Claims
- 1. A molecular computer comprising an electronic operation section and a molecular operation section, characterized in that, in addition to general computation processing, said electronic operation section controls a function of the molecular operation section substantially, and the molecular operation is performed under control thereof.
- 2. A molecular computer for performing molecular operation by chemical reaction of molecules, comprising:
a molecular operation section which has a reaction control section for performing reaction control of chemical reaction of molecules; and an electronic operation section which comprises; a control command generating section configured to convert a program described by variables, constants and functions into a series of control commands for driving the reaction control section which performs reaction control of chemical reaction of molecules which correspond to operational reaction of the coding molecules, thereby generating control command procedures, wherein the variables and the constants being defined to be associated with coding molecules obtained by coding molecules based on nucleic acid sequences, and the functions being defined to be associated with operational reaction of the coding molecules; and an output section configured to output the control command procedures.
- 3. The molecular computer according to claim 2, wherein said reaction control section comprises:
a plurality of reaction control elements to be driven based on a drive signal, thereby performing reaction; an automatic control section which sequentially outputs drive signals to said plurality of reaction control elements based on the control command procedures input from said control command generating section; and a detection section which detects the reaction results obtained in said reaction control elements.
- 4. The molecular computer according to claim 2, wherein said reaction control section comprises:
a plurality of reaction control elements to be driven based on a drive signal, thereby performing reaction; an automatic control section which sequentially outputs drive signals to said plurality of reaction control elements based on procedures for a control command input from said control command generating section; and a detection section configured to detect the reaction results obtained in said reaction control elements, and said reaction control elements include at least one of containers which contain a nucleic acid solution targeted for reaction; a nucleic acid solution dispenser configured to extract the nucleic acid solution contained in said containers; and a temperature controller configured to control the temperature of said nucleic acid solution.
- 5. The molecular computer according to claim 2, wherein said control command generating section comprises:
an operational procedure generating section configured to convert said function included in said program into reaction procedures for said molecule based on a function-operational reaction conversion table in which said function is associated with operational reaction of molecules; and a control command procedure generating section configured to convert said reaction procedures into control command procedures based on an operational reaction-control command conversion table in which operational reaction of molecules is associated with a driven operation of said reaction control section.
- 6. The molecular computer according to claim 2, wherein said control command generating section converts said function into said control command based on a data table in which at least one control command of said reaction control section is associated with said function.
- 7. The molecular computer according to claim 2, wherein said reaction control section comprises a plurality of reaction control elements, and wherein said control command generating section sets element identification data to be associated with said control command, the element identification data identifying reaction control elements targeted for driving.
- 8. The molecular computer according to claim 2, wherein said reaction control section comprises a plurality of reaction control elements, and wherein said control command generating section has:
a temporary control command generating section which generates temporary control command procedures by associating element identification data for identifying said reaction control elements with reaction control elements targeted for driving; and a restriction resolving command appending section configured to determine whether or not control in accordance with said temporary control command procedures is possible based on restriction conditions for said reaction control elements, and generate said control command by adding a restriction resolving command for resolving said restriction to said temporary control command procedures if the determined result indicates that the control is not possible.
- 9. The molecular computer according to claim 2, further comprising: a detection result output section configured to output the detection result of chemical reaction of said molecules caused by reaction control of said chemical reaction.
- 10. The molecular computer according to claim 2, further comprising:
a detection result analysis section configured to convert the detection result of chemical reaction of said molecules caused by reaction control of said chemical reaction into a description format of said program; and an analysis result output section which outputs the operation result of said detection result analysis section.
- 11. The molecular computer according to claim 2, wherein said function is defined as a first function for selecting data which includes a specific sequence or a second function for selecting data which does not include a specific sequence.
- 12. A molecular computer according to claim 2, wherein said function is defined as a third function for appending a second specific sequence to a first specific sequence included in data.
- 13. The molecular computer according to claim 2, wherein said function is defined as a fourth function for acquiring a data set which includes plural items of data having a sequence, respectively.
- 14. The molecular computer according to claim 2, wherein said function is defined as a fifth function for dividing data having a plurality of sequences into plural items of data having a sequence.
- 15. The molecular computer according to claim 2, wherein said function is defined as a sixth function for dividing a specific sequence from said sequences or a seventh function for dividing from said sequence a second sequence distant from a first specific sequence by a specified distance.
- 16. The molecular computer according to claim 2, wherein said function is defined as an eighth function for acquiring a second specific sequence associated in advance with a first specific sequence included in sequences.
- 17. The molecular computer according to claim 2, wherein said function is defined as an ninth function for acquiring second data which includes a second specific sequence associated with first specific sequence, if there exists first data including said first specific sequence.
