Oligonucleotide Adapters for Nucleic Acid Ligation
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Solution Overview
Problem
Current nucleic acid sequencing methods face inefficiencies in ligation reactions due to the limited compatibility of oligonucleotide adapters with varied or unknown nucleotide overhang sequences, leading to reduced sequencing throughput and analysis challenges.
Innovation Solution
The use of oligonucleotide adapters with a mixture of distinct single-stranded overhang sequences and lengths, allowing for the efficient ligation of nucleic acid inserts with varied overhangs, thereby facilitating the sequencing of entire DNA populations and accelerating the ligation reaction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If a single type of oligonucleotide adapter with a fixed overhang sequence is used in ligation reactions, then the ligation reaction is simple to perform, but the compatibility with varied or unknown nucleotide overhang sequences is limited
Solution Approach 1:
The adapter population is segmented into multiple distinct types, each with a specific overhang sequence (e.g., 16 different single-nucleotide overhangs or 16 different double-nucleotide overhangs). This segmentation allows the adapter mixture to collectively match a broader range of insert overhang sequences, resolving the contradiction between simplicity and versatility.
Solution Approach 2:
The adapter mixture serves multiple functions simultaneously by incorporating diverse overhang sequences. Each adapter type in the mixture can bind to different insert overhangs, making the system universally compatible with varied nucleic acid fragments while maintaining a single-step ligation protocol.
2Productivity
If adaptors with multiple distinct overhang sequences are used, then the sequencing throughput is improved, but the ligation reaction complexity increases
Solution Approach 1:
The adapter system is divided into multiple distinct adapter types, each optimized for specific overhang sequences. This segmentation enables parallel processing of diverse nucleic acid fragments during ligation, increasing sequencing throughput while keeping each individual adapter type simple in structure.
Solution Approach 2:
The overhang sequence parameter of the adaptors is varied to create a library of adapters with different sequences (e.g., all 16 possible single-nucleotide overhangs). This parameter change allows the system to accommodate diverse inserts and improve sequencing throughput without fundamentally changing the ligation mechanism.
3Adaptability or versatility
If a mixture of adaptors with distinct overhangs is used, then the range of nucleic acid fragments that can be ligated is expanded, but the difficulty of designing and implementing the ligation system increases
Solution Approach 1:
The adaptor mixture is designed to be universally compatible with various nucleic acid fragments by incorporating all possible overhang sequences (e.g., all 16 single-nucleotide or double-nucleotide combinations). This universal design expands the range of ligatable fragments while maintaining ease of manufacture through standardized synthesis protocols.
Solution Approach 2:
Systematic variation of the overhang sequence parameter creates a comprehensive set of adaptors that can match any insert. This parameter-based design approach simplifies the manufacturing process by using combinatorial synthesis methods rather than requiring custom design for each fragment type.
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 efficient ligation and sequencing of nucleic acid samples with diverse overhang sequences, enhancing sequencing throughput and data quality by accommodating a broader range of nucleic acid fragments.
Implementation Method 1
ligating the adaptors to the inserts with a ligase enzyme to generate ligated inserts
Implementation Method 2
the overhangs have random nucleotide sequences or a plurality of distinct sequences designed to hybridize to nucleotide overhangs of the inserts
Data Source
AI summary
The present disclosure relates to systems and methods for nucleic acid ligation. In particular, the present disclosure provides oligonucleotide adaptors for use in nucleic acid ligation reactions.