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1. 发明申请

US20120283139A1 METHOD OF DESIGNING ADDRESSABLE ARRAY SUITABLE FOR DETECTION OF NUCLEIC ACID SEQUENCE DIFFERENCES USING LIGASE DETECTION REACTION 有权
公开(公告)号：US20120283139A1
公开(公告)日：2012-11-08
申请号：US12252169
申请日：2008-10-15
申请人： Francis BARANY , Monib ZIRVI , Norman P. GERRY , Reyna FAVIS , Richard KLIMAN
发明人： Francis BARANY , Monib ZIRVI , Norman P. GERRY , Reyna FAVIS , Richard KLIMAN
IPC分类号： C40B40/06
CPC分类号： C12Q1/6837 , C12Q1/6827 , C12Q1/6874 , C12Q1/6886 , C12Q2527/107 , C12Q2521/501 , C12Q2521/319 , C12Q2565/501
摘要： 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 set differs from all other tetramers in the set by at least two nucleotide bases, (2) no two tetramers within a set are complementary to one another, (3) no tetramers within a set are palindromic or dinucleotide repeats, and (4) no tetramer within a 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. Alternating multimer units in the list are then divided into first and second subcollections, each arranged in order of melting temperature. After the order of the second subcollection is inverted, the first collection is linked in order to the inverted second collection to form a collection of double multimer units. From the collection of double multimer units, those units (1) having a melting temperature in ° C. 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 are removed, to form a modified collection of double multimer units. The modified collection of double multimers can be immobilized on a support and used to capture, by hybridization, the products of a ligation detection reaction. As a result, the output of a ligation detection reaction, which is useful in detecting single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences, can be formatted on a support.

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