Within the nucleus, pre-mRNA molecules are complexed with a set of proteins to form heterogeneous nuclear ribonucleoprotein complexes. Al, an abundant RNA binding protein present in these complexes, has been shown to bind selectively to single-stranded RNAs and destabilize basepairing interactions. In this study Al is shown to promote the rate of annealing of complementary RNA strands >300-fold under a wide range of salt concentration and temperature. Maximal annealing is observed under saturating or near saturating concentrations of protein, but annealing decreases sharply at both higher and lower concentrations of Al. Kinetic analysis shows that the rate of annealing is not strictly rst or second order with respect to RNA at a ratio of protein/RNA that gives optimal rates of annealing. This result suggests that Al protein may affect more than one step in the annealing reaction. Two polypeptides representing different domains of Al were also examined for annealing activity. UPl, a proteolytic fragment that represents the N-terminal two-thirds of Al, displays very limited annealing activity. In contrast, a peptide consisting of 48 amino acid residues from the glycine-rich C-terminal region promotes annealing at a rate almost onequarter that observed with intact Al. The RNARNA annealing activity of Al may play a role in pre-mRNA splicing and other aspects of nuclear mRNA metabolism.RNARNA base pairing plays a key role in regulating the transfer and expression ofgenetic information at many levels, including replication, transcription, mRNA processing, and translation (1). Although base pairing of complementary RNAs is sometimes regarded as a spontaneous process, in vitro annealing of nucleic acids of the size and complexity of naturally occurring RNA molecules is slow under conditions of ionic strength and temperature approximating those inside most cells (2, 3). In vivo, base-pairing interactions may be mediated by proteins that promote or destabilize formation of double-stranded structure.Recently, several types of proteins have been characterized that unwind or destabilize double-stranded RNA. These include helicases (4, 5), enzymes that deaminate adenosine residues in double-stranded RNA (6, 7), and single-strandspecific RNA binding proteins (8). The function of most such proteins is poorly understood, although helicases are known to be required for the splicing and translation of mRNA (4, 9). Other proteins accelerate the rate of RNARNA annealing. These include the Rom (or Rop) protein, which regulates plasmid replication (10), and a small RNA-binding protein found in retroviral cores (11). This laboratory has shown (12) that RNARNA annealing proteins are abundant in nuclear extracts active in pre-mRNA splicing. In this report we investigate the ability of an abundant nuclear protein, the heterogeneous nuclear ribonucleoprotein (hnRNP) Al (13,14), to accelerate the rate of RNA-RNA annealing under a wide range of conditions.Previous studies have shown that Al, like a number of other DNA and RNA binding...