Method of designing addressable array suitable for detection of nucleic acid sequence differences using ligase detection reaction
원문보기
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C07H-021/00
C12Q-001/68
출원번호
US-0096446
(2016-04-12)
등록번호
US-9725759
(2017-08-08)
발명자
/ 주소
Barany, Francis
Zirvi, Monib
Gerry, Norman P.
Favis, Reyna
Kliman, Richard
출원인 / 주소
Cornell Research Foundation, Inc.
대리인 / 주소
LeClairRyan, a Professional Corporation
인용정보
피인용 횟수 :
1인용 특허 :
66
초록▼
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 r
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 present invention further relates to an oligonucleotide array comprising of a support with the plurality of oligonucleotide probes immobilized on the support, a method of using the support to detect single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences, and a kit for such detection, which includes the support on which the oligonucleotides have been immobilized.
대표청구항▼
1. A collection of oligonucleotides, wherein each type of oligonucleotide of the collection comprises a zip code sequence comprising two multimer unit sequences linked together, wherein each multimer unit sequence of the oligonucleotides in the collection (1) is comprised of three consecutive subuni
1. A collection of oligonucleotides, wherein each type of oligonucleotide of the collection comprises a zip code sequence comprising two multimer unit sequences linked together, wherein each multimer unit sequence of the oligonucleotides in the collection (1) is comprised of three consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, (2) differs from all other multimer unit sequences by at least two nucleotide bases, and (3) has a Tm value greater than 24° C., wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, and wherein the collection of oligonucleotides does not contain: (1) oligonucleotides having zip code sequences with a melting temperature in ° C. less than 11 times the number of subunits and more than 15 times the number of subunits, (2) oligonucleotides having zip code sequences comprised of two identical multimer unit sequences linked together and (3) two types of oligonucleotides with zip code sequences having the same four subunit sequences linked together in the same order without interruption. 2. The collection of claim 1, wherein each oligonucleotide in the collection comprises a zip code sequence of 20-24 bases. 3. The collection of claim 1, wherein one or more of the oligonucleotides in the collection is hybridized to a nucleic acid molecule comprising a complementary nucleotide sequence. 4. The collection of claim 1, wherein the collection of oligonucleotides does not contain oligonucleotides having a zip code sequence with a melting temperature in ° C. of more than 14 times the number of subunits. 5. The collection of claim 1, wherein the collection has greater than 4000 different types of oligonucleotides. 6. A group of spheres, wherein each sphere of the group has attached to it one or more types of oligonucleotides from the collection of claim 1, wherein the group of spheres comprises at least 64 different types of oligonucleotides from said collection. 7. The group of spheres of claim 6, wherein each oligonucleotide in the collection comprises a zip code sequence of 20-24 bases. 8. The group of spheres of claim 6, wherein one or more of the oligonucleotides in the collection is hybridized to a nucleic acid molecule comprising a complementary nucleotide sequence. 9. The group of spheres of claim 6, wherein the collection has greater than 4000 different types of oligonucleotides. 10. A device comprising: a solid support having an array of positions each suitable for attachment of a oligonucleotide;a collection of oligonucleotides on the solid support at the array of positions, wherein each type of oligonucleotide on the solid support comprises a zip code sequence comprising two multimer unit sequences linked together, wherein each multimer unit sequence is comprised of three consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, wherein each multimer unit sequence has a Tm value of greater than 24° C., wherein each of the two multimer unit sequences differs from all other multimer unit sequences by at least two nucleotide bases when aligned, wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, wherein the collection of oligonucleotides on the solid support does not contain (1) oligonucleotides having zip code sequences with melting temperature in ° C. less than 11 times the number of subunits and more than 15 times the number of subunits, (2) oligonucleotides having zip code sequences comprised of two identical multimer unit sequences linked together and (3) two types of oligonucleotides with zip code sequences having the same four subunit sequences linked together in the same order without interruption; andone or more target nucleic acid molecules hybridized to complementary portions of the oligonucleotides on the solid support. 11. The device of claim 10, wherein the collection has greater than 4000 different types of oligonucleotides. 12. The device according to claim 10, wherein each oligonucleotide comprises a zip code sequence of 20-24 bases. 13. The device according to claim 10, wherein different oligonucleotides are attached at different array positions on the solid support. 14. The device according to claim 10, wherein oligonucleotides having identical zip code sequences are attached at different positions on the support. 15. The device according to claim 10, wherein the solid support comprises particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, discs, membranes, or any combination or composite thereof. 16. The device according to claim 10, wherein a linker couples the oligonucleotides to the solid support. 17. The device according to claim 16, wherein the linker comprises a silane on a surface of the solid support. 