US-20260125745-A1 - BIOLOGICAL BASED WIRING OF ELECTRONIC CIRCUITS FOR MOLECULAR SENSING APPLICATIONS

US20260125745A1US 20260125745 A1US20260125745 A1US 20260125745A1US-20260125745-A1

Abstract

In some embodiments, an apparatus comprises a first electrode and a second electrode defining a gap therebetween; a molecular wire disposed across the gap, and configured to electrically connect the first electrode and the second electrode, the molecular wire including: at least one molecule of deoxyribonucleic acid (DNA) including a double stranded portion; and a plurality of functional groups coupled to nucleotides of the at least one molecule of DNA at predetermined positions along the at least one molecule of DNA, the plurality of functional groups configured to cause electron delocalization along the molecular wire to increase an electrical conductivity of the molecular wire; and a first molecular linker configured to couple a first portion of the molecular wire to the first electrode and a second molecular linker configured to couple a second portion of the molecular wire to the second electrode.

Inventors

Michael Shane Bowen

Assignees

ATLAS DATA STORAGE, INC.

Dates

Publication Date: 20260507
Application Date: 20251107

Claims (20)

1 . An apparatus, comprising: a first electrode and a second electrode defining a gap therebetween; a molecular wire disposed across the gap, and configured to electrically connect the first electrode and the second electrode, the molecular wire including: at least one molecule of deoxyribonucleic acid (DNA) including a double stranded portion; and a plurality of functional groups coupled to nucleotides of the at least one molecule of DNA at predetermined positions along the at least one molecule of DNA, the plurality of functional groups configured to cause electron delocalization along the molecular wire to increase an electrical conductivity of the molecular wire; and a first molecular linker configured to couple a first portion of the molecular wire to the first electrode and a second molecular linker configured to couple a second portion of the molecular wire to the second electrode.
2 . The apparatus of claim 1 , wherein the plurality of functional groups include aromatic rings, the aromatic rings spaced along the molecular wire such that a pi orbital of each aromatic ring overlaps with a pi orbital of an adjacent aromatic ring.
3 . The apparatus of claim 1 , wherein the plurality of functional groups include a metal atom.
4 . The apparatus of claim 1 , wherein the at least one molecule of DNA of the molecular wire includes a DNA origami structure.
5 . The apparatus of claim 1 , wherein at least one of the first molecular linker and the second molecular linker include a DNA origami linker, the DNA origami linker including a plurality of sites each having a predetermined DNA sequence.
6 . The apparatus of claim 5 , wherein the molecular wire includes a first binding region configured to hybridize to a first site of the plurality of sites, and a second binding region configured to hybridize to a second site of the plurality of sites to couple the molecular wire to the first electrode and the second electrode.
7 . The apparatus of claim 1 , further comprising: a transduction agent coupled to the molecular wire, the transduction agent configured to change a current directed between the first electrode and the second electrode in response to a chemical event occurring in an environment surrounding the transduction agent.
8 . The apparatus of claim 7 , wherein the transduction agent includes a polymerase, the polymerase configured to undergo a conformation change in response to reacting with a nucleotide in the environment binding to a binding site of the polymerase, the conformation change of the polymerase configured to cause the change in current directed between the first electrode and the second electrode.
9 . The apparatus of claim 1 , wherein at least one of the molecular wire, the first molecular linker, or the second molecular linker include toehold regions such that one or more portions of the molecular wire can be replace via toehold mediated strand displacement.
10 .- 30 . (canceled)
31 . The apparatus of claim 5 , wherein the DNA origami linker further includes: a plurality of scaffolding sections configured to organize into a predetermined structure; and a plurality of staples configured to attach the plurality of scaffolding sections to one another, the plurality of staples including the plurality of binding sites.
32 . The apparatus of claim 31 , wherein the plurality of functional groups is a first plurality of functional groups, the DNA origami linker further including: a second plurality of functional groups coupled to nucleotides of the DNA origami linker, the second plurality of functional groups configured to increase conductivity through the DNA origami linker.
33 . The apparatus of claim 32 , wherein the second plurality of functional groups are coupled to nucleotides within the plurality of binding sites.
34 . The apparatus of claim 32 , wherein the second plurality of functional groups include aromatic rings coupled to nucleotides of the DNA origami linker such that a pi orbital of aromatic rings are oriented to form an electron pathway between the electrode and the molecular wire.
35 . The apparatus of claim 1 , wherein the first electrode and the second electrode are disposed on a semiconductor chip including a plurality of electrodes, the semiconductor chip further including a plurality of molecular wires configured to electrically connect one or more sets of electrodes of the plurality of electrodes to form one or more circuits.
