Method For Searching Target Base Sequence Of Rna Interference, Method For Designing Base Sequence Of Polynucleotide For Causing Rna Interference, Method For Producing Double-Stranded Polynucleotide, Method For Inhibiting Gene Expression, Base Sequence Processing Apparatus, Program For Running Base Sequence Processing Method On Computer, Recording Medium, And Base Sequence Processing System

A method for designing a base sequence of a polynucleotide for causing RNA interference comprising:

• searching a base sequence, conforming to the rules (a) to (d) below, from the base sequences of a target gene and designing a base sequence homologous to the searched base sequence:
• (a) The 3′ end base is adenine, thymine, or uracil,
• (b) The 5′ end base is guanine or cytosine,
• (c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and
• (d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

A method for producing a double-stranded polynucleotide comprising:

• forming one strand by providing an overhanging portion to the 3′ end of a base sequence homologous to a prescribed sequence which is contained in the base sequences of a target gene and which conforms to the following rules (a) to (d);
• and
• forming the other strand by providing an overhanging portion to the 3′ end of a base sequence complementary to the base sequence homologous to the prescribed sequence, wherein the number of bases in each strand is 15 to 30:
• (a) The 3′ end base is adenine, thymine, or uracil,
• (b) The 5′ end base is guanine or cytosine,
• (c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and
• (d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

A double-stranded polynucleotide synthesized by searching a sequence segment having 13 to 28 bases, conforming to the following rules (a) to (d), from the base sequences of a target gene for RNA interference,

• forming one strand by providing an overhanging portion to the 3′ end of a base sequence homologous to a prescribed sequence which is contained in the base sequences of the target gene and which conforms to the following rules (a) to (d), and
• forming the other strand by providing an overhanging portion to the 3′ end of a base sequence complementary to the base sequence homologous to the prescribed sequence, wherein the number of bases in each strand is 15 to 30:
• (a) The 3′ end base is adenine, thymine, or uracil,
• (b) The 5′ end base is guanine or cytosine,
• (c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and
• (d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

A method for inhibiting gene expression comprising the steps of:

• searching a sequence segment having 13 to 28 bases, conforming to the following rules (a) to (d), from the base sequences of a target gene for RNA interference;
• synthesizing a double-stranded polynucleotide such that one strand is formed by providing an overhanging portion to the 3′ end of a base sequence homologous to a prescribed sequence which is contained in the base sequences of the target gene and which conforms to the following rules (a) to (d), the other strand is formed by providing an overhanging portion to the 3′ end of a base sequence complementary to the base sequence homologous to the prescribed sequence, and the number of bases in each strand is 15 to 30;
• and
• introducing the synthesized double-stranded polynucleotide into an expression system of the target gene of which expression is to be inhibited to inhibit the expression of the target gene:
• (a) The 3′ end base is adenine, thymine, or uracil,
• (b) The 5′ end base is guanine or cytosine,
• (c) A 7-base sequence from the 3′ end is rich in one or more types of bases selected from the group consisting of adenine, thymine, and uracil, and
• (d) The number of bases is within a range that allows RNA interference to occur without causing cytotoxicity.

A base sequence processing apparatus characterized in that it comprises:

• partial base sequence creation means for acquiring base sequence information of a target gene for RNA interference and creating partial base sequence information corresponding to a sequence segment having 19 bases in the base sequence information;
• 3′ end base determination means for determining whether the 3′ end base in the partial base sequence information of a sense strand created by the partial base sequence creation means is adenine, thymine, or uracil;
• 5′ end base determination means for determining whether the 5′ end base in the partial base sequence information of a sense strand created by the partial base sequence creation means is guanine or cytosine;
• predetermined base inclusion determination means for determining whether in a 7 bases from the 3′ end in the partial base sequence information of a sense strand created by the partial base sequence creation means, at least four bases among the seven bases are one or more types of bases selected from the group consisting of adenine, thymine, and uracil;
• and
• prescribed sequence selection means for selecting prescribed sequence information which specifically causes RNA interference in the target gene from the partial base sequence information created by the partial base sequence creation means, based on the results determined by the 3′ base determination means, the 5′ end base determination means, and the predetermined base inclusion determination means;
• wherein the partial sequence information has a following general formula
• 5′- S NNNNNNNNNNN XXXXXX W - 3′
• 3′- S NNNNNNNNNNN XXXXXX W - 5′
• S is G or C
• N is G, C, A, T or U
• at least three of X is A, T or U
• W is A, T or U.

