Undergraduate Honors Theses

Thesis Defended

Spring 2018

Document Type


Type of Thesis

Departmental Honors



First Advisor

Robert Batey


Riboswitches are RNA-based genetic regulatory elements that control gene expression without the need for protein cofactors. These RNA motifs are found within the 5’ untranslated regions of mRNA and promote genetic regulation by altering the structure of RNA through binding small molecule effector ligands that cause conformational changes that repress or activate translation/transcription. The env8 cobalamin riboswitch binds cyanocobalamin (CNCbl) to repress gene expression of the downstream mRNA. It accomplishes this through an interplay of two separate domains; an aptamer domain which binds the effector ligand and a regulatory domain which contains the genetic switch. Within the aptamer domain, there are several important constructs that promote the tertiary structure of the cobalamin binding pocket as well as the T-loop that interacts with the regulatory domain. This study is aimed to observe the effect of variation within the L4-L6 T-loop interaction that organizes the structure of the cobalamin binding pocket.

It was observed that a highly conserved consensus sequence is required for maintenance of riboswitch functionality. Specifically, nucleotides 30 and 33 on the L4 in addition to nucleotide 61 on the L6 are highly conserved and therefore must play a key role in the formation of the binding pocket. This region of the riboswitch was seen to be conserved regardless of the efficiency of the riboswitch and can be assumed to have critical importance in overall functionality.