Oligonucleotide Construct with Coding Element for Non-Destructive Sequencing
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Solution Overview
Problem
Current methods for identifying modified oligonucleotides, such as X-aptamers and SELEX, face limitations due to the need for unmodified copies for amplification, which restricts the range of chemical modifications and requires destructive decoding processes, making it challenging to determine the sequence of functional oligonucleotides with high affinity and specificity.
Innovation Solution
An oligonucleotide construct comprising a functional element with structural modifications and a coding element that remains associated, allowing enzymatic amplification and sequencing without destruction, enabling the selection and identification of oligonucleotides with desired properties and target binding affinity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If polymerase based amplification is used to determine the sequence of modified oligonucleotides, then the sequence can be identified, but the range of chemical modifications is limited to those that can be accepted by the polymerase enzyme
Solution Approach 1:
The patent uses an unmodified copy (proxy) of the oligonucleotide to represent the modified version. The proxy contains coding information that indicates which unmodified nucleotides correspond to modified nucleotides in the selected oligonucleotide. This allows the modified oligonucleotide to be screened and selected while its sequence is determined through amplification of the unmodified proxy, thereby expanding the range of acceptable chemical modifications without compromising amplification capability.
2Reliability
If unmodified copies are used for amplification to identify modified oligonucleotides, then amplification can proceed, but the process requires destructive decoding to determine the sequence of the modified oligonucleotide
Solution Approach 1:
The patent introduces a coding information system that acts as an intermediary between the modified oligonucleotide and the amplification process. The coding information, associated with the unmodified proxy, encodes the modification pattern. This intermediary allows non-destructive determination of the modified oligonucleotide sequence by reading the coding information from the proxy, eliminating the need for destructive decoding processes while maintaining amplification capability.
3Measurement precision
If bead based combinatorial library is used to screen modified oligonucleotides, then individual beads can be selected, but each bead requires more than one copy of unique oligonucleotide increasing complexity
Solution Approach 1:
The patent merges the functional oligonucleotide and its coding information into a single integrated structure. The coding information is associated with the oligonucleotide in such a way that both the functional element and the sequence information are present together. This integration allows individual beads to contain complete information for both screening and sequence determination, reducing the need for multiple copies per unique oligonucleotide and simplifying the library structure while maintaining selection accuracy.
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
Enables the determination of the sequence structure of functional oligonucleotides without destruction, allowing for the synthesis of modified oligonucleotides with high affinity and specificity, and facilitates the creation of diverse libraries for target binding, overcoming the limitations of existing methods.
Implementation Method 1
amplified (e.g. by the polymerase chain reaction (PCR))
Data Source
AI summary
Oligonucleotide constructs are described, each comprising a functional element and a coding element, wherein the functional element comprises a functional sequence, the functional sequence comprising a sequence of nucleotides in which one or more, or each, nucleotide is modified and the coding element comprises a coding sequence, the coding sequence comprising a sequence of nucleotides which do not contain the modifications of the functional sequence, wherein the coding sequence encodes the sequence structure of the functional sequence.