Method of designing addressable array for detection of nucleic acid sequence differences using ligase detection reaction

• US 7,455,965 B2
• Filed: 04/04/2001
• Issued: 11/25/2008
• Est. Priority Date: 04/14/2000
• Status: Expired due to Fees

• Current Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Original Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Inventors: Barany, Francis, Zirvi, Monib, Kliman, Richard, Favis, Reyna, Gerry, Norman P.
• Primary Examiner(s): Johannsen; Diana B.
• Assistant Examiner(s): Crow; Robert T
• Application Number:
  US10/257,158
• Publication Number:
  US 20050142543A1
• Time in Patent Office: 2,792 Days
• Field of Search: 435/6, 435/91.1, 435/91.2
• US Class Current: 435/6.16
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2527/107 Temperature of melting, i.e. Tm
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: H05K 999/99 dummy group

Abstract

The present invention is directed to a method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, where the plural capture oligonucleotide probes have melting temperatures within a narrow range. The first step of the method involves providing a first set of a plurality of tetramers of four nucleotides linked together, where (1) each tetramer within the first set differs from all other tetramers in the first set by at least two nucleotide bases, (2) no two tetramers within the first set are complementary to one another, (3) no tetramers within the first set are palindromic or dinucleotide repeats, and (4) no tetramer within the first set has one or less or three or more G or C nucleotides. Groups of 2 to 4 of the tetramers from the first set are linked together to form a collection of multimer units. From the collection of multimer units, all multimer units formed from the same tetramer and all multimer units having a melting temperature in ° C. of less than 4 times the number of tetramers forming a multimer unit are removed to form a modified collection of multimer units. The modified collection of multimer units is arranged in a list in order of melting temperature. The order of the modified collection of multimer units is randomized in 2° C. increments of melting temperature.

Claims

1. A method of designing a plurality of capture oligonucleotide probes for use on a support to which complementary oligonucleotide probes will hybridize with little mismatch, wherein the plurality of capture oligonucleotide probes have melting temperatures within a narrow range, said method comprising:

providing a first set of a plurality of tetramers of four nucleotides linked together, wherein (1) each tetramer within the first set differs from all other tetramers in the first set by at least two nucleotide bases, (2) no two tetramers within the first set are complementary to one another, (3) no tetramers within the first set are palindromic or dinucleotide repeats, and (4) no tetramer within the first set has less than one or more than three G or C nucleotides;

linking groups of 2 to 4 of the tetramers from the first set together to form a collection of multimer units;

calculating the predicted melting temperatures of the linked groups of 2 to 4 of the tetramers in the collection of multimer units;

removing from the collection of multimer units all multimer units formed from the same tetramer and all multimer units having a melting temperature in °

C. of less than 4 times the number of tetramers forming a multimer unit, to form a modified collection of multimer units;

arranging the modified collection of multimer units into groups differing by 2°

C. increments in melting temperature;

randomizing the order of the groups of multimer units;

dividing alternating groups of multimer units into first and second subcollections;

arranging each of the first and the second subcollections in order of melting temperature;

inverting the order of the second subcollection;

linking the multimer units of the first subcollection to the multimer units of the inverted second subcollection to form a collection of double multimer units;

calculating the melting temperature of the linked multimer units in the collection of double multimer units;

removing from the collection of double multimer units all double multimer units (1) having a melting temperature in °

C. of less than 11 times the number of tetramers and more than 15 times the number of tetramers, (2) double multimer units with the same 3 tetramers linked together, and (3) double multimer units with the same 4 tetramers linked together with or without interruption, to form a modified collection of double multimer units; and

producing the modified collection of double multimer units.

2. A method according to claim 1 further comprising:

placing the modified collection of double multimer units at positions on a support.

3. A method according to claim 2, wherein the collection of double multimer units removed has a melting temperature in °

C. of less than 12.5 times the number of tetramers and more than 14 times the number of tetramers.

4. A method according to claim 1, wherein the collection of multimer units have 12 mers, the double multimer units have 24 mers, and the melting point of the double multimer units is 75-84°

C.

5. A method according to claim 1 further comprising:

reclaiming double multimer units having a melting temperature in °

C. of less than 11 times the number of tetramers and more than 15 times the number of tetramers;

unlinking the reclaimed double multimers units to each form a pair of reclaimed multimer units;

selecting reclaimed multimer units with a melting temperature in °

C. of more than 11 times the number of tetramers and less than 17 times the number of tetramers; and

reintegrating the reclaimed selected multimer units into said method.

6. A method according to claim 5, wherein the method is repeated.

7. A method according to claim 1 further comprising:

making additional different sets of a plurality of tetramers by producing, base by base, circular permutations of the tetramers within the first set and complements thereof.

8. A method according to claim 1, wherein the collection of double multimer units has a melting temperature in °

C of less than 12.5 times the number of tetramers and more than 14 times the number of tetramers.