Polymer Sequence Decoding via Fluorescence Signal Sequencing
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Solution Overview
Problem
Existing methods for decoding information stored on DNA strands or other polymers are slow, time-consuming, and inefficient, particularly when dealing with varying sizes of polymer sequences, as they require sequencing individual bases rather than blocks or sections.
Innovation Solution
An optical method that involves attaching sequence-encoded molecular probes to polymer sequences, which emit fluorescence signals as they are unwound, allowing for real-time decoding of information by observing the sequence of fluorescence signals produced.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If individual bases are sequenced using conventional methods, then measurement precision is achieved, but productivity is significantly reduced
Solution Approach 1:
The patent divides the polymer sequence into discrete blocks or sections, each containing multiple component molecules. Instead of sequencing individual bases, the method sequences entire blocks as units. This segmentation approach maintains measurement precision by accurately determining block composition while dramatically improving productivity by reducing the total number of sequencing operations required.
Solution Approach 2:
The patent combines multiple component molecules into single functional blocks that can be sequenced together. By merging individual bases into blocks and using combined labeling approaches (multiple labels on the same polymer), the system achieves high-throughput sequencing that maintains accuracy while increasing readout rate by orders of magnitude.
2Adaptability or versatility
If polymer sequences of varying sizes are processed, then adaptability is improved, but device complexity increases
Solution Approach 1:
The patent employs dynamic control of label unbinding through enzymatic digestion that can be precisely regulated in real-time. The enzyme activity can be adjusted to process polymer sequences of varying lengths and compositions, allowing the system to adapt to different input sizes without requiring separate processing pathways, thereby managing complexity while maintaining versatility.
Solution Approach 2:
The system changes key parameters including enzyme concentration, digestion time, and label design to accommodate polymer sequences of varying sizes. By adjusting these parameters, the same basic apparatus can handle diverse polymer lengths and compositions, achieving adaptability without proportionally increasing device complexity.
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
This method significantly increases the rate of readout and enables high-throughput decoding of information stored on polymer sequences by focusing on blocks or sections rather than individual bases, improving efficiency and speed.
Implementation Method 1
The molecular probe includes a fluorophore at the leading end that emits a fluorescence signal at a wavelength based on the corresponding pattern of component molecules
Implementation Method 2
a quencher that inhibits a fluorescence signal emitted by an adjacent fluorophore at a leading end of a trailing adjacent molecular probe
Data Source
AI summary
A method and system to decode information stored on a polymer sequence, such as a DNA strand, is described herein. The method and system use molecular probes to label sections of the polymer sequence. Each molecular probe includes a fluorophore and a quencher. The fluorophore produces light with a color and wavelength corresponding to the information stored on the section of the polymer sequence the molecular probe labels. The quencher inhibits the production of light by an adjacent fluorophore. When adjacent sections of the polymer sequence are labeled with molecular probes, the fluorophore of the leading molecular probe produces light while the trailing molecular probe's light is quenched. The method and system then sequentially unbind the molecular probes from the sections of the polymer sequence within a waveguide, producing a sequence of observable fluorescence signals. The sequence can be used to determine the information stored on a polymer sequence.