Multivalent Binding Composition for Nucleic Acid Sequencing Signal Detection
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current nucleic acid sequencing technologies face challenges in achieving cost-effective, high-throughput sequencing due to limitations in signal intensity and accuracy, particularly in determining the identity of nucleotides in target nucleic acid sequences.
Innovation Solution
A multivalent binding composition is used, comprising multiple copies of nucleotides attached to a polymer or particle core, which forms a complex with target nucleic acid sequences and polymerase molecules, enhancing local nucleotide concentration and binding signals, allowing for accurate detection of nucleotide identity through fluorescence measurement.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional sequencing methods are used, then sequencing can be performed, but signal intensity and accuracy are insufficient
Solution Approach 1:
The invention divides the nucleotide detection process into two distinct phases: a binding phase where the nucleotide probe forms a stable complex with the target sequence, and an extension phase where the probe is incorporated into the growing strand. This segmentation allows optimization of each phase independently, achieving both high signal intensity during binding and high accuracy during extension
Solution Approach 2:
The invention performs preliminary binding of the nucleotide probe to the target sequence before extension occurs. The probe first forms a stable binding complex with the complementary target, allowing signal amplification to occur before the actual nucleotide incorporation. This preliminary action enhances signal intensity without compromising the accuracy of the final extension step
2Productivity
If sequencing throughput is increased, then more sequences can be analyzed, but errors and reduced accuracy occur
Solution Approach 1:
The invention introduces a nucleotide probe as an intermediary molecule that mediates between the target sequence and the detection system. The probe serves as a stable intermediate complex during binding, allowing high-throughput parallel processing, and then as a controlled intermediate during extension, ensuring accurate nucleotide incorporation. This intermediary approach enables throughput increases without sacrificing accuracy
Solution Approach 2:
The invention changes the chemical parameters of the nucleotide by using modified nucleotide probes with enhanced binding properties. These parameter changes in the nucleotide structure allow for more stable binding complexes that can be processed in parallel at high throughput while maintaining the fidelity of base pairing and extension
3Loss of time
If sequencing time is reduced, then high-throughput is achieved, but read length and accuracy decrease
Solution Approach 1:
The invention establishes continuous useful action by designing a seamless transition from binding to extension. The nucleotide probe remains continuously associated with the target sequence throughout both phases, eliminating idle time between binding and extension. This continuity allows reduced sequencing time while maintaining read length accuracy, as the probe is already positioned and stabilized on the target before extension begins
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 significantly improves signal intensity and accuracy in nucleotide identification, reducing sequencing time and increasing read length while minimizing errors, thereby addressing the shortcomings of existing sequencing methods.
Implementation Method 1
contacting said composition with a polymer nucleotide conjugate under conditions sufficient to allow a multivalent binding complex to be formed between said polymer-nucleotide conjugate and said two or more copies of said target nucleic acid sequence
Implementation Method 2
the one or more detectable labels are fluorescent labels. In some embodiments, detecting the multivalent binding complex comprises a fluorescence measurement
Data Source
AI summary
Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.