Scaffold Adapter Composition for Single-Stranded Nucleic Acid Libraries
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing methods for preparing nucleic acid libraries, particularly single-stranded nucleic acid libraries, are labor-intensive, time-consuming, and require expensive, exotic reagents, limiting their widespread use in high-throughput sequencing.
Innovation Solution
A composition comprising scaffold adapters with unique molecular identifiers (UMIs) and scaffold polynucleotides that hybridize to single-stranded nucleic acids, allowing for efficient library preparation without the need for labor-intensive protocols and exotic reagents, using oligonucleotides with GC-rich regions and complementary sequences for hybridization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If traditional single-stranded library preparation methods are used, then library quality and complexity are improved, but labor intensity, time consumption, and reagent cost increase
Solution Approach 1:
The library preparation process is divided into distinct functional modules: fragmentation, end modification with scaffold adapters containing UMIs, and sequencing. Each module can be independently optimized and performed, allowing parallel processing and reducing overall preparation time while maintaining library quality
Solution Approach 2:
Scaffold adapters with unique molecular identifiers (UMIs) are pre-designed and synthesized with specific functional regions (ssNA hybridization region, oligonucleotide hybridization region, UMI region) before use. This preliminary preparation of standardized adapters eliminates the need for complex, custom reagent preparation during the library construction process, reducing both time and labor requirements
2Manufacturing precision
If single-stranded library preparation is performed, then library complexity is improved, but reagent cost and protocol complexity increase
Solution Approach 1:
The scaffold adapter design incorporates multiple functional regions within a single universal structure: the ssNA hybridization region for capturing single-stranded nucleic acids, the oligonucleotide hybridization region for adapter-adapter annealing, and the UMI region for molecular identification. This multi-functional design allows a single adapter type to perform multiple functions, simplifying the protocol while maintaining the ability to generate complex libraries
Solution Approach 2:
The invention changes the key parameter of adapter design from traditional complex, multi-component structures to a simplified single-stranded scaffold adapter with defined functional regions. By altering the structural parameters (single-stranded vs. double-stranded, modular functional regions), the protocol becomes less complex while still achieving high library complexity through the UMI-based molecular identification system
3Adaptability or versatility
If nucleic acid ends are modified for library preparation, then sequencing compatibility is improved, but information preservation at ends deteriorates
Solution Approach 1:
The scaffold adapter acts as an intermediary between the native nucleic acid fragment and the sequencing platform requirements. The adapter's ssNA hybridization region binds to the nucleic acid end without altering it, while the oligonucleotide hybridization region and UMI region provide the necessary sequencing compatibility. This intermediary approach adds sequencing functionality while preserving the original nucleic acid end information
Solution Approach 2:
The scaffold adapter is designed with pre-defined functional regions including a UMI region that is incorporated at the nucleic acid end before sequencing. This preliminary incorporation of identification markers and sequencing adapters ensures that the native nucleic acid information is preserved and captured, while the added regions provide necessary sequencing 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
Facilitates the generation of high-quality, complex nucleic acid libraries with reduced costs and time, preserving valuable information at nucleic acid ends, suitable for various sequencing platforms.
Implementation Method 1
a plurality of first scaffold polynucleotide species each comprising an ssNA hybridization region and a first oligonucleotide hybridization region
Implementation Method 2
the first oligonucleotide hybridization region comprises (i) a polynucleotide complementary to the first flank region, and (ii) a polynucleotide complementary to the second flank region
Implementation Method 3
the first flank region comprises about 70% guanine and cytosine nucleotides, or the first flank region comprises about 90% guanine and cytosine nucleotides
Data Source
Figure 1
Figure 2
Figure 3
AI summary
The present invention relates in part to methods and compositions for analyzing nucleic acid. In some aspects, the technology relates to methods and compositions for preparing a nucleic acid library from single-stranded nucleic acid fragments.