Myopic Nucleic Acid Binding Estimation Algorithm
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Solution Overview
Problem
Current nucleic acid design methods face challenges in efficiently determining desired interactions and avoiding undesired binding patterns in nucleic acid systems, particularly due to the large search space and computational expense of evaluating binding probabilities for each mutation cycle.
Innovation Solution
The approach involves using a cost function that considers binding behavior in a limited neighborhood surrounding each nucleotide, precomputing binding probabilities for these neighborhoods, and incrementally updating the scoring matrix as mutations are made, reducing computational complexity to O(n) and enabling time-efficient global optimization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If binding probabilities are evaluated for each mutation cycle to ensure accurate nucleic acid design, then design accuracy is improved, but computational time and resources increase significantly
Solution Approach 1:
The patent precomputes binding probabilities for all possible nucleotide pairs and stores them in lookup tables before the design process begins. This preliminary computation allows the algorithm to retrieve pre-stored values during mutation cycles rather than recalculating binding probabilities, dramatically reducing computational time while maintaining accuracy
Solution Approach 2:
The patent implements a myopic evaluation approach that focuses computational resources on local neighborhoods around mutation sites rather than evaluating the entire sequence. By computing binding probabilities only for affected local regions and using precomputed values for unchanged regions, the method achieves accurate local evaluation with reduced overall computational burden
2Measurement precision
If the entire nucleic acid sequence is evaluated for binding patterns in each mutation cycle, then comprehensive design accuracy is improved, but computational complexity increases to O(n^2) or higher
Solution Approach 1:
The patent divides the nucleic acid sequence into local neighborhoods or windows around mutation sites. Instead of evaluating the entire sequence globally, the algorithm segments the problem into manageable local regions, evaluating binding patterns only where mutations occur and using precomputed values for the rest, reducing complexity from O(n^2) to O(n)
Solution Approach 2:
The patent performs partial evaluation by computing binding probabilities only for the minimal necessary regions affected by mutations rather than the complete sequence. This partial action approach maintains design accuracy for critical regions while avoiding redundant computations in unchanged regions, achieving O(n) complexity
Data Source
AI summary
Systems and methods for capturing desired interactions and non-interactions of a set of strands (e.g., DNA strands, RNA strands) that may be used in various technological applications, including DNA molecular probes used in medical diagnostics, forensics, microbial ecology, molecular computation, DNA origami, and numerous other applications. Given a nucleic acid system with a certain defined binding pattern, the implementations of the present disclosure automatically generate nucleotide sequences that achieve the intended binding pattern and not other binding patterns, subject to miscellaneous other constraints of the system. Advantageously, given nucleotides i and j, the implementations of the present disclosure consider the binding behavior only in a limited neighborhood of nucleotides surrounding each nucleotide in their respective strands, rather than the binding behavior of whole assignment of which they are a part. These features provide a time-efficient and incremental algorithm that is suitable for numerous practical applications.