Nucleic acid base pairing occurs during DNA repair (San Filippo et al., 2008), splicing (Black, 2003), ribosomal RNA modification (Weinstein and Steitz, 1999) and gene regulation by small silencing RNAs (Ghildiyal and Zamore, 2009). Recent work by Ha and colleagues (Cisse et al., 2012) on the association and dissociation of complementary nucleic acids provides new insight into how short regions of nucleic acid complementarity mediate these biological functions. Ha and coworkers measured the annealing and melting of complementary oligonucleotides using fluorescence resonance energy transfer (FRET). Unlike classical FRET studies, these authors enclosed a single pair of complementary nucleic acid molecules in liposomes of defined volume. The liposomes were then adhered to a glass slide, allowing the dye-labeled nucleic acid contents to be imaged by Total Internal Reflection Fluorescence (TIRF) microscopy. With one of the strands tagged with Cy3 (donor) and the other with Cy5 (acceptor), annealing between the two strands brings the dyes together, producing a high FRET state; their dissociation produces a low FRET state. DNA or RNA strands with less than 7 nt of contiguous base pairing displayed an association rate 2 orders of magnitude smaller than those with seven or more base pairs. A minimum of 7 nt is therefore required for a duplex to form quickly.
The number seven immediately brings to mind the seven-to-eight-nucleotide “seed sequence” of miRNAs and siRNAs. The seed sequence, spanning nucleotides 2 to 8 of a small silencing RNA guide, is created when the RNA guide binds an Argonaute protein; the seed sequence provides nearly all the binding specificity of the Argonaute: small RNA silencing complex. Remarkably, studies of the bacterial CRISPR system also point to a seven-nucleotide seed that allows the machinery to bind foreign nucleic acids (Bhaya et al., 2011). Thus, regulation by Argonaute-bound small RNAs or the CRISPR machinery may have evolved to harness the natural biophysical properties of nucleic acid pairing: the minimal 7 nt pairing rule allows them to rapidly lock in on their targets.—Liang-Meng Wee, University of Massachusetts Medical School