Here, we report the isolation, identification, and whole-genome sequences of 12 bacterial strains associated with four mushroom species. The study was done as an inquiry-based exercise in an undergraduate genomics course (BIOL 340) in the Thomas H. Gosnell School of Life Sciences at the Rochester Institute of Technology.
Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A + -A + base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homoduplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100-fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2 ′ ′ ′ ′ ′ -O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2 ′ ′ ′ ′ ′ -O-methyl-adenylic strand, formed a hetero-duplex with a polyriboadenylic strand. Overall, our work validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification.
Polyadenylic molecules (poly A) are single stranded nucleic acids containing a series of repeating adenine bases. Polyriboadenylic (poly (rA)) strands form parallel duplexed helices in acidic conditions. Our group has generated and utilized a technique to determine if polyadenylic sequences can pair when each sequence differs in composition. We have adapted a DNA nanoswitch developed by others to detect duplex formation where we can control the composition of each strand that is being tested for interaction. This method is superior to traditional UV melting studies, given the low specificity for detection of duplex species in a complex mixture of polyadenylic strands with different compositions. Our results show that nanoswitches can be used to detect poly(rA) duplex formation as a function of pH and we have identified interesting binding between polyadenylic strands that have different compositions. Our methodology not only provides fundamental information regarding parallel polyadenylic duplex formation, but also can help in design of future and potentially pH‐sensing biological nanotechnology.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
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