Acrylamide Copolymerization for Scalable ssDNA Production

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Solution Overview

Problem

The production of long, high-purity single-stranded DNA (ssDNA) is expensive and difficult to perform on a large scale, hindering the use of DNA-based nanomaterials in various applications due to the challenges in synthesizing ssDNA, which is a critical building block for DNA-based materials and technologies.

Innovation Solution

A method involving the sequestration of double-stranded DNA (dsDNA) in solution to form a copolymer, followed by denaturation to release ssDNA, and subsequent selective precipitation using methanol, allowing for the scalable and cost-effective production of long, highly pure ssDNA strands using acrylamide-labeled dsDNA and acrylamide monomers.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If conventional molecular biology methods are used to produce ssDNA, then ssDNA can be synthesized, but the process is expensive and difficult to perform on a large scale

Engineering Contradiction:

Improvescalability of ssDNA productionVSAvoidcost-effectiveness of ssDNA production

Core Design Contradiction:

ProductivityVSEase of manufacture

Solution Approach 1:

The invention segments the DNA production process into two distinct stages: first, synthesis of double-stranded DNA (dsDNA) using conventional methods; second, conversion of dsDNA to single-stranded DNA (ssDNA) through denaturation. This segmentation allows each stage to be optimized independently, with dsDNA synthesis scaled up efficiently and ssDNA generation performed through simple thermal or chemical treatment, thereby achieving large-scale production at reduced cost.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The invention performs preliminary synthesis of dsDNA before converting to ssDNA. By pre-synthesizing the double-stranded form using well-established, scalable molecular biology techniques, the patent eliminates the need for direct ssDNA synthesis, which is more complex and costly. The preliminary dsDNA step serves as a foundation that simplifies subsequent ssDNA generation through denaturation.

Inventive Principle:

Principle #10Preliminary action

2Manufacturing precision

If long ssDNA strands with high purity are required, then the quality of DNA-based nanomaterials is improved, but the production process becomes more difficult and expensive

Engineering Contradiction:

Improvepurity of ssDNAVSAvoidcomplexity of ssDNA production process

Core Design Contradiction:

Manufacturing precisionVSDevice complexity

Solution Approach 1:

The invention extracts and removes the complementary strand from dsDNA through denaturation processes such as thermal treatment or chemical exposure. By selectively separating and removing one strand, the method produces high-purity ssDNA without requiring complex purification steps. The extraction of the unwanted strand simplifies the overall process while maintaining high product quality.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The invention utilizes parameter changes in terms of temperature, pH, or chemical conditions to facilitate denaturation of dsDNA into ssDNA. By adjusting these parameters, the patent achieves efficient strand separation and high-purity ssDNA production. The parameter changes enable simple, scalable conversion without complex equipment or procedures.

Inventive Principle:

Principle #35Parameter changes

3Ease of manufacture

If dsDNA is used as starting material, then the production process is simplified, but the ability to produce long ssDNA strands directly is limited

Engineering Contradiction:

Improvesimplicity of production processVSAvoidlength of ssDNA strands

Core Design Contradiction:

Ease of manufactureVSLength of moving object

Solution Approach 1:

The invention performs preliminary synthesis of long dsDNA strands using conventional molecular biology methods, which are optimized for producing long double-stranded molecules. After obtaining the long dsDNA, the patent applies denaturation to generate ssDNA of equivalent length. This preliminary action leverages the strengths of existing dsDNA synthesis capabilities while achieving the desired long ssDNA product through a simple subsequent step.

Inventive Principle:

Principle #10Preliminary action

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 enables the efficient production of long ssDNA strands, facilitating applications in DNA origami, guide RNA templates, direct DNA sequencing, and DNA-based therapeutics, while also enabling the capture and release of nucleic acid targets, thus expanding the scope of DNA nanotechnology and biotechnological applications.

Implementation Method 1

combining in solution acrylamide-labeled double-stranded deoxyribonucleic acid (dsDNA) and acrylamide (AA) to form copolymer-linked dsDNA

Methodology Applied

Scientific EffectCopolymerization: Chemical Bonding

Implementation Method 2

dsDNA may be sequestered in solution to form a copolymer containing the dsDNA, using a solution-phase polymerization process of the present disclosure

Methodology Applied

Scientific EffectDenaturation: Heat Treatment