Abstract
A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.
Highlights
When the monomers added to a growing polymer chain depend on signals in the environment, such as the ion fluxes during an action potential, the polymer sequence stores a record of the environmental signal’s variation over time, much like a ticker tape [1,2]
We recently proposed a molecular device for recording time-varying ion concentration signals: DNA polymerases (DNAPs) copy known template DNA strands with an error rate dependent on the local ion concentration
We focus on (1) the kinetic parameters of polymerization by DNAP: the average single-base elongation time, average pause time, and pause probability (P); (2) the number of simultaneously replicated DNA template strands; and (3) the concentration to misincorporation link function (CMLF), which relates the per-base misincorporation probability to the local ion concentration
Summary
When the monomers added to a growing polymer chain depend on signals in the environment, such as the ion fluxes during an action potential, the polymer sequence stores a record of the environmental signal’s variation over time, much like a ticker tape [1,2]. DNA polymerases (DNAPs), enzymes that catalyze replication of DNA, possess nucleotide misincorporation probabilities that can be modulated by local ion concentrations [3,4], making them candidates for ion-sensitive molecular ticker tapes that encode signals into DNA strands in the form of base misincorporation patterns. In DNAP misincorporation-based recording, information is stored in the form of a string of copied nucleotides, which can be sequenced and compared to the known template sequence to identify the sites of misincorporations. One can estimate the state of the environment – e.g. ion concentration – as a function of time, based on the observed misincorporation pattern.
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