I am looking for a folded domain or protein able to recognize single stranded RNA independently of the sequence. Most of the ones that I have found are specific to sequences. I need it to engineer a delivery vehicle. Thanks for your help.
What proteins have you looked at? Does it have to be a protein? There are other delivery vehicles. It may seem a bit odd, but have you considered proteins such as oxidised / scrambled RNAse (I don't know if it binds RNA, but it has no RNAse activity). Antibodies ? (to uridine ?), RNPs?
http://rbpdb.ccbr.utoronto.ca/
I always thought that the RGG motif was non-specific. And even an RBD-type domain might in itself be non-specific, if you eliminate any of the surrounding sequence which could add specificity. I should also add that the p34/37 proteins I studied bound ssDNA non-specifically, so it wouldn't surprise me if it also bound all ssRNA more or less with non-specificity, with the 5S rRNA as its primary target. Most RBD-type proteins probably act the same way.
The nucleocapsid protein of certain negative-strand RNA viruses, such as respiratory syncytial virus, bind single-stranded RNA in a sequence-independent manner. The RNA is wrapped around the outside of a helical structure composed of polymerized protein.
The nuclear auto antigen La/SS-B binds almost all RNAs. We have used it for delivery of RNA to dendritic cells to trigger maturation via TLRs. Although anti-La coprecipitation brings down mainly oligouridylated PolIII transcripts and some viral RNAs such as EBERI/II and VA RNAs, recombinantly expressed La binds to almost all externally added RNAs including short oligos. Most likely, even the N-terminal 29 kD domain of La is sufficient.
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