5'-Cohesive End Base Sequence Design for Nucleic Acid Nanostructures
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Solution Overview
Problem
The use of T4 ligation enzymes for synthesizing nucleic acid nanostructures results in low product yield and high probability of errors due to mismatch ligations, making it difficult to achieve precise structures, especially when used in vivo.
Innovation Solution
A method involving the selection of candidate groups of base sequences with specific guanine-cytosine content and Gibb's free energy values for the 5' cohesive end, followed by ligation experiments to identify sequences with high yield and low mismatch ligation probability, using enzymes like T4, Thermus thermophilus, or Vaccinia virus DNA ligation enzymes in optimized buffer conditions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If T4 ligation enzymes are used for synthesizing nucleic acid nanostructures, then the synthesis process can be performed, but the product yield is low and the probability of mismatch ligations increases
Solution Approach 1:
The patent changes the base sequence parameters of the 5'-cohesive end to have 3-5 different successive bases instead of repetitive sequences, and optimizes GC content to 50-60%, which improves both ligation efficiency and accuracy simultaneously
Solution Approach 2:
The patent uses computational design to create optimized base sequences that copy successful patterns identified through screening, allowing replication of high-yield, low-mismatch sequences across multiple applications
2Manufacturing precision
If conventional base sequences are used for 5'-cohesive end, then the synthesis can proceed, but mismatch ligations occur frequently reducing manufacturing precision
Solution Approach 1:
The patent modifies the base sequence parameters by introducing 3-5 different successive bases and optimizing GC content, which eliminates mismatch ligations and improves manufacturing precision of nucleic acid nanostructures
Solution Approach 2:
The patent converts the potential harm of mismatch ligations into a benefit by designing sequences where the 5'-cohesive end base sequences are specifically optimized to prevent mismatches, turning a problematic aspect into a controlled feature
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 synthetic yield of dendrimer-like nucleic acid nanostructures by up to 20-25% and reduces the probability of mismatch ligation products, resulting in high-purity and high-yield nucleic acid nanostructures.
Implementation Method 1
T4 ligation enzymes have been widely used to construct new structures in addition to the natural nucleic acid structures
Data Source
AI summary
A method of preparing a base sequence for synthesis of a nucleic acid nanostructure, a method of synthesizing a nucleic acid nanostructure, a candidate base sequence pair, and a nucleic acid nanostructure are provided. A method of preparing a base sequence includes selecting candidate groups of base sequences of 5′-cohesive end having at least 50% GC content, calculating Gibb's free energy values of the selected candidate groups to re-select the candidate groups, and selecting the candidate groups, that have a sequence of 3 different successive bases among the base sequences from the re-selected candidate groups.