US 2026/0065010 A1 · Thermodynamically Favoured Molecular Computations

Abstract

A method 800 for making molecular computations comprises: i) providing a mixture 100 comprising a scaffold 110 comprising N scaffold positions 120; ii) designing a set of computing tiles to drive a desired computation, the set of computing tiles comprising at least N different computing tile types, wherein the computing tile types are selected to be used for the computation, in such a way that a target output has a higher probability of being reached than the probability for any other potential output, wherein for each computing tile 140, a bottom position domain 160 is arranged to bind directly to a matching scaffold position 120 with a first binding strength, and to the compute domains 150 of other computing tiles 140 with a set of second binding strengths, which are each weaker than the first binding strength; iii) adding the designed set of computing tiles to the mixture 100; iv) allowing computing tiles 140 to bind to scaffold positions 120 until all scaffold positions 120 required for the computation have been filled; v) allowing replacement of all mismatched computing tiles 140, based on correct compute domain bindings being enthalpically favoured over incorrect compute domain bindings; and vi) reaching an output configuration.

Claims38

Dependent claims

A method (800) for making molecular computations, the method (800) comprising:

i. providing (810) a mixture (100) comprising a scaffold (110), comprised of a long information-encoding molecule or strand, such as e.g. a long polynucleotide strand or a long amino acid sequence, and comprising N binding domains, wherein each binding domain constitutes a scaffold position (120);
ii. designing (820) a set of computing tiles to drive a desired computation, the set of computing tiles comprising at least N different computing tile types, wherein the computing tile types are selected to be used for the computation, in such a way that a target output has a higher probability of being reached than the probability for any other potential output, where each computing tile (140) is comprised of a short information-encoding molecule or strand, such as e.g. a short polynucleotide or a short amino acid sequence, and comprises a bottom position domain (160) and at least one compute domain (150), wherein for each computing tile (140), the bottom position domain (160) is arranged to bind directly to a matching scaffold position (120) on the scaffold (110) with a first binding strength, and to the compute domains (150) of other computing tiles (140) with a set of second binding strengths, which are each weaker than the first binding strength;
iii. adding (830) the set of computing tiles to the mixture (100);
iv. allowing (850) bottom position domains (160) of computing tiles (140) to bind to scaffold positions (120), until all scaffold positions (120) required for the computation have been filled;
v. allowing (860) replacement of all mismatched computing tiles (140), based on correct compute domain bindings being enthalpically favoured over incorrect compute domain bindings;
and
vi. reaching (870) an output configuration.

4 more elements

Arrangement (200) for making molecular computations, the arrangement (200) comprising:

a mixture (100) comprising a scaffold (110), comprised of a long information-encoding molecule or strand, such as e.g. a long polynucleotide strand or a long amino acid sequence, and comprising N binding domains, each binding domain constituting a scaffold position (120);
and
a set of computing tiles, which has been designed to drive a desired computation, wherein the designed set of computing tiles comprises at least N different computing tile types, which have been selected to be used for the computation in such a way that a target output has a higher probability of being reached than the probability for any other potential output, each computing tile (140) comprised of a short information-encoding molecule or strand, such as e.g. a short polynucleotide or a short amino acid sequence, and comprising a bottom position domain (160) and at least one compute domain (150), wherein for each computing tile (140), the bottom position domain (160) is arranged to bind directly to a matching scaffold position (120) on the scaffold (110) with a first binding strength, and to the compute domains (150) of other computing tiles (140) with a set of second binding strengths, which are each weaker than the first binding strength;
wherein the arrangement (200) is configured to:
allow bottom position domains (160) of computing tiles (140) to bind to scaffold positions (120) until all scaffold positions (120) required for the computation have been filled;
and
allow replacement of all mismatched computing tiles (140), based on correct compute domain bindings being arranged to be enthalpically favoured over incorrect compute domain bindings, thereby allowing an output configuration to be reached.

4 more elements

Method (900) for determining the status of a target molecule (340) in a molecular mixture (100), the method comprising:

adding (910) a reporting strand (350) to a molecular mixture (100);
designing (920) a result indicating strand (310) to bind to a predetermined extent to a target molecule (340);
adding (930) the result indicating strand (310) to the molecular mixture (100);
detecting (940) the fluorescence signal caused by the energy transfer between the reporting strand (350) and the result indicating strand (310);
and
determining (950) the status of the target molecule (340) based on a comparison of the fluorescence signal with a predetermined range corresponding to a predetermined status of the target molecule (340).

3 more elements

Arrangement (300) for determining the status of a target molecule (340) in a molecular mixture (100), the arrangement (300) comprising a molecular mixture (100) comprising a reporting strand (350) and a result indicating strand (310), which has been designed to bind to a predetermined extent to the target molecule (340), wherein the arrangement (300) is configured to detect the fluorescence signal caused by the energy transfer between the reporting strand (350) and the result indicating strand (310), and determine the status of the target molecule (340) based on a comparison of the fluorescence signal with a predetermined range corresponding to a predetermined status of the target molecule (340).

Dependencies are inferred from the claim text.

Thermodynamically Favoured Molecular Computations

Life of this patent

Thermodynamically Favoured Molecular Computations

Life of this patent

Abstract

Claims38