Role of helical constraints of the EBS1–IBS1 duplex of a group II intron on demarcation of the 5′ splice site

Circular dichroism (CD) spectra of the ID3 stem–loop at 100 mM NaCl. Ellipticity was shown in mdeg for all spectra. Spectral features of the ID3 stem–loop, e.g., a minimum at 210 nm and maximum 265 nm, were typical of an A-form RNA helix; a shoulder at 280 nm suggested a single-stranded region. Addition of MgCl₂ resulted in a slight increase in the intensity of the band at 265 nm, consistent with an enhancement of stacking. Addition of the IBS1 target induced an increase in the positive ellipticity at 265 nm, consistent with additional helix formation. Addition of Mg²⁺ to the ID3–IBS1 complex did not result in further spectral changes.