2001 Annual Science Report

Scripps Research Institute Reporting  |  JUL 2000 – JUN 2001

Executive Summary

Executive Summary – SCR (dm)

What constitutes life, requirements for the origins of life and evolution, and how living systems may be identified elsewhere in the universe are some of the most fundamental questions in astrobiology. Under the auspices of the Scripps Research Institute, a “vitual institute” has been assembled to explore multidisciplinary experimental approaches to self-replicating molecular species and Darwinian chemistry, the most important hallmarks of life. By comparing and contrasting the results of diverse but complementary set of experiments, we seek to garner a better understanding of life and its origins. In the past year our team has made significant progress in several areas of research.

Benner’s group at the University of Florida has confirmed that hydrogen bonding is central to base pairing in DNA, laying to rest a five-year discussion suggesting that specific base pairing might be had between two DNA strands without the involvement of hydrogen bonds. This result provides an important piece of a model to help us guess how non-terrean genetic systems might be structured, and how they might be detected on Mars, Europa, and elsewhere. They have also made significant progress in developing polymerases to support in vitro selection with functionalized nucleic acids on an expanded genetic alphabet, directed towards generating in the laboratory artificial experimental models for life. In an effort to couple geology to genomics, Benner’s group has organized database of protein sequences containing a complete history of macromolecular life on Earth in order to extract genomic clues that couple events in the molecular record with mass extinctions, paleoecology biosphere transitions, and planetary events. Benner’s group has also developed simple assays to detect organic chemicals on the surface of Mars.

Ghadiri’s group has continued their efforts in the design and characterization of novel self-organized molecular systems that display emergent properties such as replication and parasitism. Furthermore, they provided an important experimental evidence for the origin of homochirality in living systems. Origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules, but none of the possible physiochemical processes considered can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material, or for a nonenzymatic process by which biopolymers undergo chiroselective molecular replication. Given that molecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature. Ghadiri’s group reported recently that a 32-residue peptide replicator is capable of efficiently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective amplification process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical “editing” function; it makes use of heterochiral sequences that arise through uncatalyzed background reactions to catalyze the production of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.

Ellington’s group has made significant strides in filling in several key intermediates in a hypothetical ascent of molecules from simplistic origins to complex catalysts presumed present in the RNA world. They have described in vitro selection of a simple deoxyribozyme that may have resembled some of the earliest self-replicators. In addition, Ellington’s group evolved a ribonucleoprotein enzyme that may have resembled cataysts found at the boundary between the ancient RNA and modern protein worlds. Finally, their studies, directed at generating an unnatural organism, have gone far in testing the bounds of terrestrial chemistry.

Rebek’s group continues to evaluate molecular requirements for the process of self-replication in abiotic systems. They have devised a system that shows a new form of autocatalysis. It involves encapsulated reagents that work on the principles of molecular recognition but without any direct contact between reagents and products. The emergent properties of this system are related to those of self-replicating molecules.

Switzer’s group has expanded efforts directed at design and discovery of alternative nucleic acids strcutures. They demonstrated that the iso-Coiso-G base-pair exhibits intrinsic fidelity during non-enzymatic transcription. This result is in complete contrast with the limited fidelity seen during past experiments involving replication, transcription and translation using natural enzymes and the unnatural iso-Coiso-G base-pair, and implies iso-Coiso-G could have contributed to early biopolymer replication on Earth or elsewhere. In addition they established that the non-standard iso-Coiso-G nucleotide base-pair can support recombination. This is the first time the question of recombination ability has been assessed for an unnatural base-pair, and is an important component of base-pair fitness. Switzer’s group has also shown that an acyclic, phosphodiester linked, glycerol nucleotide template (an attractive pre-RNA candidate) can participate in non-enzymatic template-directed copying reactions. Prior to this study, such a result was considered unlikely, and implies this primitive nucleotide candidate could have contributed to early biopolymer replication.