Structure and dynamics of adenosine loops in RNA bulge duplexes as revealed by linked application of thermodynamics, spectrofluorimetry and simulation of molecular dynamics

Structure and dynamics of adenosine loops in RNA bulge duplexes was studied using time-resolved spectrofluorimetry and in aqua simulation of molecular dynamics. Thermodynamics revealed that 2-aminopurine riboside is an non-invasive fluorescent probe when built within the bulge region of chemically synthesized RNA duplexes.