- 18. The molecular computer according to claim 2, wherein said function is defined as a tenth function for acquiring characteristics included in sequences.
- 19. The molecular computer according to claim 2, wherein said molecular operation section comprises a synthesizing section configured to synthesize a coding molecule.
- 20. The molecular computer according to claim 2, wherein said molecule is a nucleic acid.
- 21. A molecular operation plan-designing apparatus for setting up a plan for molecular operation in which molecular operation is performed by chemical reaction of molecules, comprising:
a control command generating section configured to convert a program described by variables, constants and functions into a series of control commands for driving a reaction control section which performs reaction control of chemical reaction of molecules which correspond to operational reaction of the coding molecules, thereby generating control command procedures, wherein the variables and the constants being defined to be associated with coding molecules obtained by coding molecules based on nucleic acid sequences, and the functions being defined to be associated with operational reaction of the coding molecules; and an output section configured to output the control command procedures.
- 22. A molecular computation method for performing molecular operation by chemical reaction of molecules, comprising:
converting a program described by variables, constants and functions into a series of control commands for driving a reaction control section which performs reaction control of chemical reaction of molecules which correspond to operational reaction of the coding molecules, thereby generating control command procedures, wherein the variables and the constants being defined to be associated with coding molecules obtained by coding molecules based on nucleic acid sequences, and the functions being defined to be associated with operational reaction of the coding molecules; outputting the control command procedures; and performing reaction control of chemical reaction of molecules based on the control command procedures.
- 23. The molecular computation method according to claim 22, wherein said reaction control sequentially outputs a drive signal which drives a plurality of reaction control elements to reaction control elements specified by the control command.
- 24. The molecular computation method according to claim 22, further comprising:
detecting the reaction result of chemical reaction of molecules performed by said reaction control.
- 25. The molecular computation method according to claim 22, further comprising:
detecting the reaction result of chemical reaction of molecules performed by said reaction control; and converting a description format of said program based on said detection result, thereby deriving the operation result of said program.
- 26. A molecular computation method integrally functioning an electrical operation section and a molecular operation section on the basis of molecular information recognizable by an electronic program.
- 27. A molecular computation program product causing a computer system to control execution of molecular operation caused by chemical reaction of molecules, comprising:
a recording medium; first means recorded in said recording medium, the first means for assigning to said computer system a command for converting a program described by variables, constants and functions into a series of control commands for driving a reaction control section which performs reaction control of chemical reaction of molecules which correspond to operational reaction of the coding molecules, thereby generating control command procedures, wherein the variables and the constants being defined to be associated with coding molecules obtained by coding molecules based on nucleic acid sequences, and the functions being defined to be associated with operational reaction of the coding molecules; second means recorded in said recording medium, the second means for assigning a command for outputting the control command procedures; and third means recorded in said recording medium, said third means for assigning to said computer system a command for receiving the detection result of chemical reaction of molecules performed by reaction control caused by said reaction control section, and converting the received result into a description format of said program, thereby deriving the operation result of said program.
- 28. A molecular computation program product causing a molecular computer which comprises an electronic operation section and a molecular operation section to perform molecular operation caused by chemical reaction of molecules, comprising:
a recording medium; and means recorded in said recording medium, the means being applied to said electronic operation section and/or said molecular operation section, the means for assigning to said each operation section a command for initiating a computational work caused by said electronic operation section and a computational work caused by said molecular operation section in an information format which can be electrically recognized by said each operation section.
- 29. A molecular operation result analysis program product for assigning a command to an electronic operation section which assigns a command for a molecular operation section to assign a command for performing molecular operation caused by chemical reaction of molecules, the program comprising:
a recording medium; and means recorded in said recording medium, the means for assigning to said electronic operation section a command for converting information computed by said molecular operation section into an information format so as to conform with an electronic program of said electronic operation section.
- 30. A molecular operation result analysis program product for assigning a command to an electronic operation section which assigns a command for a molecular operation section to assign a command for performing molecular operation caused by chemical reaction of molecules, said program product comprising:
a recording medium; and means recorded in said recording medium, the means for assigning to said electronic operation section a command for converting the information computed by said electronic operation section so as to conform with a computational work of said molecular operation section.
- 31. A method of processing information by using an operational nucleic acid, comprising
(a) converting arbitrary information into a nucleic acid molecule; (b) hybridizing the nucleic acid molecule obtained in said (a) to an operational nucleic acid designed so as to express a logical equation indicating a condition to be detected, and extending the nucleic acid molecule hybridized; and (c) detecting a binding profile of the nucleic acid molecule included in the nucleic acid molecule extended in said (b), thereby evaluating whether a solution of the logical equation is true or false.
