A number of bacterial small RNAs which have been shown to bind to Hfq have been characterised (see list).

Many of these RNAs share a similar structure composed of three stem-loops.

[1] Several studies have expanded this list, and experimentally validated a total of 64 Hfq binding sRNA in Salmonella Typhimurium.

[5] Genomic SELEX has been used to show that Hfq binding RNAs are enriched in the sequence motif 5′-AAYAAYAA-3′.

[6] Genome-wide study identified 40 candidate Hfq-dependent sRNAs in plant pathogen Erwinia amylovora.