id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-001337-a3y1rfas	Sharma, Virag	Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli	2014-07-01		.txt	text/plain	10079	515	60	The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. Prokaryotic signals sometimes possess another type of stimulatory element upstream of the frameshift motif: a Shine-Dalgarno (SD)-like sequence normally involved in translation initiation through pairing with the CCUCC sequence at the 3 end of 16S ribosomal RNA (32) (33) (34) . A preliminary study of 271 IS3 family members (see Supplementary Figure S2 ) led us to choose the following empirical rules: the structure is (i) a simple or branched hairpin of a length ranging from 17 to 140 nt, (ii) that starts 4-10 nt after the last base of the motif , (iii) with a G-C(or C-G) base-pair followed by at least three consecutive Watson-Crick or G-U or U-G base-pairs and (iv) has a G unfold@37 • C ≥ 7.6 kcal.mol −1 ; the G @37 • C value was determined using the default parameters of the RNAfold program from version 1.8.5 of the Vienna RNA package (47) .	./cache/cord-001337-a3y1rfas.txt	./txt/cord-001337-a3y1rfas.txt