Systems comprising non-immunogenic and nuclease resistant nucleic acid origami devices for molecular computation

Patent metadata

Field	Value
Publication number	US-10316320-B2
Application number	US-201414785201-A
Country	US
Kind code	B2
Filing date	Apr 13, 2014
Priority date	Apr 18, 2013
Publication date	Jun 11, 2019
Grant date	Jun 11, 2019

Abstract

Systems acting as logic gates and systems exhibiting quorum sensing are provided, wherein said systems comprise at least one effector nucleic acid origami device, at least one regulator nucleic acid origami device, at least one input and at least one output, and the nucleic acid origami devices are non-immunogenic and/or resistant to nucleases.

First claim

The invention claimed is:

1. A system acting as a logic gate, said system comprising at least one effector device, at least one regulator device, at least one input and at least one output,
wherein each one of said at least one effector device and at least one regulator device is a nucleic acid origami device comprising a scaffold strand and a plurality of staple strands, and independently has the structure A, B or C, wherein:
in the structure A:
(i) one of the staple strands comprises either (a) an aptamer domain capable of binding to a binding partner comprising a first of said at least one input; (b) an oligonucleotide capable of binding to a binding partner comprising a DNA binding protein, said DNA binding protein comprising a second of said at least one input; or (c) an oligonucleotide attached to a nano-antenna capable of receiving an electromagnetic field comprising a third of said at least one input, or one of the staple strands comprises an aptamer domain of (a) and another of the staple strands comprises an oligonucleotide of (c);
(ii) another of the staple strands comprises a latch domain hybridized or bound to said aptamer domain of (a) or oligonucleotide of (b) or (c), the sequence of the latch domain being selected such that the aptamer domain of (a) is capable of binding to the binding partner such that the binding partner displaces the latch domain, or the latch domain is capable of hybridizing with an external oligonucleotide selected such that the external oligonucleotide displaces the aptamer domain; said latch domain is linked to a binding partner that is selected such that the binding partner has a first configuration under a first condition and a different second configuration under a different second condition, and the aptamer of (a) or the oligonucleotide of (b) is capable of binding to the binding partner having the first configuration but incapable of binding to the binding partner having the second configuration such that the latch domain is displaced from the aptamer of (a) or the oligonucleotide of (b) when the binding partner transitions from the first to the second configuration; or the nano-antenna of (c), upon receipt of said electromagnetic field, undergoes inductive coupling and subsequent heating thereby displacing the latch domain from the oligonucleotide of (c); and
(iii) the aptamer domain of (a) or the oligonucleotide of (b) or (c), and the latch domain, when hybridized or bound to one another, hold the device in a closed configuration; and the device transitions to an open configuration when the aptamer domain of (a) or the oligonucleotide of (b) or (c), and the latch domain, are not hybridized or bound to one another,
in the structure B:
(i) one of the staple strands comprises a first aptamer domain capable of binding to a first binding partner comprising one of said at least one input;
(ii) another of the staple strands comprises a second aptamer domain capable of binding to a second binding partner comprising another one of said at least one input;
(iii) still another of the staple strands comprises a first latch domain hybridized to the first aptamer domain, the sequence of the first latch domain being selected such that the first aptamer domain is capable of binding to the first binding partner such that the first binding partner displaces the first latch domain, or the first latch domain is capable of hybridizing with an external oligonucleotide selected such that the external oligonucleotide displaces the aptamer domain;
(iv) yet another of the staple strands comprises a second latch domain hybridized to the second aptamer domain, the sequence of the second latch domain being selected such that the second aptamer domain is capable of binding to the second binding partner such that the second binding partner displaces the second latch domain, or the second latch domain is capable of hybridizing with an external oligonucleotide selected such that the external oligonucleotide displaces the aptamer domain; and
(v) said nucleic acid origami device is in a closed configuration when the first aptamer domain is hybridized to the first latch domain and/or the second aptamer domain is hybridized to the second latch domain; and the device transitions to an open configuration when the first aptamer domain is not hybridized to the first latch domain and the second aptamer domain is not hybridized to the second latch domain,
in the structure C:
(i) two of the staple strands each comprises a latch domain linked to an oligonucleotide capable of hybridizing with an external oligonucleotide, said external oligonucleotide is positioned on another one of said nucleic acid origami devices; and
(ii) said nucleic acid origami device is in an open configuration when each one of the oligonucleotide capable of hybridizing with an external oligonucleotide is not hybridized to said external oligonucleotide; and the device transitions to a closed configuration when each oligonucleotide capable of hybridizing with an external oligonucleotide is hybridized to said external oligonucleotide,
wherein
each one of said at least one effector nucleic acid origami device and at least one regulator nucleic acid origami device is either alkylated, acylated or hydroxylated, or interacts with a compound capable of non-covalently binding to the major- or minor-groove of a double stranded nucleic acid, and therefore is resistant to nucleases, or
each one of said at least one effector nucleic acid origami device and at least one regulator nucleic acid origami device lacks TLR9 recognition elements or the TLR9 recognition elements of said nucleic acid origami device are masked or modified and therefore said nucleic acid origami device is non-immunogenic.

2. The system of claim 1 , wherein each one of said nucleic acid origami devices is methylated.

3. The system of claim 2 , wherein said compound capable of non-covalently binding to the major- or minor-groove of a double stranded nucleic acid is selected from the group consisting of netropsin, distamycin, an oligoamide, a sugar-oligoamide conjugate and a bis-amidine.

4. The system of claim 1 , wherein one or more further staple strands in at least one of said nucleic acid origami devices each comprises a handle domain bound to a payload, optionally via a linker, thereby providing for one or more payloads in at least one of said nucleic acid origami devices, wherein at least one of said payload(s) is one of said at least one output, and optionally, at least one of said payload(s) is one of said at least one input or emulates one of said at least one input.

5. The system of claim 4 , wherein said linker comprises an oligonucleotide having a sequence complementary to the sequence of the handle domain and optionally comprising a further domain comprising a recognition site for enzymatic cleavage, and the payload is bound to the handle domain through the hybridization of the oligonucleotide to the handle domain, said further domain optionally comprising a peptide linker comprising a protease recognition site for cleavage by a protease or wherein said linker comprises a protein capable of binding a small-molecule.

6. The system of claim 4 , wherein said payload each independently is a drug selected from the group consisting of insulin, an antibody or a fragment thereof, a cell surface receptor ligand or a biologically active fragment thereof, a small molecule, a nucleic acid molecule, an oligonucleotide, a nuclease, an aptamer, a lipid, a glycan, a protein, a glycoprotein, a glycolipid, a nanoparticle, a fluorophore, a radioactive compound, a nano-antenna, and a liposome.

7. The system of claim 4 , wherein the plurality of staple strands are selected such that at least one of the payloads is positioned on an inner surface of the n

Assignees

• Univ Bar Ilan

Inventors

• Bachelet Ido
• Abu-Horowitz Almogit
• Ben-Ishay Eldad
• Amir Yaniv
• De Beer Joel
• Ittah Shmulik

Classifications

• B82Y5/00

  Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery · CPC title

• A61K47/6923

  the form being an inorganic particle, e.g. ceramic particles, silica particles, ferrite or synsorb · CPC title

• C12N2310/3519

  Fusion with another nucleic acid · CPC title

• C12N2310/16

  Aptamers · CPC title

• A61K47/6901

  Conjugates being cells, cell fragments, viruses, ghosts, red blood cells or viral vectors · CPC title