Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published October 4, 2011 | Published + Supplemental Material
Journal Article Open

Timing molecular motion and production with a synthetic transcriptional clock

Abstract

The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of "load" processes such as the operation of a DNA-based nanomechanical device ("DNA tweezers") or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an "insulator circuit" was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems.

Additional Information

© 2011 by the National Academy of Sciences. Freely available online through the PNAS open access option. Edited by David Baker, University of Washington, Seattle, WA, and approved August 9, 2011 (received for review January 17, 2011). We are especially grateful to Eric Klavins for coining the irresistible moniker "genelets," to Maximilian Weitz for control measurements, and to Franco Blanchini for mathematical advice. The authors acknowledge financial support by the Human Frontier Science Program (HFSP) grant no. RGY 74/2006, the European Commission FP7 grant no. 248919 (BACTOCOM), the National Science Foundation (NSF) grants nos. NIRT-0608889 and CCF-0832824 (The Molecular Programming Project), the Institute for Collaborative Biotechnologies (grant DAAD19-03-D-0004 from the Army Research Office), and the Nanosystems Initiative Munich (NIM). Author contributions: E. Franco, E. Friedrichs, J.K., E.W., and F.C.S. designed research; E. Franco and E. Friedrichs performed research; E. Franco, E. Friedrichs, J.K., R.J., R.M., E.W., and F.C.S. analyzed data; and E. Franco, E. Friedrichs, J.K., R.J., E.W., and F.C.S. wrote the paper.

Attached Files

Published - PNAS-2011-Franco-E784-93_1_.pdf

Supplemental Material - Appendix.pdf

Files

Appendix.pdf
Files (18.1 MB)
Name Size Download all
md5:7c78da9bc73139671383ab7d65834401
10.4 MB Preview Download
md5:17b97dc448de4e3d9e82cd1d9afc71fd
7.7 MB Preview Download

Additional details

Created:
August 22, 2023
Modified:
October 24, 2023