Poly(A)-binding protein binds to A-rich sequences via RNA-binding domains 1+2 and 3+4

Poly(A) binding protein (PABP) binds non-protein-coding BC1 RNA and BC200 RNA, which contain adenosine-rich domains. Two combinations of the four PABP RNA recognition motifs (RRMs), RRMs 1+2 and RRMs 3+4, bind with very strong affinities to various transcripts with long stretches of adenosine residues, whereas RRMs 2+3 bind weakly. While RRMs 1+2 preferentially bind to stretches that contain only adenosines, RRMs 3+4 exhibit relatively high affinities towards sequences that are interspersed with other nucleotides. Binding studies with oligoribonucleotide(A)(65) and oligoribonucleotide(A)(25) showed that the shorter RNA is not an ideal substrate for binding studies to model the interactions with mRNAs, which in general harbor long poly(A) tails.