Microarray Selection Device with Dual Thermal Zones
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Solution Overview
Problem
Current microarray-based genome selection methods fail to quantitatively recover target DNA sequences due to back-hybridization of complementary strands, leading to incomplete recovery of target regions, which hampers reliable mutation detection in re-sequencing approaches.
Innovation Solution
A device with a hybridization zone and a denaturation zone, connected by a fluid transportation means, allows for repeated reactivation of unbound target molecules while maintaining bound molecules at optimal hybridization temperatures, enhancing the enrichment of specifically bound molecules and reducing non-specific binding.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If target molecules are hybridized to capture molecules in a microarray, then target enrichment is achieved, but complementary strands undergo back-hybridization reducing recovery efficiency
Solution Approach 1:
The patent implements periodic temperature cycling between hybridization zone (lower temperature for binding) and denaturation zone (higher temperature for strand separation). This periodic thermal action prevents back-hybridization by continuously denaturing complementary strands that attempt to re-bind, thereby improving target recovery efficiency from 80-90% to near-complete recovery
Solution Approach 2:
The system dynamically changes the temperature parameter along the fluid path, creating distinct thermal zones. The hybridization zone maintains temperatures optimal for probe-target binding, while the denaturation zone uses elevated temperatures to prevent complemented strand re-hybridization. This spatial parameter variation resolves the contradiction between achieving specific binding and preventing back-hybridization
2Reliability
If temperature is maintained for prolonged hybridization, then binding efficiency increases, but time consumption increases
Solution Approach 1:
The continuous cycling of target molecules through hybridization and denaturation zones creates multiple brief interaction opportunities rather than requiring one prolonged incubation. This periodic exposure achieves comparable or superior binding efficiency in reduced time, as unbound molecules receive repeated chances to hybridize during each circulation cycle
Solution Approach 2:
The system maintains continuous fluid flow and continuous temperature cycling, eliminating idle time between hybridization attempts. Target molecules are constantly presented to capture probes in the hybridization zone, maximizing binding efficiency per unit time compared to batch processing methods with idle incubation periods
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 the recovery of target DNA sequences by allowing repeated interaction opportunities for unbound molecules, leading to enhanced specificity and efficiency in target molecule selection and enrichment.
Implementation Method 1
one or more temperature control and/or regulating units for controlling and/or regulating the temperature within the zone
Implementation Method 2
at least one transportation means capable of generating and/or regulating a fluid flow between said reaction zone (a) and said zone comprising one or more temperature control and/or regulating units (b)
Implementation Method 3
performing interaction reactions in a reaction zone... allowing hybridization of nucleic acids to said capture molecules
Implementation Method 4
performing additional interaction reactions with the reactivated target molecules... zone allowing reactivation of the target molecules
Data Source
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AI summary
The present invention relates to a device for the specific selection of target molecules, comprising: (a) at least one reaction zone comprising a microarray, wherein the microarray comprises a substrate, on which one or more species of capture molecules are immobilized, comprising one or more temperature control and/or regulating units for controlling and/or regulating the temperature within the zone; (b) at least one non-reaction zone comprising one or more temperature control and/or regulating units for controlling and/or regulating the temperature within the zone, which is in fluid connection with the reaction zone; and (c) at least one transportation means capable of generating and/or regulating a fluid flow between said reaction zone (a) and said non-reaction zone comprising one or more temperature control and/or regulating units (b). The present invention further relates to a device for the specific selection of target molecules wherein the immobilized capture molecules are organized in the microarray in the form of spots, elongated spots and/or lines. In a further aspect the present invention relates to a method of specifically selecting target molecules, comprising the introducing a medium to such a device, performing interaction reactions in a reaction zone, transporting not interacted or not bound target molecules to a zone allowing reactivation of the target molecules and performing additional interaction reactions with the reactivated target molecules at the reaction zone, as well as the use of such a device for specifically selecting target molecules, e.g. for target enrichment also referred to as microarray based genome selection (MGS) in the literature.