Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Naoto Hori; Natalia A. Denesyuk; D. Thirumalai

The multifarious roles RNA molecules play in controlling a myriad of cellular functions [1] have made it important to understand in quantitative terms their folding [2] [3] [4] [5] [6] and how they respond to external stresses [7] . Among them, one of the simplest structural motifs is the RNA pseudoknot (PK), which is involved in many biological functions. The simplest type, referred to as H-type PK, consists of two stems connected by two loops in which one of the stems forms base pairs with the loop of the other. The PK motif, found in many RNA molecules such as telomerase [8] , mRNA [9] , ribosomal RNA [10] , transfer-messenger RNA, and viral RNA [11] , is functionally important [12] . For instance, a PK in the human telomerase RNA is essential for enzyme (a ribonucleoprotein complex) activity [13] . Many pathogenic mutations in the human telomerase RNA are found in the wellconserved PK region of the RNA, further underscoring the importance of the PK [8, 13] . The presence of PKs is also important in ribozyme catalysis and inhibition of ribosome translation.