Blocking Oligonucleotide Adaptors for Nucleic Acid Joining
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Solution Overview
Problem
Current nucleic acid workflows face challenges in efficiently joining polynucleotides due to the formation of undesirable adaptor dimers or trimers, which reduces the yield of desirable polynucleotide-adaptor products.
Innovation Solution
The use of blocking oligonucleotide adaptors, which are designed to hybridize with nucleic acid overhangs, reducing the formation of dimers or trimers by annealing with each other instead, thereby improving the yield of desirable products through specific hybridization and subsequent manipulation steps.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If standard nucleic acid adaptors are used for joining polynucleotides, then the joining process can proceed, but adaptor dimers or trimers form which reduces the yield of desirable polynucleotide-adaptor products
Solution Approach 1:
The blocking adaptor incorporates a blocking oligonucleotide sequence that preemptively prevents adaptor dimers or trimers from forming by hybridizing with and blocking the adaptor's overhang sequence. This preliminary anti-action stops the harmful concatemerization process before it can occur, thereby improving the yield of desirable polynucleotide-adaptor products.
Solution Approach 2:
The blocking oligonucleotide sequence acts as an intermediary element within the blocking adaptor. It mediates the prevention of harmful adaptor-adaptor interactions by specifically binding to the adaptor overhang, thereby blocking unwanted concatemerization while allowing the adaptor to still perform its intended function of joining polynucleotides.
2Productivity
If blocking oligonucleotide adaptors are used to prevent dimer formation, then the yield of desirable products improves, but the device complexity increases due to additional blocking sequences
Solution Approach 1:
The blocking adaptor merges multiple functions into a single oligonucleotide structure: it contains both the functional adaptor sequence needed for polynucleotide joining and the blocking oligonucleotide sequence needed to prevent dimer formation. This consolidation reduces the number of separate components needed while achieving both goals.
Solution Approach 2:
The blocking adaptor is designed as a multi-functional molecule that simultaneously serves as both an adaptor for joining polynucleotides and a blocking agent to prevent unwanted concatemerization. The single blocking adaptor structure performs multiple roles, reducing overall system complexity despite the added functionality.
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 enhances the yield of desirable polynucleotide-adaptor products by preventing unwanted concatemerization, allowing for more effective joining of polynucleotides and circularization, thereby improving the efficiency of nucleic acid workflows.
Implementation Method 1
Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products
Data Source
AI summary
Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. Also provided herein are compositions generated using the blocking oligonucleotide adapters, including circularized polynucleotides, that may be manipulated, for example, through nick translation, to yield a linear mate pair construct.