NERPE
Non-Enzymatic RNA Primer Extension
Faculty Advisor/PI: Prof. Jack Szostak/Dr. Daniel Duzdevich (U. Chicago); Christopher E. Carr (Georgia Tech, Collaborator)
Start Date: Mid 2018
Current Status: Active
Collaborators: This is a collaborative project led by the Szostak lab at University of Chicago
All known life is related to a common ancestor as evidenced by sequence conservation of nucleic acids, the basis for heredity and evolution. In modern life, DNA codes for RNA, which is translated into proteins that are the molecular machinery of a cell. This translation is performed by the ribosome, a molecular machine made of RNA, and later proteins, which provides evidence of an ancient RNA world that preexisted the DNA world. In such an RNA world, life would have had to evolve translation before proteins could be made, a classic chicken and egg problem. This implies RNA would have needed to copy itself in the absence of enzymes.
Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes (functional RNAs) such as the ribosome. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we have introduced a deep-sequencing methodology for studying RNA primer extension and are applying it to address these questions and assess the plausibility of non-enzymatic RNA copying in a planetary context.
[Some text above adapted from Duzdevich et al. 2020.]
Funding: Supported by H.H.M.I. awards to Szostak.
Publications:
[Journal] Daniel Duzdevich, Christopher E. Carr, Dian Ding, Stephanie J. Zhang, Travis S. Walton, and Jack W. Szostak. Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Research, 49(7):3681-91, 19 April 2021 https://doi.org/10.1093/nar/gkab173 Preprint BioRxiv https://www.biorxiv.org/content/10.1101/2021.01.02.425068v1
[Journal] Daniel Duzdevich*, Christopher E. Carr* and Jack W. Szostak. Deep sequencing of nonenzymatic RNA primer extension. Nucleic Acids Research (2020), gkaa400, https://doi.org/10.1093/nar/gkaa400. Preprint: bioRxiv 10.1101/2020.02.18.955120 *Joint authors. Correction Code: https://github.com/CarrCE/NERPE-Seq
[Preprint] Stephanie J. Zhang, Daniel Duzdevich, Christopher E. Carr, and Jack W. Szostak. Freeze-thaw Cycles Enable a Prebiotically Plausible and Self-contained Pathway from Nucleotide Activation to Nonenzymatic Template-directed RNA Polymerization. Preprint: bioRxiv https://doi.org/10.1101/2021.09.07.459201
[Talk] Daniel Duzdevich, Christopher E. Carr, Jack W. Szostak. Studying the Sequence Space of Nonenzymatic RNA Polymerization Using Deep Sequencing. 23rd SANKEN International Symposium, Awaji, Japan, January 9-10, 2020 (abstract, invited talk).
[Poster] Duzdevich D, Carr CE, Szostak JW. A Novel Approach to Studying the Sequence Space of Nonenzymatic RNA Primer Extension Using Deep Sequencing. Astrobiology Science Conference, June 24-28, 2019. Abstract + Poster.
[Poster] Daniel Duzdevich, Christopher E. Carr, and Jack Szostak. Studying the Emergence of Heredity at the Origin of Life: A New Deep-sequencing Analysis of Nonenzymatic RNA Primer Extension. Harvard Origins of Life Initiative, Spring Poster Session, May 8, 2019.