Zenith Grant Awardee

Dr. Thomas LaBean

Duke University

Co-Investigators

Erik A. Schultes, <i>Duke University</i><br>Peter Hraber, <i>Los Alamos National Lab</i>

Project Title

Experimentally Probing the Origins of Macromolecular Structure

Project Summary

Darwin's theory of evolution describes the close fit between adaptations and the environment, but what is the ultimate source of these adaptations from which natural selection must choose? For macromolecules such as proteins and the nucleic acids RNA and DNA, no amount of genomic or phylogentic data can answer this question because genealogical relationships among macromolecules confound the ultimate physiochemical properties creating adaptations and the historically contingent constraints that limit them. To understand the ultimate origins of macromolecular structures, it is therefore necessary to explore the much larger space of sequence possibilities from which particular evolutionary lineages are derived. This FQXi proposal will utilize new technology to literally "print" tens-of-thousands of closely-related DNA sequences on a "chip" so their functional adaptations can be directly analyzed using automated instrumentation. By systematically scanning through large regions sequence space, it will be possible to identify the entire spectrum of adaptations that are possible and to directly evaluate the likelihood that new structures and functions can emerge in the course of evolution. This experimental approach opens up a new kind of evolutionary analysis based not on what has happened in the past, but what is possible independent of any particular evolutionary lineage.

Technical Abstract

Although there is a well-developed theory describing molecular evolution, there is at present no rigorous theory explaining the ultimate origins of complex macromolecular structure. Previous analyses have suggested that networks of sequences that encode the same structure (so-called neutral networks) permeate nucleic acid sequence space. It has been conjectured that new structures (and functions) may arise in the course of evolution by small mutational changes near the intersections of distinct neutral networks. Intersecting networks have been experimentally demonstrated (Schultes & Bartel 2000), but how important this mechanism is to the emergence of new folds in evolution remains an open question. It ultimately depends on the degree of interconnectivity of neutral networks, a parameter that could not be measured using previous methods. Here, we use high-throughput DNA microarrays to directly measure the proximity and interconnectivity of multiple neutral networks. Microarrays displaying the entire single- and double-step mutational neighborhoods of a DNA aptamer will be assayed for biding to the cognate peptide substrate as well as alternative peptide substrates. By systematically evaluating the multiple functionalities of a local mutational neighborhood, it will be possible to directly measure the network parameters governing the emergence of new structures in the course of evolution.