A program for running base sequence processing method on computer, characterized in that it comprises:

• a partial base sequence creation step of acquiring base sequence information of a target gene for RNA interference and creating partial base sequence information corresponding to a sequence segment having 19 bases in the base sequence information;
• a 3′ end base determination step of determining whether the 3′ end base in the partial base sequence information of a sense strand created in the partial base sequence creation step is adenine, thymine, or uracil;
• a 5′ end base determination step of determining whether the 5′ end base in the partial base sequence information of a sense strand created in the partial base sequence creation step is guanine or cytosine;
• a predetermined base inclusion determination step of determining whether in a 7 bases from the 3′ end in the partial base sequence information of a sense strand created by the partial base sequence creation means, at least four bases among the seven bases are one or more types of bases selected from the group consisting of adenine, thymine, and uracil;
• and
• a prescribed sequence selection step of selecting, based on the results determined in the 3′ base determination step, the 5′ end base determination step, and the predetermined base inclusion determination step, prescribed sequence information which specifically causes RNA interference in the target gene from the partial base sequence information created in the partial base sequence creation step;
• wherein the partial sequence information has a following general formula
• 5′- S NNNNNNNNNNN XXXXXX W - 3′
• 3′- S NNNNNNNNNNN XXXXXX W - 5′
• S is G or C
• N is G, C, A, T or U
• at least three of X is A, T or U
• W is A, T or U.

A base sequence processing system which comprises a base sequence processing apparatus processing base sequence information of a target gene for RNA interference and a client apparatus, the base sequence processing apparatus and the client apparatus being connected to each other via a network in a communicable manner, characterized in that

• the client apparatus comprises:
• base sequence transmission means for transmitting a name of the target gene or the base sequence information to the base sequence processing apparatus;
• and
• prescribed sequence acquisition means for acquiring prescribed sequence information which is transmitted from the base sequence processing apparatus and which specifically causes RNA interference in the target gene, and
• the base sequence processing apparatus comprises:
• partial base sequence creation means for acquiring base sequence information corresponding to the name of the target gene or the base sequence information transmitted from the client apparatus and creating partial base sequence information corresponding to a sequence segment having 19 bases in the base sequence information;
• 3′ end base determination means for determining whether the 3′ end base in the partial base sequence information of a sense strand created by the partial base sequence creation means is adenine, thymine, or uracil;
• 5′ end base determination means for determining whether the 5′ end base in the partial base sequence information of a sense strand created by the partial base sequence creation means is guanine or cytosine;
• predetermined base inclusion determination means for determining whether in a 7 bases from the 3′ end in the partial base sequence information means, at least four bases among the seven bases are one or more types of bases selected from the group consisting of adenine, thymine, and uracil;
• prescribed sequence selection means for selecting the prescribed sequence information from the partial base sequence information created by the partial base sequence creation means, based on the results determined by the 3′ base determination means, the 5′ end base determination means, and the predetermined base inclusion determination means;
• and
• prescribed sequence transmission means for transmitting the prescribed sequence information selected by the prescribed sequence selection means to the client apparatus;
• wherein the partial sequence information has a following general formula
• 5′- S NNNNNNNNNNN XXXXXX W - 3′
• 3′- S NNNNNNNNNNN XXXXXX W - 5′
• S is G or C
• N is G, C, A, T or U
• at least three of X is A, T or U
• W is A, T or U.