Research
Projects in the Hud Lab
Intercalation-Mediated Nucleic Acid Assembly
We are investigating how intercalation by small molecules can be
used to assemble RNA-like polymers. Our initial experiments in this area have
revealed that coralyne, a small crescent-shaped molecule, causes the
disproportionation of duplex poly(dT):poly(dA). That is, coralyne causes the
strands of duplex poly(dT):poly(dA) to repartition into equal molar equivalents
of triplex poly(dT):poly(dA):poly(dT) and poly(dA) (see figure above). We have
also discovered that poly(dA) forms a self-structure in the presence of
coralyne with a melting temperature of around 47oC. This poly(dA) self-structure binds coralyne with an
affinity that is comparable to that of triplex poly(dT):poly(dA):poly(dT).
These studies represent the first time that a small molecule at micromolar
concentrations has been shown to cause a nucleic acid sample to completely, and
spontaneously, change its secondary structure. More importantly, our findings
illustrate the great potential for intercalation to act as a molecular switch
of nucleic acid structures. This provides supports for our theories for the
origin of the RNA world (see below).
The
Molecular Midwife and the Origin of Life
It is now widely accepted that life evolved from a far simpler self-replicating molecular system. However, the origin of life and the evolutionary path that led to life as we know it remain obscure. In contemporary biological systems only RNA functions in both the transfer of genetic information and chemical catalysis, two properties essential for self-replication. Consequently, a period in biological evolution has been proposed when all information storage and chemical catalysis was carried out by RNA (the "RNA world" hypothesis). There are presently a number of efforts underway to verify and possibly recreate elements of the RNA world, however, none have produced a true self-replicating system. We have recently published a detailed theory for how plausible molecular constituents of the primordial soup could have brought about the RNA world. The central figure in our theory is what we have dubbed the Molecular Midwife (shown above schematically in blue). This was a molecule that we believe acted as a template for the initial assembly and replication of RNA-like polymers. Much of the activity of the Molecular Midwife is associated with its ability to intercalate RNA-like polymers. Unlike many previous theories for the origin of life, the details of this theory lend themselves to experimental verification and suggest a potential method for the replication of RNA that is consistent with recognized principles of molecular self-assembly. As part of our laboratory's emphasis on nucleic acid structure and assembly, work is being carried out towards the realization of protein-free replication of RNA-like polymers. Success in this endeavor would open a new area of combinatorial chemistry and in vitro evolution. This would in turn have numerous applications in the development of therapeutics and novel catalysts. [publications on this topic] [An interview with Prof. Hud regarding the origin of life]
Nucleic
Acid-Cation Interactions
The polyanionic nature of nucleic acids mandates that cations play an essential role in the stabilization of RNA and DNA structures. With NMR spectroscopy it is often possible to determine both the solution state structure of a nucleic acid molecule and the location of their cation binding sites. This approach complements studies conducted using x-ray crystallography, for in the solution state kinetic and thermodynamic aspects of cation binding can also be studied. In our laboratory we are studying the cation binding properties of various nucleic acid molecules. [publications on this topic]
