DNA Array Sequencing with Interspersed Adaptors
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Solution Overview
Problem
Traditional high-throughput sequencing techniques are limited by short sequence read lengths and random positioning of DNA targets, which reduces packing efficiency and overall sequencing efficiency.
Innovation Solution
The method involves creating concatemers with interspersed adaptors that are immobilized on a surface, allowing for the use of sequencing probes to identify nucleotides by hybridization and extension reactions, thereby increasing sequence information per cycle and improving read lengths.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If random positioning of DNA targets is used over an array surface, then ease of operation is improved, but manufacturing precision deteriorates due to reduced packing efficiency
Solution Approach 1:
The patent applies preliminary action by pre-defining specific attachment sites on the array surface before DNA targets are introduced. The surface is prepared with predetermined binding locations that guide DNA attachment, ensuring optimal packing efficiency before the actual sequencing process begins. This pre-arrangement resolves the contradiction by establishing precise positions in advance while maintaining operational simplicity.
2Device complexity
If traditional sequencing chemistry is used, then device complexity is reduced, but productivity deteriorates due to limited sequence information per cycle
Solution Approach 1:
The patent applies segmentation by dividing the sequencing process into multiple sequential steps within each cycle. Instead of attempting to read multiple nucleotides simultaneously, the method segments the detection into sequential rounds where different nucleotide types are detected in succession. This allows traditional sequencing chemistry to be enhanced with multi-step protocols that increase information output per cycle without requiring complex new chemistry.
Solution Approach 2:
The patent implements periodic action by repeating cycles of nucleotide incorporation and detection multiple times. Each cycle follows a periodic pattern of adding specific nucleotides, washing, and detecting signals. By repeating these periodic cycles with different nucleotide compositions, the system accumulates sequence information over multiple iterations, increasing productivity while maintaining relatively simple device architecture.
3Manufacturing precision
If short read lengths are accepted, then manufacturing precision requirements are reduced, but loss of information increases due to limited contiguous sequence determination
Solution Approach 1:
The patent applies continuity of useful action by extending the sequencing read length through continuous sequential detection. Instead of stopping after a few nucleotides, the method maintains continuous detection capability by repeating the nucleotide addition and signal detection cycles multiple times in succession. This continuous process accumulates sequence information over longer stretches, reducing information loss while managing precision requirements through incremental rather than simultaneous measurement.
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 the determination of longer contiguous sequences by reading nucleotides adjacent to adaptors, enhancing sequencing efficiency and information output.
Implementation Method 1
identifying the first nucleotide comprises contacting the concatemers with a set of sequencing probes
Implementation Method 2
contacting the concatemers with a set of sequencing probes. In an exemplary embodiment, the sequencing probes each comprise a first domain complementary to one of the adaptors, a unique nucleotide at a first interrogation position, and a label
Data Source
AI summary
The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.