Original Patent details on DNA Origami Molecular buckets which enables nanomedicine

Ido Bachelet, Shawn Douglas and George Church filed a patent in 2011 for DNA origami devices useful in the targeted delivery of biologically active entities to specific cell populations.

This is the patent for the DNA nanorobot for molecular precise delivery of treatments to cells. This has been covered several times by Nextbigfuture

Their DNA origami device comprises a scaffold strand and a plurality of staple strands, wherein:

  • one of the staple strands comprises an aptamer domain capable of binding to an antigen;
  • another of the staple strands comprises a latch domain hybridized to the aptamer domain, the latch domain sequence selected such that the aptamer domain is capable of binding to the antigen such that the antigen displaces the latch domain;
  • the aptamer domain and the latch domain, when hybridized to one another, hold the device in a closed configuration; and
  • the device transitions to an open configuration when the aptamer domain and the latch domain are not hybridized to one another.

In some embodiments, the staples of the DNA origami devices are selected such that the DNA origami device is held in a particular conformation by a molecular latch. In general, such latches are formed from two or more staple stands, including at least one staple strand having at least one stimulus-binding domain that is able to bind to an external stimulus, such as a nucleic acid, a lipid or a protein, and at least one other staple strand having at least one latch domain that binds to the stimulus binding domain. The binding of the stimulus-binding domain to the latch domain supports the stability of a first conformation of the DNA origami device. The contacting of one or more of the stimulus-binding domains by an external stimulus to which it can bind displaces the latch domain from the stimulus-binding domain. This disruption of the molecular latch weakens the stability of the first conformation and may cause the DNA origami device to transition to a second conformation. In certain embodiments, this conformational change may result in previously sequestered moieties becoming externally presented and thereby rendering them capable of exerting a biological effect upon proximal cells.

In certain embodiments, the staple strands of a DNA origami device are selected such that the DNA origami device includes multiple molecular latches. For example, in certain embodiments, the DNA origami device includes two molecular latches. In some embodiments the various molecular latches may recognize different external stimuli, while in certain embodiments they recognize the same external stimuli. In certain embodiments, multiple external-stimuli binding domains and/or latch domains may be present on a single staple strand. In some embodiments, a stimuli-binding domain or a latch domain may span multiple staple strands which come together when the stimulus binds. In some embodiments, a stimuli-binding domain may bind multiple latch domains, or multiple stimuli-binding domains may bind a single latch domain.

The external stimulus to which the stimulus-binding domain can be any type of molecule including, but not limited to, a protein, a nucleic acid, a lipid, a carbohydrate and a small molecule. In certain embodiments, the external stimulus is preferentially expressed by a particular population of cells to be targeted by the DNA origami device. In such embodiments, the external stimulus may be present on or near the surface of the targeted cell population. For example, in certain embodiments the external stimulus is a cancer cell-specific antigen. In some embodiments the external stimulus is a molecule that is able to specifically bind to a particular population of cells. For example, the external stimulus can be a moiety bound to an antibody specific for an antigen expressed by a particular population of cells (e.g. a cancer cell-specific antigen).

The stimulus-binding domain is capable of forming a bond with a latch domain that is displaced upon the binding of an external stimulus. In certain embodiments, the stimulus binding domain binds to the external stimulus with a higher affinity than it binds to the latch domain.

A method of delivering one or more moieties to a cell having an external stimulus (e.g. an antigen) on or near its surface may include contacting the cell with a latched DNA origami device that is carrying the moiety, thereby allowing the external stimulus to displace a latch domain from an stimulus-binding domain, and allowing the moiety to contact the cell.

As described above, in certain embodiments, contacting a DNA origami device with an external stimulus present on the surface of a cell causes the DNA origami device to transition from a closed configuration to an open configuration. In such embodiments, this conformational change will cause previously internal handle domains to become external handle domains, thereby allowing their bound moieties to interact with the cell. In certain embodiments, the moieties remain bound to the handle domains after the transition to an open configuration. Thus, in certain embodiments a method of treating a disease or disorder in a subject may include administering to the subject a DNA origami device as disclosed herein that delivers an effective amount of a therapeutic moiety to one or more targeted cell in the subject. Multi-drug therapy may be delivered by these methods by attaching different drug moieties to various handles. The relative amounts of moieties may be precisely controlled in this manner, because each handle can be made receptive to specific moieties. So, for example, if three moieties A, B, and C are to be delivered in a stoichiometric ratio of 2:1:3, a DNA origami device can be made with staple strands having domains such that there are two handles specific for moiety A, and three handles specific for moiety C, for every handle that is specific for moiety B.

A wide variety of diseases and disorders are susceptible to treatment by these methods. Diseases or disorders characterized by the absence of a tangible mass that can be physically targeted may be especially well-suited to the present methods of treatment. Examples include blood-borne illnesses, such as a blood-borne cancer (e.g. a leukemia) or an autoimmune disease.

In some embodiments, the transition to the open configuration or the interaction with the cell causes the moiety to be released by the handle domain. For example, the handle domain can include an aptamer sequence specific for an antigen present on the surface of the cell. In such embodiments, the binding of the antigen to the handle domain displaces the moiety from the handle domain. Thus, in these embodiments, the DNA origami device not only delivers the therapeutic moiety to a cell, it can achieve a high local concentration of the therapeutic moiety around intended targets while sparing unintended targets from undesirable side-effects. The released therapeutic moiety will also be freer to interact with the cell, possibly being internalized for therapeutic effect.

Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising
Nucleic acids binding to non-nucleic acids, e.g. aptamers

SOURCE – US Patents