RT. The selected aptamer (PF1) c

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