Stacked Nanopore Structure for DNA Sequencing
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Solution Overview
Problem
Current DNA sequencing technologies face limitations in speed and accuracy, particularly in determining the precise order of nucleotides in DNA molecules, as they often require multiple passes and can be affected by non-uniformity of nanopore structures.
Innovation Solution
A stacked nanopore structure is fabricated with alternating conductive lines and dielectric layers, forming a staircase or tapered pattern, which allows for multiple sensing of DNA molecules in a single pass by creating sharp conductive tips on opposite sides of the nanopore, with one tip grounded and the other biased, enabling precise measurement of tunneling current changes caused by different nucleobases.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If a single nanopore structure is used for DNA sequencing, then the device complexity is low, but the sequencing speed and accuracy are limited
Solution Approach 1:
The invention divides a single nanopore into multiple stacked nanopore layers (e.g., 3-10 layers), where each layer contains conductive lines forming sensing electrodes. This segmentation allows parallel sensing of DNA molecules across multiple layers, increasing sequencing throughput and speed while maintaining a manageable structural complexity through systematic stacking.
Solution Approach 2:
The invention transitions from a two-dimensional single nanopore plane to a three-dimensional stacked structure by adding the vertical dimension. Multiple nanopore layers are stacked along the vertical axis, enabling simultaneous sensing at different depths and positions, thereby increasing productivity without proportionally increasing lateral device complexity.
2Productivity
If multiple nanopore layers are stacked to increase sequencing speed, then the productivity improves, but the manufacturing precision requirements increase
Solution Approach 1:
The invention combines multiple nanopore layers into a single integrated stacked structure where conductive lines and dielectric layers are alternately deposited and patterned together. This merging approach allows simultaneous formation and alignment of multiple nanopores during a single fabrication process, improving manufacturing precision by reducing the number of separate alignment steps required.
Solution Approach 2:
The invention performs preliminary patterning of conductive lines and dielectric layers in alternating stacks before final nanopore formation. This preliminary structuring establishes precise geometric templates that guide subsequent etching and nanopore creation, ensuring accurate alignment across multiple layers while simplifying the overall manufacturing process.
3Measurement precision
If a stacked nanopore structure is used to improve sequencing accuracy, then the measurement precision improves, but the device complexity increases
Solution Approach 1:
The invention segments the measurement function across multiple nanopore layers, where each layer contributes to sensing different portions or aspects of the DNA molecule. This segmentation enables signal averaging and cross-validation across layers, improving measurement precision for nucleotide identification while distributing the functional complexity across identical modular units.
Solution Approach 2:
The invention varies parameters such as conductive line lengths, spacing, and stacking distances to optimize sensing performance. By adjusting these geometric parameters, the device achieves improved measurement precision through enhanced signal detection and differentiation, while maintaining a relatively simple repetitive stack structure that limits overall complexity.
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 enhances sequencing speed and accuracy by averaging signals from multiple nanopore layers, minimizing variations due to non-uniformity and allowing for parallel DNA sequencing, thereby improving the precision of nucleotide identification.
Implementation Method 1
enabling precise measurement of tunneling current changes caused by different nucleobases
Data Source
AI summary
A method for fabricating a stacked nanopore includes forming a stack of layers having alternating conductive lines and dielectric layers on a substrate, and patterning the stack to form a staircase structure with the conductive lines having a length gradually changing at each level in the stack. The method also includes depositing and planarizing a dielectric material over the staircase structure, forming contacts through the dielectric material to the conductive lines for each level of conductive lines, etching a nanopore through the stack of layers to form pairs of opposing electrodes across the nanopore using the conductive lines; and opening up the substrate to expose the nanopore.