- 32. The method of processing information according to claim 31, wherein said nucleic acid molecule is from an orthonormal set of nucleic acid molecules.
- 33. The method of processing information according to claim 31, wherein said operational nucleic acid molecule is configured of a plurality of sequence units, a sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation, and the truth or falsehood of the logical equation is evaluated based on the binding of the nucleic acid molecule to each unit and extension thereof.
- 34. The method of processing information according to claim 31, wherein said operational nucleic acid is configured of a plurality of sequence units and a marker binding portion, the sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation, when said nucleic acid molecule binds to one of the units and is extended so that a marker does not bind to the marker binding portion, determination of the truth or falsehood of the logical equation is made whether or not a marker binds to the marker binding portion.
- 35. The method of processing information according to claim 31, wherein said operational nucleic acid is configured of a plurality of sequence units and a marker binding portion, a sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation which is formulated on the basis of the combination of presence and absence of a set of target nucleic acid molecules, when said nucleic acid molecule binds to one of the units and is extended so that a marker does not bind the marker binding portion, determination of truth or falsehood of the logical equation is made whether or not a marker binds to the marker binding portion.
- 36. A method of processing information using an operational nucleic acid, comprising
(a) selecting target sequences, and further selecting “presence” or “absence” of the target sequences as a condition, formulating a logical equation based on the selected sequences and combination of the presence or absence of the target sequences selected, and designing and preparing an operational nucleic acid molecule in accordance with the logical equation; (b) when the target sequence selected in said (a), is present, information “the target sequence is present” being converted into a “presence molecule”, whereas, when the target sequence is absent, information “the target sequence is absent” being converted into an absence molecule; (c) hybridizing a presence/absence oligonucleotide previously prepared on the basis of the condition selected in said (a)with the presence molecule obtained in said (b) and extending the presence molecule; (d) after step (c), recovering a single-stranded presence/absence oligonucleotide which has failed in forming a double strand because a desired information is absent; (e) hybridizing the absence molecule to the presence/absence oligonucleotide recovered in (d), thereby extracting the absence molecule; (f) hybridizing the presence molecule and absence molecule extracted in said (b) and (e), respectively, to the operational nucleic acid prepared in said (a) and expending the presence molecule and absence molecule; and (g) detecting binding profiles of the presence molecule and the absence molecule in the extended molecule obtained in said (f), thereby evaluating the truth or falsehood of a solution of the logical equation.
- 37. The method of processing information according to claim 36, wherein said presence molecule and said absence molecule are from a set of orthonormal nucleic acid molecules.
- 38. The method of processing information according to claim 36, wherein said operational nucleic acid molecule is configured of a plurality of sequence units, a sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation, and the truth or falsehood of the logical equation is evaluated based on the binding of the nucleic acid molecule to each unit and extension thereof.
- 39. The method of processing information according to claim 36, wherein said operational nucleic acid is configured of a plurality of sequence units and a marker binding portion, a sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation, when said nucleic acid molecule binds to one of the units and is extended so that a marker does not bind to the marker binding portion, and determination of the truth or falsehood of the logical equation is made whether or not a marker binds to the marker binding portion.
- 40. The method of processing information according to claim 36, wherein said operational nucleic acid molecule is configured of a plurality of sequence units and a marker binding portion, a sequence of each of the sequence units and the arrangement of the sequence units can be designed in accordance with the logical equation which is formulated on the basis of the combination of presence and absence of a set of target nucleic acid molecules, when said nucleic acid molecule binds to one of the units and is extended so that a marker does not bind to the marker binding portion, determination of the truth or falsehood of the logical equation is made whether or not a marker,binds to the marker binding portion.
- 41. The method of processing information according to claim 36, wherein said molecule is a nucleic acid molecule.
- 42. A method of processing information using an operational nucleic acid for evaluating a logical OR or logical AND which corresponds to the presence or absence of the nucleic acid molecule having a specific sequence or using an operational nucleic acid molecule for evaluating a logical OR and a logical AND.
Priority Claims (2)
Number |
Date |
Country |
Kind |
2000-382449 |
Dec 2000 |
JP |
|
2000-399415 |
Dec 2000 |
JP |
|
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This is a Continuation-in-Part application of U.S. patent application Ser. No. 09/893,205, filed Jun. 27, 2001, the entire contents of which are incorporated herein by reference.
[0002] This application is based upon and claims the benefit of priority from the prior Japanese Patent Applications No. 2000-382449, filed Dec. 15, 2000; No. 2000-399415, filed Dec. 27, 2000, the entire contents of both of which are incorporated herein by reference.
Continuation in Parts (1)
|
Number |
Date |
Country |
Parent |
09893205 |
Jun 2001 |
US |
Child |
10159475 |
May 2002 |
US |