The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch.

ABSTRACT: Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation. Overall, our studies show the apo-aptamer acts as (i) a pre-organized aptamer competent to bind ligand and undergo structural collapse and (ii) a conformation that is more accessible to anti-terminator formation. We show that both Mg(2+) ions and SAM are required for a collapse transition to occur. We then use competition between the aptamer and expression platform for shared sequence to characterize the stability o

SUBMITTER: Hennelly SP 

PROVIDER: S-EPMC3562059 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature