Method of automatically selecting oligonucleotide hybridization probes

• US 6,475,737 B1
• Filed: 11/21/2000
• Issued: 11/05/2002
• Est. Priority Date: 11/24/1999
• Status: Expired due to Fees

• Current Assignee: Nicolas Von Ahsen, Schütz, Ekkehard
• Original Assignee: Nicolas Von Ahsen, Schütz, Ekkehard
• Inventors: von Ahsen, Nicolas, Schütz, Ekkehard
• Primary Examiner(s): Siew, Jeffrey
• Application Number:
  US09/717,569
• Time in Patent Office: 714 Days
• Field of Search: 435/6, 435/7.1, 435/91.1, 435/91.2, 435/287.2, 536/22.1, 536/23.1, 536/24.3, 536/24.31, 536/24.32, 536/24.33, 702/19, 702/20
• US Class Current: 435/6.1
• 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
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

A method for automatically selecting oligonucleotide hybridization probes for detecting a mutation causing a mismatch in a DNA duplex is based on a thermodynamic nearest-neighbour model for calculating a melting point, which is a temperature at which a predetermined percentage of a multitude of identical hybridized pairs of a certain hybridization probe and a DNA strand is in an annealed state. Using this model a first melting point of the respective probe hybridized with its complementary mutant DNA strand or opposite sense mutant DNA strand, a second melting point of the respective probe hybridized with its complementary wild-type DNA strand or opposite sense wild-type DNA strand, respectively, and a temperature difference between the first and second melting points are calculated for all possible hybridization probes. Then, the possible hybridization probes are ranked with regard to the calculated temperature difference.

Claims

1. A method of selecting oligonucleotide hybridization probes for detecting a mutation causing a mismatch in a DNA duplex, the method comprising the steps of:

defining the mutation to be detected by

a DNA sequence of a mutant DNA strand and

a DNA sequence of a wild-type DNA strand corresponding to the mutant DNA strand;

defining an integer variable L1 for a first length of the oligonucleotide hybridization probes from the place of mutation in a first direction;

defining a range from m1 to n1 of possible values of the variable L1;

defining an integer variable L2 for a second length of the oligonucleotide hybridization probes from the place of mutation in a second direction opposite to the first direction;

defining a range from m2 to n2 of possible values of the variable L2;

selecting at least one oligonucleotide hybridization probe from the group consisting of

probes which are fully complementary to the mutant DNA strand,

probes which are fully complementary to the wild-type DNA strand corresponing to the mutant DNA strand,

probes which are fully complementary to an opposite sense mutant DNA strand which is the complementary DNA strand to the mutant DNA strand, and

probes which are fully complementary to an opposite sense wild-type DNA strand which is the complementary DNA strand to the wild-type DNA strand corresponding to the mutant DNA strand;

determining all possible hybridization probes from the possible values of the variables L1 and L2, and the selected probes;

defining a thermodynamic nearest-neighbor model for calculating a melting point of a certain hybridization probe hybridized to a DNA strand, the melting point being a temperature at which a predetermined percentage of a multitude of identical pairs of said certain hybridization probe and said DNA strand is in an annealed state;

calculating, on basis of the thermodynamic nearest-neighbor model, for all possible hybridization probes

a first melting point of the respective probe hybridized with its complementary mutant DNA strand or opposite sense mutant DNA strand, respectively,

a second melting point of the respective probe hybridized with its complementary wild-type DNA strand or opposite sense wild-type DNA strand, respectively, and

a temperature difference between the second melting point and the first melting point; and

ranking the possible hybridization probes with regard to the temperature difference.

2. The method of claim 1, and firther comprising the steps of:

defining a temperature range of a hybridization assay to be employed for detecting the mutation using the oligonucleotide hybridization probes; and

checking for each of the possible hybridization probes whether both the first and the second melting points are within the temperature range of the hybridization assay;

wherein the step of ranking the possible hybridization probes with regard to the temperature difference includes;

ranking only those possible hybridization probes which have both their melting points within the temperature range of the hybridization assay.

3. The method of claim 2, wherein the step of defining the temperature range of the hybridization assay to be employed for detecting the mutation includes:

defining the temperature range within a range from 20 to 80°

C.

4. The method according to claim 1, and further comprising the step of:

defining at least one physico-chemical parameter of a hybridization assay to be employed for detecting the mutation using the oligonucleotide hybridization probes;

wherein the step of defining a thermodynamic nearest-neighbor model includes;

defining the thermodynamic nearest-neighbor model based on at least one physico-chemical parameter of the hybridization assay.

5. The method of claim 4, wherein the step of defining at least one physico-chemical parameter of the hybridization assay to be employed for detecting the mutation includes:

defining at least one ion concentration as one of the physico-chemical parameters.

6. The method of claim 5, wherein the step of defining at least one ion concentration as one of the physico-chemical parameters includes:

defining a Na+ cation equivalent concentration.

7. The method according to claim 1, and further comprising the steps of:

defining an integer number N of the hybridization probes to be automatically selected; and

making a list of the N top ranked possible hybridization probes.

8. The method according to claim 1, wherein the step of ranking the possible hybridization probes with regard to the temperature difference includes:

ranking the possible hybridization probes separately for each of the kinds of the oligonucleotide hybridization probes.

9. The method according to claim 1, and further comprising the step of:

checking, for each of the possible hybridization probes, whether it is able to hybridize either to the mutant DNA strand and the opposite sense mutant DNA strand, or to the wild-type DNA strand and the opposite sense wild-type DNA strand in more than one way;

wherein the step of ranking the possible hybridization probes with regard to the temperature difference includes;

ranking only those possible hybridization probes which are neither able to hybridize to the mutant DNA strand and the opposite sense mutant DNA strand, nor to the wild-type DNA strand and the opposite sense wild-type DNA strand in more than one way.

10. The method according to claim 1, and further comprising the steps of:

defining at least one further mutation which may occur on the mutant DNA strand or the wild-type DNA-strand or the opposite sense wild-type DNA strand;

checking, for each of the possible hybridization probes, whether it is sensitive to the further mutation in the same way as to the mutation;

wherein the step of ranking the possible hybridization probes with regard to the temperature difference includes;

ranking only those possible hybridization probes which are not sensitive to the further mutation in the same way as to the mutation.