Telomerase is essential for maintaining telomere length and chromosome stability in stem cells, germline cells, and cancer cells. The telomerase ribonucleoprotein complex consists of two essential components, a catalytic protein component and an RNA molecule that provides the template for telomeric repeat synthesis. A pseudoknot structure in the human telomerase RNA is conserved in all vertebrates and is essential for telomerase activity. It has been proposed that this highly conserved structure functions as a dynamic structure with conformational interchange between the pseudoknot and a hairpin with intraloop base pairings. To examine the structural and functional requirements of the pseudoknot structure, we made mutations in the proposed base-paired regions in the pseudoknot. Although mutations that disrupted the pseudoknot P3 helix abolished activity as predicted, mutations that disrupted the intraloop hairpin base pairings did not reduce telomerase activity, indicating that the intraloop hairpin is not required for telomerase function. This functional study thus provides evidence against the previous proposed molecular-switch model of telomerase pseudoknot function and supports a static pseudoknot structure. The mutational analysis further suggests that telomerase RNA can function independent of the proposed intermolecular pairings between pseudoknot regions on two RNA molecules.reverse transcriptase ͉ ribonucleoprotein ͉ telomere T elomerase is a unique ribonucleoprotein complex that is essential for telomere maintenance. Vertebrate telomeres are required for the stable chromosome maintenance; they consist of simple tandemly repeated TTAGGG sequences and telomere-associated proteins. Telomerase maintains telomeres by adding telomeric repeats to chromosome ends to counterbalance the natural shortening that occurs during DNA replication. Telomerase consists of two essential core components, the catalytic protein component telomerase reverse transcriptase (TERT), and the telomerase RNA (TR) that specifies the repeat sequence added. Vertebrate TR comprises three highly conserved structural domains: the template͞pseudoknot domain, CR4-CR5 domain, and the small Cajal-body RNA domain (1-4). The template͞pseudoknot domain contains the template region for telomeric DNA synthesis and a conserved pseudoknot structure essential for telomerase activity (Fig. 1A). The template region and the pseudoknot structure are brought into proximity by long-range base pairing interactions, i.e., the P1 helix. The integrity of the P1 helix plays an important role in template boundary definition (5). The presence of the pseudoknot structure formed by helices P2b and P3 was predicted based on phylogenetic analysis (1) and confirmed by mutational analysis (6). Although the pseudoknot structures are conserved in ciliate and vertebrate TRs, the molecular mechanism of their function in telomerase activity is unclear. A ''molecular switch'' hypothesis for pseudoknot function was proposed based on a NMR structure of the P2b stem-loop (Fig. ...