For this blog entry I wanted to write about one of the talks from the NAI Workshop that I saw on Monday given by Ram Krishnamurty from the Scripps Research Institute on his research into structural alternatives for RNA. The basic motivation of his research is to study the potential of novel oligomer systems to act as informational systems similar to RNA. One of the major goals of Krishnamurty’s team is to systematically synthesize, by chemical methods, potentially self-replicating chemical systems that may have been competitors to RNA in a primordial world. At the conference he presented a system he recently synthesized in which he expected the strands of the molecule to pair well with DNA and RNA as well as with its partner; however, some of the strands failed to bind which led to the discovery an additional criterion for strands that may shed light on why RNA prevailed in the primordial world.
So, Ram and his team initially set out to identify potential RNA alternatives, but what they found was a very interesting new criterion to better understand RNA and DNA and further the search for alternatives or precursors. The pKa itself may not be responsible for the relative bonding strengths of different bases, the results do suggest that pKa differences are a good and relativle convenient indicator for potential bases that will have the proper bonding strength. An interesting time is upon us, where pKa may now be one of the first considerations in work to identify alternative bases.