Ethylene Glycol Linkers in Nucleic Acids

Abstract

Single stranded RNA folds upon itself to create structural motifs, such as, hairpin loops, internal loops and bulge loops. Additional hydrogen bonding and ion interactions occur in the loops regions forming unique structural features that are recognized in RNA‐protein interactions. A helical structure interrupted by bulges is typically lower in stability than a continuous helix. In this study we designed RNA and DNA constructs containing varying length of ethylene glycol linkers to measure the stability of constructs that have no additional hydrogen bonding interactions in the bulge regions. The role of metal ions in RNA and DNA is complex as the negatively charged phosphate backbone of RNA and DNA molecules interacts with positively charged metal ions. In addition, loop regions often bind to metal ions to stabilize particular structural features. Thus, examining the stability of linker constructs in various ionic conditions provides further insights into factors that contribute to RNA and DNA stability. Thermodynamic denaturation experiments were performed in 10 mM MgCl 2 and 1M KCl buffer solutions at a pH of 7. DNA internal loops and bulge loops showed a decrease in stability with an increase in linker size. Most constructs showed an increase in stability in the presence of magnesium ions as compared to 1 M KCl. A comparative analysis of RNA and DNA bulge loops and internal loops constructs with linkers will be presented. Support or Funding Information Neena Grover and Colorado College Biochemistry Department