Novel computation with nucleic acid molecules, computer and software for computing

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 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 extract 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 true or false of a solution of the logical equation.

A molecular computer comprising an electronic operation section and a molecular operation section;

• wherein, in said electronic operation section, a constant and a variable of a computation program are converted into coding molecules, and a procedure and a function of the computation program are converted into an operation reaction;
• implementation steps of the operation reaction are prepared from the computation program;
• and
• in said molecular operation section, in which coding molecules are stored, the operation reaction of the coding molecules is performed in accordance with the implementation steps, whereby the results of the operation reaction are obtained or further detected.

A molecular computer comprising an electronic operation section and a molecular operation section;

• wherein said electronic operation section comprises
• means inputting a computation program, a constant and a variable of a computation program;
• means converting the constant and variable of the computation program into a coding molecule;
• means converting a procedure and a function of the computation program into a corresponding operational reaction of a coding molecule;
• performing an operation of a part of the computation program;
• means preparing an implementation procedure of the operation reaction in accordance with the computation program or the operation results of the molecular operation section;
• and
• means controlling the operation reaction to be performed in the molecular operation section in accordance with the implementation procedure of the operation reaction;
• and
• said molecular operation section comprises
• operation means performing the operation reaction by using the coding molecule;
• and
• detection means detecting the operation result performed by the operation means.

A molecular computer comprising an electronic operation section and a molecular operation section;

• wherein said electronic operation section comprises
• means inputting a computation program, a constant and a variable of a computation program;
• means converting the constant and variable of the computation program into a coding molecule;
• means converting a procedure and a function of the computation program into a corresponding operational reaction of a coding molecule;
• performing an operation of a part of the computation program;
• means preparing an implementation procedure of the operation reaction in accordance with the computation program or the operation results of the molecular operation section;
• and
• means controlling the operation reaction to be performed in the molecular operation section in accordance with the implementation procedure of the operation reaction;
• and
• means displaying the operation results detected by the molecular operation section;
• and
• said molecular operation section comprises
• operation means performing the operation reaction by using the coding molecule;
• and
• detection means detecting the operation result performed by the operation means.

A molecular computer comprising

• input means inputting a computation program for computation;
• storage means storing the computation program input
• operation means operating a part of the computation program;
• storage means storing a molecule conversion table for assigning the computation program, and a constant and a variable of the computation program to coding molecules;
• conversion means converting the computation program, and the constant and the variable of the computation program to coding molecules by reading the molecule conversion table and screening and reading out corresponding data stored therein;
• synthesis means synthesizing the coding molecule;
• storage means storing a procedure conversion table for converting the computation program into an experimental operation of the coding molecule;
• plan preparation means preparing an experimental design by reading out the procedure conversion table, screening and reading out the corresponding data and converting the corresponding data into an experimental operation;
• automatic control means outputting a driving signal in accordance with the experimental means prepared;
• experimental means operating the experimental operation in accordance with the driving signal from the automatic control means by using the coding molecule synthesized;
• detection means detecting the coding molecule obtained from the experimental operation;
• processing means processing detection results into a form written in the computation program;
• and
• an output means outputting results obtained by the processing means.