RNA aptamer is similar to protein antibody. If you are to use RNA aptamer, you will have to get a RNA aptmer that specifically binds to the target protein. If you simply want to isolate the RNA-binidng protein that you know the RNA sequences for binding, you had better use the RNA oligonucleotide with defined sequences. Hope this help your experimental set up.

Aptamers are amazing molecules that could bind specifically (aditionally to its complementary sequences) small molecules such as cations, aminoacids, neurotransmitters and certain small proteins as thrombin or lysozyme, among others compounds. Aptamers are synthethic oligonucleotides "customized" for the binding of specific target molecules. The advantages of aptamers are huge compared to others affinity-binding molecules (i.e. antibodies). That is the main reason because of several research groups use aptamers as affinit-binding tools in order to isolate specifically a number of proteins (or another type of compounds).

for practical reasons, I would go with a pool of several biotinylated oligonucleotides to pull-down your RNA. Aptamers are great, but biotin-streptavidin and base-pairing are solid and predictable interactions and are fairly affordable. Experimental design will be easier. choose base-pairing regions for your biotinylated oligos that you expect to have low structure or protein binding. A good aptamer system though, already validated, might be better. it depends on your ultimate goal.

DNA or RNA aptamers directed against a given target are usually obtained through a in vitro selection method known as SELEX which is very easy to understand but may take a while to implement. Although that in many instances aptamers can result as good or even better than antibodies, you may spend a lot of time and money trying to isolate one. On the other hand, many ribosomal proteins naturally attach to specific sequences within the rRNA skeleton and thus using unselected and minimally modified RNA oligonucleotides in combination with some sort of capture method (i.e. pull down, columns, etc.) as suggested may be the most direct strategy to your needs.

Thanks all for the useful info. I'll go down the oligonucleotide strategy.