Error Detection in Hybridisation of Nucleic Acid Sequences
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Solution Overview
Problem
Current methods for synthesizing double-stranded nucleic acids, such as DNA, face challenges due to high error rates in nucleotide incorporation, leading to low yields and limitations in synthesizing longer sequences, as errors accumulate and reduce the efficiency of hybridization processes, making it costly and time-consuming to produce error-free sequences.
Innovation Solution
The method involves a series of hybridization steps with error-detecting operations to identify and discard erroneous fragments, using a controlled apparatus with temperature control and fluid flow to manage fragment hybridization and error detection, ensuring that only error-free fragments are used in subsequent steps, thereby improving the yield of target double-stranded nucleic acids.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional hybridization methods are used to synthesize double-stranded nucleic acids, then the process is simple and fast, but the yield of error-free sequences is low due to accumulation of incorporation errors
Solution Approach 1:
The patent divides the synthesis process into multiple sequential hybridization stages, where fragments are assembled step-by-step rather than all at once. Each stage allows for error detection and removal before proceeding to the next stage, preventing error accumulation and improving the overall yield of error-free sequences.
Solution Approach 2:
The patent performs error detection and removal operations before final assembly of the complete nucleic acid sequence. By identifying and discarding erroneous fragments in advance during intermediate stages, the system ensures that only error-free fragments proceed to subsequent hybridization steps, thereby improving reliability without sacrificing productivity.
2Reliability
If cloning-based techniques are used to correct errors, then error-free sequences can be obtained, but the process becomes expensive and time-consuming
Solution Approach 1:
The patent implements self-service error correction through automated error detection and removal operations that are integrated into the hybridization process itself. The system automatically identifies erroneous fragments and removes them without requiring external cloning or manual intervention, thereby maintaining high reliability while significantly reducing the time and cost associated with traditional error correction methods.
Solution Approach 2:
The patent extracts erroneous fragments from the hybridization mixture through selective removal operations. By identifying and taking out only the erroneous sequences at each stage, the system efficiently corrects errors without needing to process or clone the entire population of sequences, thus reducing time and resource requirements compared to conventional cloning-based approaches.
3Reliability
If multiple cloning lines are used to increase the chance of obtaining error-free samples, then reliability improves, but the cost and complexity increase significantly
Solution Approach 1:
The patent incorporates feedback mechanisms where the results of error detection at each hybridization stage inform subsequent processing steps. By using feedback to guide selective removal of erroneous fragments and to adjust subsequent hybridization conditions, the system achieves high reliability through a single controlled process rather than requiring multiple parallel cloning lines, thereby reducing complexity while maintaining or improving error-free sequence production.
Data Source
AI summary
A series of hybridisations is performed for forming a target double-stranded nucleic acid from initial fragments, where each further hybridisation step hybridises the direct products of a pair of earlier hybridisation steps. For at least one further hybridisation step HF, both of the corresponding pair of earlier hybridisation steps HE comprise an error-detecting type of hybridisation step, which includes an error detecting operation to detect whether the hybridised fragments formed in the error-detecting type of hybridisation step HE comprise at least one erroneous hybridised fragment, and discarding at least part of the erroneous fragment to exclude it from a subsequent further hybridisation step. By detecting and removing erroneous fragments throughout a staged and controlled hybridisation process, erroneous fragments are prevented from diluting the pool of error-free fragments at each hybridisation step, to improve yield.