Method of designing probe from polynucleotide group comprising plurality of polynucleotides

• US 20060110757A1
• Filed: 10/26/2005
• Published: 05/25/2006
• Est. Priority Date: 10/26/2004
• Status: Active Grant

• Current Assignee: Samsung Electronics Co. Ltd. (Samsung Group)
• Original Assignee: Samsung Electronics Co. Ltd. (Samsung Group)
• Inventors: Ahn, Tae-jin
• Granted Patent: US 7,321,832 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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:

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.

2. The method of claim 1, wherein the providing of the sequence specific identification number comprises:

providing bases of nucleotides A, T, G and C with values of 0, 4^(L-i)/4, 4^(L-i)/2 and 4^(L-i)×

(3/4), respectively, where L is the length of each 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;

combining the provided values;

adding values from 4¹ to 4^(L-1) to the sum; and

providing the obtained value as the identification numbers of the polynucleotide fragment.

3. The method of claim 1, wherein the probe is a sequence specific to a polynucleotide or a common sequence of polynucleotides.

4. The method of claim 1, wherein, when a specific probe having mismatched nucleotides is selected, the providing the sequence specific identification number to each of the polynucleotide fragments 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 produced polynucelotides with sequence specific identification numbers.

5. The method of claim 4, wherein the providing of the sequence specific identification number comprises:

providing bases of nucleotides A, T, G and C with values of 0, 4^(L-i)/4, 4^(L-i)/2 and 4^(L-i)×

(3/4), respectively, where L is the length of each 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;

combining the provided values;

adding values from 4′

to 4^(L-1) to the sum; and

providing the obtained value as the identification numbers of the polynucleotide fragment.

6. The method of claim 4, wherein, when the selected sequence specific probe comprises sequence specific probes having mismatched nucleotides, the method further comprises:

producing polynucleotide fragments having a certain length produced from a sequence specific probe having mismatched nucleotides;

obtaining sequence and position information of the produced polynucleotide fragments;

providing the polynucleotide fragments with sequence specific identification numbers based on the sequence and position information; and

comparing the sequence specific identification numbers of the polynucleotide fragments obtained from each of the sequence specific probes having mismatched nucleotides to select the most frequently appearing sequence specific probe having a mismatched nucleotide.

7. The method of claim 1, wherein a region where a probe specific to a target polynucleotide appears frequently is selected using position information of the polynucleotide fragments, and probes present in the region are selected as sequence specific probes.