id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-275859-ix8du1er	Mouzakis, Kathryn D.	HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome	2012-12-15		.txt	text/plain	6721	322	50	In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Instead, we observe a strong correlation (R 2 = 0.88) between frameshift efficiency and local stability of the first 3 bp at the base of the stem-loop using a one-phase exponential decay function ( Figure 3C and Supplementary Table S3 ).	./cache/cord-275859-ix8du1er.txt	./txt/cord-275859-ix8du1er.txt