36 . The apparatus of claim 35 , wherein at least a portion of the plurality of molecular wires are configured to be replaced via toehold strand displacement such that the one or more circuits formed by the plurality of molecular wires can be regenerated or reprogrammed.
37 . The apparatus of claim 35 , wherein the one or more circuits includes a plurality of circuits configured to perform molecular sensing.
38 . The apparatus of claim 35 , wherein the one or more circuits includes a plurality of circuits configured to perform DNA sequencing.
39 . The apparatus of claim 38 , wherein the plurality of circuits are configured to operate in parallel.
40 . The apparatus of claim 38 , wherein the plurality of circuits are distributed across the semiconductor chip with a pitch of about 200 nm to about 500 nm.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to and the benefit of U.S. Provisional Application No. 63/717,727, filed Nov. 7, 2024, and entitled “Biological Based Wiring of Electronic Circuits for Molecular Sensing Applications,” and U.S. Provisional Application No. 63/764,479, filed Feb. 27, 2025, and entitled “Biological Based Programmable Arrays,” the disclosure of each of which is incorporated by reference herein in its entirety. TECHNICAL FIELD Embodiments described herein relate to molecular sensors including biological wires. More specifically, the embodiments described herein relate to DNA based wires for molecular sensing applications. BACKGROUND Molecular sensors can be used for many applications including affinity binder-based proteomics (e.g., protein identification and quantification) via aptamers or antibodies, Enzyme linked immunosorbent assay (ELISA) type measurements of proteins (e.g., using affinity binders to form sandwich assays), Genotyping, deoxyribonucleic acid (DNA) sequencing, DNA decoding, and/or DNA data storage. Current approaches include use fluorescence to indicate the occurrence of a molecular event (e.g., binding of an affinity binder to a probe or incorporation of a base into DNA) or use of nanopores for electronic readout. However, these approaches have limitations around throughput, cost, and ability to reprogram the platform for different uses. SUMMARY In some embodiments, an apparatus comprises a first electrode and a second electrode defining a gap therebetween; a molecular wire disposed across the gap, and configured to electrically connect the first electrode and the second electrode, the molecular wire including: at least one molecule of deoxyribonucleic acid (DNA) including a double stranded portion; and a plurality of functional groups coupled to nucleotides of the at least one molecule of DNA at predetermined positions along the at least one molecule of DNA, the plurality of functional groups configured to cause electron delocalization along the molecular wire to increase an electrical conductivity of the molecular wire; and a first molecular linker configured to couple a first portion of the molecular wire to the first electrode and a second molecular linker configured to couple a second portion of the molecular wire to the second electrode. In some embodiments, an apparatus comprises: an electrode; a molecular wire configured to be coupled to the electrode to conduct an electrical signal to and from the electrode, the molecular wire including at least one molecule of deoxyribonucleic acid (DNA) including a double stranded portion; and a linker disposed on the electrode and configured to couple the molecular wire to the electrode, the linker including: a DNA origami structure including a plurality of binding sites, the plurality of binding sites including at least one binding site including a first DNA sequence configured to hybridize to a binding region of the molecular wire having a second DNA sequence complementary to the first DNA sequence. In some embodiments, an apparatus comprises a semiconductor chip including a plurality of electrodes; a plurality of molecular wires, each molecular wire of the plurality of molecular wires configured to electrically connect a set of electrodes of the plurality of electrodes to form one or more circuits, the plurality of molecular wires including at least one deoxyribonucleic (DNA) molecule; and a plurality of molecular linkers disposed on the plurality of electrodes, the plurality of molecular linkers configured to attach a respective portion of each molecular wire of the plurality of molecular wires to a respective electrode of the plurality of electrodes, at least a portion of the plurality of molecular wires configured to be replaced via toehold strand displacement such that the one or more circuits formed by the plurality of molecular wires can be regenerated or reprogrammed. In some embodiments, a system comprises a semiconductor chip including a plurality of molecular circuits, each molecular circuit of the plurality of molecular circuits including: a pair of electrodes defining a gap therebetween; a molecular wire disposed across the gap and configured to electrically connect the pair of electrodes, the molecular wire including at least one molecule of deoxyribonucleic (DNA); and a polymerase including a binding site separate from an active portion of the polymerase, the binding site configured to bind to a portion of the molecular wire, the polymerase configured to undergo a conformation change in response to interacting with a nucleotide of a target strand of DNA to be sequenced, the conformation change configured to cause a change in a level of current directed between the pair of electrodes; and a processor operatively coupled to the semiconductor chip, the processor configured to: receive, as polymerase sequentially interacts with nucleotides of the target strand of DNA to be sequen