Method of designing probe from polynucleotide group comprising plurality of polynucleotides

• US 7,321,832 B2
• Filed: 10/26/2005
• Issued: 01/22/2008
• Est. Priority Date: 10/26/2004
• Status: Expired due to Fees

• Current Assignee: Samsung Electronics Co. Ltd.
• Original Assignee: Samsung Electronics Co. Ltd.
• Inventors: Ahn, Tae-jin
• Primary Examiner(s): Shukla; Ram R.
• Assistant Examiner(s): Skibinsky; Anna
• Application Number:
  US11/259,730
• Publication Number:
  US 20060110757A1
• Time in Patent Office: 818 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

There is provided a method of designing a probe from a polynucleotide group comprising a plurality of polynucleotides, the method including: forming a polynucleotide group by selecting polynucleotides having a certain sequence; producing polynucleotide fragments having a certain length from each of the polynucleotides of the polynucleotide group and obtaining sequence and position information on the polynucleotide fragments; providing each polynucleotide fragment with a sequence specific identification number using the obtained sequence and position information of the polynucleotide fragments; and comparing the identification numbers of the fragments to select the probe.

Claims

1. A method of designing a probe from a polynucleotide group comprising a plurality of polynucleotides, the method comprising:

providing a sequence for each polynucleotide in a plurality of polynucleotides;

forming a polynucleotide group consisting of all the sequences;

producing polynucleotide fragments having a certain length from each of the sequences of the polynucleotide group;

obtaining a sequence for each polynucleotide fragment;

providing, for each polynucleotide fragment, a sequence specific identification number using the sequence for the polynucleotide fragment;

comparing the sequence specific identification numbers of the polynucleotide fragments to each other to select a probe; and

displaying the selected probe;

wherein the sequence specific identification number is calculated by

providing bases of nucleotides A, T, G, and C in the sequence of the polynucleotide fragment with values of 0, 4<sup>(L−

i)</sup>/4, 4<sup>(L−

i)</sup>/2, and 4<sup>(L−

i)</sup>×

(3/4), respectively, where L is the length of the polynucleotide fragment and i sequentially increases from i=0 at a 5′

-end nucleotide of the polynucleotide to i=L−

1 at a 3′

-end nucleotide of the polynucleotide fragment;

adding the provided values for each base in the sequence and values from 4¹ to obtain a sum; and

providing the sum as the sequence specific identification number of the polynucleotide fragment.

2. The method of claim 1, wherein the probe is a specific probe or a common probe.

3. The method of claim 1, wherein, if the selected probe is a specific probe comprising mismatched nucleotides, the method further comprises:

producing polynucleotide fragments having at least one nucleotide mismatched to one of the polynucleotide fragments having a sequence specific identification number; and

providing the mismatched polynucleotide fragments with sequence specific identification numbers.

4. The method of claim 3, wherein providing a mismatched polynucleotide fragment with a sequence specific identification number comprises:

providing bases of nucleotides A, T, G and C in a sequence of the mismatched polynucleotide fragment with values of 0, 4<sup>(L−

i)</sup>/4, 4<sup>(L−

i)</sup>/2 and 4<sup>(L−

i)</sup>×

(3/4), respectively, where L is the length of the mismatched polynucleotide fragment and i sequentially increases from i=0 at a 5′

-end nucledotide of the mismatched polynucleotide fragment to i=L−

1 at a 3′

-end nucleotide of the mismatched polynucleotide fragment;

adding the provided values for the sequence of the mismatched polynucleotide fragment and values from 4¹ to 4<sup>(L−

1)</sup> to obtain a sum; and

providing the sum as the sequence specific identification number of the mismatched polynucleotide fragment.

5. The method of claim 3, further comprising:

producing polynucleotide fragments comprising mismatched nucleotide and having a certain length from the selected specific probe;

obtaining a sequence for each of the produced polynucleotide fragments;

providing each of the produced polynucleotide fragments with sequence specific identification numbers based on the sequence; and

comparing the sequence specific identification numbers of the produced polynucleotide fragments obtained from each of the selected specific probes; and

selecting the most frequently appearing specific probe comprising a mismatched nucleotide.

6. The method of claim 1, further comprising

selecting a region of a polynucleotide in which a probe specific to the polynucleotide appears frequently using position information of the polynucleotide fragments, and probes present in the region are selected as sequence specific probes.