Base sequence for control probe and method of designing the same

• US 20060269933A1
• Filed: 02/10/2006
• Published: 11/30/2006
• Est. Priority Date: 02/14/2005
• Status: Active Grant

• Current Assignee: Canon Kabushiki Kaisha (Canon Inc.)
• Original Assignee: Canon Kabushiki Kaisha (Canon Inc.)
• Inventors: Inui, Mimune
• Granted Patent: US 7,923,546 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

There are provided a sequence for a control probe having a sequence rarely forming a secondary structure and rarely hybridizing with an undesired target and a method of designing thereof. There is further provided a probe carrier employing a control probe designed by the designing method. To provide these, a palindromic sequence is selected based on a sequence of which frequency is low in a database for a predetermined base sequence and used as the sequence of the control probe.

Claims

1. A control probe, comprising one base sequence heading from the center of the sequence of the control probe toward an end thereof and another base sequence heading from said center toward the other end thereof, both sequences being uncomplementary.

2. The control probe according to claim 1, wherein said one sequence heading toward an end thereof has a sequence of which frequency is lowest and length of which average number of frequency (Na)is lowest(Na is not 0) in the NCBI database.

4. The control probe according to claim 1, comprising a base sequence represented by SEQ. ID No. 1.

12. The probe carrier, wherein the probe carrier is a solid phase carrier having a control probe according to any one of claims 1 to 4 and a probe for detecting a target sequence contained in a specimen, said both probes being immobilized on the solid phase carrier.

15. A nucleic acid detection kit, comprising the probe carrier according to claim 12 and an artificial nucleic acid having a complementary sequence to that of the control probe.

3. A control probe comprising a palindromic base sequence.

5. A method designing for a control probe sequence comprising the steps of:

selecting the lowest frequent sequence, of which frequency is lowest among the sequences of genes stored in a database; and

selecting a sequence containing the lowest frequent sequence as a control probe sequence, wherein the sequence comprises one base sequence heading from the center of the probe sequence toward one end thereof, and another base sequence heading from said center toward the other end thereof, both of the base sequences being uncomplementary to each other, thereby determining the sequence of the control probe.

6. A method designing for a control probe sequence comprising the steps of:

obtaining an average number of frequency (N) of each of the base sequences of not less than three bases in the sequences of genes stored in a database;

determining a base length of which average number of frequency (Na) is lowest (Na is not

     0);

selecting a lowest frequent sequence, of which frequency is lowest, from among the sequences having the base length of which average number of frequency (Na) is lowest; and

determining the sequence of the control probe by selecting a palindromic sequence containing the lowest frequent sequence as a control probe.

7. The method according to claim 6, wherein the database is the NCBI UniGene genomic sequence database.

8. The method according to claim 7, the base length is 9, wherein average number of frequency is lowest.

9. The method according to claim 8, wherein the lowest frequent sequence is CGTACGATC.

10. The method according to claim 6, wherein the average number of frequency is calculated by replacing A, T, C, and G of a genomic sequence comprising A, T, C and G in combination by four different numeric characters, respectively, to represent sequences having a predetermined length by numeric sequences containing said numeric characters, counting the numeric sequences, and calculating an average number of frequency.

11. A probe carrier, wherein the probe carrier is a solid phase carrier having a control probe comprising the sequence designed by the method according to claim 6 and a probe for detecting a target sequence contained in a specimen, said both probes being immobilized on the solid phase carrier.

13. A detection method for a target nucleic acid using hybridization reaction of the target nucleic acid with a probe nucleic acid capable of capturing the target nucleic acid, wherein the hybridization of the target nucleic acid with the probe nucleic acid is detected based on a hybridization reaction between a control probe having a palindromic base sequence and an artificial nucleic acid having a complementary sequence to that of the control probe.

14. The detection method according to claim 13, wherein the hybridization reaction is performed in the simultaneous presence of the control probe, the artificial nucleic acid having a complementary sequence to that of the control probe, the target nucleic acid, and the probe nucleic acid.