Locked Nucleic Acid - miRNA in situ using LNA probes (Jan/15/2008 )
Does anyone know why a probe containing LNA's has increased thermal stability and improved affinities for complementary sequences. The only thing I can find is in a paper by Dwaine A. Braasch and David R. Corey which states that "The bridge results in a locked 3P-endo conformation, reducing the conformational fexibility of the ribose and increasing the local organization of the phosphate backbone." Intuitively, one would think that a less flexible probe would be less likley to bind strongly, right?
Any info would be appreciated. Thanks.
Okay, I'll give a shot at a prose description.
A single stranded nucleic acid has some freedom to wiggle about. The bases can unstack and wave around in the water, though that takes overcoming the hydrophobicity of the bases -- with a little thermal energy the unstacked configurations happen. Even with the bases stacked, the backbone can wind tighter or loosen up, holding the bases in non-ideal configurations for Watson-Crick pairing. By adding the bridge to lock the backbone, the motion of the backbone is constrained and the bases are confined within a range of motion closer to the ideal stacking for Watson-Crick binding. This makes the pairing of a complementary heteroduplex more rapid, since you don't need to wait around for the bases to be in a near-ideal conformation, increasing the odds that a given strand-strand collision will be productive (that is, will result in formation of hydrogen bonds by Watson-Crick pairing). Once a complementary heteroduplex is established, if thermal motion melts apart a base pair then the locked backbone keeps the LNA base in a near-pairing confirmation and favors reannealing.