Asynchronous DNA Sequencing via Parallel Polymerization

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Solution Overview

Problem

Current DNA sequencing methods are labor-intensive, time-consuming, and require significant amounts of DNA, limiting their ability to achieve rapid, high-throughput sequencing with minimal starting material, especially for clinical applications and large-scale genome projects.

Innovation Solution

The method involves asynchronous polymerization reactions using multiple nucleic acid molecules with the same sequence, each complexed with a primer and polymerase, where the polymerization reactions are conducted in optical confinements to generate overlapping nascent strands, allowing for the compilation of sequence information without the need for extensive DNA amplification or cloning.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If traditional Sanger or Maxam-Gilbert sequencing methods are used, then sequence accuracy is achieved, but the process is labor-intensive and time-consuming

Engineering Contradiction:
Improvesequencing speedVSAvoidtime required for sequencing run
Core Design Contradiction:
ProductivityVSLoss of time

Solution Approach 1:

The patent segments the sequencing process by using multiple independent polymerase reactions occurring in parallel within a single flow cell. Each polymerase independently synthesizes a nascent strand, and multiple such reactions are conducted simultaneously, dividing the overall sequencing task into concurrent segments that collectively produce the complete sequence data much faster than sequential methods.

Inventive Principle:
Principle #1Segmentation

2Quantity of substance

If PCR amplification is performed to increase DNA quantity, then sufficient template DNA is available for sequencing, but the process becomes more complex and time-consuming

Engineering Contradiction:
Improveamount of DNA templateVSAvoidcomplexity of pretreatment steps
Core Design Contradiction:
Quantity of substanceVSDevice complexity

Solution Approach 1:

The patent applies self-service by designing a system where the sequencing reaction itself generates sufficient signal without requiring prior PCR amplification. The asynchronous polymerization reactions produce multiple nascent strands that collectively provide enough template for accurate sequence determination, eliminating the need for separate amplification steps and reducing overall process complexity.

Inventive Principle:
Principle #25Self-service

3Length of moving object

If synchronous polymerization is used as in previous methods, then sequence reading is simplified, but sequence read length is restricted to about 40 nucleotides

Engineering Contradiction:
Improvesequence read lengthVSAvoidsynchronization requirement
Core Design Contradiction:
Length of moving objectVSEase of operation

Solution Approach 1:

The patent employs dynamics by allowing polymerases to operate asynchronously rather than in strict synchronization. Each polymerase progresses through the template at its own rate, and the system dynamically captures sequence information from multiple polymerases at different stages of synthesis. This dynamic approach enables reading of much longer sequences because the data from asynchronously progressing polymerases can be integrated to reconstruct the complete sequence.

Inventive Principle:
Principle #15Dynamics

4Quantity of substance

If extensive DNA amplification and cloning into sequencing vectors is performed, then sufficient DNA material is obtained for sequencing, but the cost increases making it unrealistic for large-scale projects

Engineering Contradiction:
Improveamount of DNA materialVSAvoidcost of sequencing
Core Design Contradiction:
Quantity of substanceVSEase of manufacture

Solution Approach 1:

The patent applies preliminary action by performing minimal pretreatment of the DNA source - simply preparing the template DNA without extensive amplification or cloning. The system is designed to work efficiently with the available template DNA, using asynchronous polymerization to generate sufficient sequence information directly from the original sample, thereby eliminating costly and time-consuming preliminary steps.

Inventive Principle:
Principle #10Preliminary action

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 approach enables efficient, rapid, and accurate DNA sequencing with reduced DNA requirements, improving throughput and minimizing errors through redundant sequence data analysis, thereby addressing the limitations of traditional sequencing techniques.

Implementation Method 1

The first nucleic acid molecule is subjected to a first polymerization reaction to yield a first strand complementary to the first nucleic acid molecule. The second nucleic acid molecule is subjected to a second polymerization reaction to yield a second strand complementary to the second nucleic acid molecule.

Methodology Applied
Scientific EffectPolymerization:

Implementation Method 2

Time sequences of incorporation of nucleotides or nucleotide analogs into the first strand and the second strand during the asynchronous polymerization reactions are obtained

Methodology Applied
Scientific EffectOptical detection:

Data Source

PatentUS8993230B2Asynchronous sequencing of biological polymers
Publication Date: 2015.03.31 PACIFIC BIOSCIENCES OF CALIFORNIA INC
  • US8993230B2 patent drawing

AI summary

The present invention provides methods, reagents and apparatus for conducting single molecule sequencing in an asynchronous manner. The subject methods and compositions are particularly useful for high throughput and multiplexed sequencing.