Single-Base Editor DNA Clock for Cellular Time Measurement
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Solution Overview
Problem
Current methods face challenges in accurately tracking and measuring elapsed time within cells due to the complexity and transient nature of biological signals, making it difficult to monitor and study molecular events in their native context.
Innovation Solution
A composition comprising a single-base editor and guide RNA targeting human genome sequences with a protospacer adjacent motif (PAM), allowing for the measurement of elapsed time by transducing the composition into cells, culturing them, and calculating the time elapsed using the frequency of edited sequences through A-to-G conversion.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional methods are used to track biological signals, then measurement can be performed, but accuracy and precision are insufficient due to the complexity and transient nature of biological signals
Solution Approach 1:
The patent extracts the time measurement function from complex biological signal tracking by using a simplified DNA-based recording system. The single-base editor and guide RNA system selectively edits specific DNA targets, creating a simplified molecular clock that directly measures time without needing to track complex transient biological signals.
Solution Approach 2:
The patent changes the measurement parameter from tracking dynamic biological signals to measuring the cumulative frequency of DNA editing events. By monitoring the proportion of edited versus unedited DNA targets over time, the system converts a dynamic measurement problem into a stable compositional measurement that can be accurately quantified.
2Device complexity
If a small number of targets are used in the DNA clock, then the system is simpler and more practical, but measurement accuracy may be compromised
Solution Approach 1:
The patent performs preliminary action by designing the DNA clock system with pre-selected target sites that are optimized for accurate time measurement. The guide RNA and single-base editor are configured beforehand to target specific genomic locations, ensuring that even with a limited number of targets, the system can accurately track time through the cumulative editing frequency.
3Loss of information
If CRISPR Cas-based molecular recording devices are used, then molecular events can be recorded, but the system is complex and requires multiple components
Solution Approach 1:
The patent extracts only the essential time-recording function from the CRISPR Cas system by using a single-base editor instead of the full CRISPR Cas machinery. This simplified approach retains the ability to record molecular events through DNA editing while eliminating the need for multiple Cas proteins, gRNAs, and other complex components.
Solution Approach 2:
The patent replaces the mechanical CRISPR Cas complex with a simpler single-base editor system that achieves the same information recording function through a different mechanism. The single-base editor directly modifies DNA bases without requiring the complex Cas protein machinery, thereby substituting a simpler molecular mechanism for the more complex CRISPR system.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables precise estimation of elapsed time by exploiting the exponential decay of intact target sequences, allowing for accurate time measurement even in isolated cells using a small number of targets, thereby overcoming the limitations of traditional methods.
Implementation Method 1
a single-base editor or a nucleic acid encoding the same... measuring the copy number frequency of a sequence edited by the composition, that is, the A-to-G conversion frequency
Data Source
AI summary
Please enter in the present application the English translation of the abstract of the Korean language application that was filed in the USPTO on Jun. 12, 2024, as contained in the English translation of the application in Appendix B of the Translator Certificate filed herewith, and as separately filed herewith in .docx format (728_Patent_Application_ABSTRACT.docx).