Investigation of the Properties of Stem-Loop DNA

Abstract

Deoxyribonucleic acid (DNA) is the genetic material of almost all living organisms and a polymer of deoxynucleotide monomers. Stem-loop DNA (slDNA) is a type of secondary structure formed when a single strand of DNA folds over on itself and contains complementary deoxynucleotides that form base pairs in the stem while the deoxynucleotides that are not complementary to each other forms the loop. SlDNA sizes in this study varied in the stem to loop ratios with ranges from 10 to 20 base pairs in the stem and from 3 to 60 nucleotides in the loop. The behavior of these slDNAs in native polyacrylamide gel electrophoresis (PAGE) and denaturing PAGE with different urea and formamide concentrations, common denaturing agents used to destabilize DNA, were studied to determine that slDNAs with higher stem-loop ratios did not denature while the ones with lower stem-loop ratios successfully denatured at an optimal condition of 12% PAGE 9.0 M Urea and 10% PAGE 16 M formamide. Polymerase chain reactions (PCR) using slDNA molecules were studied to determine if the slDNAs of similar stem to loop ratios will have a similar response to PCR as gel electrophoresis, but the analysis of the products on PAGE conveyed obscure results.