18. A collection of oligonucleotides, wherein each type of oligonucleotide of the collection comprises a zip code sequence having either five consecutive subunits linked together or six consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, wherein (1) the sequence of any three consecutive subunits of the oligonucleotide sequence of one type of oligonucleotide in the collection differs from the sequence of any three consecutive subunits of the oligonucleotide sequence of any other type of oligonucleotide in the collection by at least two nucleotide bases and (2) the sequence of any three consecutive subunits of the oligonucleotide sequence in the collection of oligonucleotides has a Tm value greater than 24° C., wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, and wherein the collection of oligonucleotides does not contain: (1) oligonucleotides having zip code sequences with a melting temperature in ° C. less than 11 times the number of subunits and more than 15 times the number of subunits, (2) oligonucleotides having zip code sequences where the sequence of the first three consecutive subunits is identical to the sequence of the last three consecutive subunits of the same oligonucleotide sequence, and (3) two types of oligonucleotides with zip code sequences having the same four subunit sequences linked together in the same order with or without interruption. 19. The collection of claim 18, wherein the collection has greater than 4000 different types of oligonucleotides. 20. A device comprising: a solid support having an array of positions each suitable for attachment of a oligonucleotide;a collection of oligonucleotides on the solid support at the array of positions, wherein each type of oligonucleotide on the solid support comprises a zip code sequence having either five consecutive subunits linked together or six consecutive subunits linked together, each subunit independently selected from the group consisting of a trimer, tetramer, pentamer, or hexamer sequence, wherein (1) the sequence of any three consecutive subunits of the oligonucleotide sequence of one type of oligonucleotide in the collection differs from the sequence of any three consecutive subunits of the oligonucleotide sequence of any other type of oligonucleotide in the collection by at least two nucleotide bases and (2) the sequence of any three consecutive subunits of the oligonucleotide sequence in the collection of oligonucleotides has a Tm value greater than 24° C., wherein the collection of oligonucleotides has at least 64 different types of oligonucleotides, and wherein the collection of oligonucleotides does not contain: (1) oligonucleotides having zip code sequences with a melting temperature in ° C. less than 11 times the number of subunits and more than 15 times the number of subunits, (2) oligonucleotides having zip code sequences where the sequence of the first three consecutive subunits is identical to the sequence of the last three consecutive subunits of the same oligonucleotide sequence, and (3) two types of oligonucleotides with zip code sequences having the same four subunit sequences linked together in the same order with or without interruption; andone or more target nucleic acid molecules hybridized to complementary portions of the oligonucleotides on the solid support. 21. The device of claim 20, wherein the collection has greater than 4000 different types of oligonucleotides. 22. The device according to claim 20, each oligonucleotide comprises a zip code sequence of 20-24 bases. 23. The device according to claim 20, wherein different oligonucleotides are attached at different array positions on the solid support. 24. The device according to claim 20, wherein oligonucleotides having identical sequences are attached at different positions on the support. 25. The device according to claim 20, wherein the solid support comprises particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, discs, membranes, or any combination or composite thereof.
연구과제 타임라인
LOADING...
LOADING...
LOADING...
LOADING...
LOADING...
이 특허에 인용된 특허 (66)
Chakraborty Prasanta R. (Scotch Plains NJ) Elbrecht Alex (Watchung NJ) Dashkevicz Michael (Jamesburg NJ) Feighner Scott D. (Scotch Plains NJ) Liberator Paul A. (Jackson NJ) Profous-Juchelka Helen (St, Eimeria brunetti 16s rDNA probes.
Bhatnagar Satish K. (Gaithersburg MD) George ; Jr. Albert L. (Gaithersburg MD) Nazarenko Irina (Gaithersburg MD), Amplification of nucleic acid sequences.
Zaun Peter (Libertyville IL) Bouma Stanley R. (Grayslake IL) Gordon Julian (Lake Bluff IL) Kotlarik John J. (Vernon Hills IL), Apparatus and method for amplifying and detecting target nucleic acids.
Fodor Stephen P. A. (Palo Alto CA) Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Stryer Lubert (Stanford CA), Array of oligonucleotides on a solid substrate.
McGall Glenn Hugh ; Miyada Charles Garrett ; Cronin Maureen T. ; Tan Jennifer Dee ; Chee Mark S., Arrays of modified nucleic acid probes and methods of use.
Chee Mark ; Cronin Maureen T. ; Fodor Stephen P. A. ; Huang Xiaohua X. ; Hubbell Earl A. ; Lipshutz Robert J. ; Lobban Peter E. ; Morris MacDonald S. ; Sheldon Edward L., Arrays of nucleic acid probes on biological chips.
Ekins Roger P. (Department of Molecular Endocrinology University College and Middlesex School of Medicine Mortimer Street London W1N 8AA GBX) Chu Frederick W. (Department of Molecular Endocrinology U, Binding assay employing labelled reagent.
Fraiser Melinda S. (Durham NC) Walker George T. (Chapel Hill NC) Schram James L. (Knightdale NC), Decontamination of nucleic acid amplification reactions using uracil-N-glycosylase (UDG).
Barany, Francis; Gerry, Norman P.; Witowski, Nancy E.; Day, Joseph; Hammer, Robert P.; Barany, George, Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays.
Whiteley Norman M. (San Carlos CA) Hunkapiller Michael W. (San Carlos CA) Glazer Alexander N. (Orinda CA), Detection of specific sequences in nucleic acids.
Froehler Brian (Belmont CA) Matteucci Mark (Burlingame CA), Enhanced triple-helix and double-helix formation with oligomers containing modified purines.
Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Fodor Stephen P. A. (Palo Alto CA) Stryer Lubert (Stanford CA), Large scale photolithographic solid phase synthesis of an array of polymers.
Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Fodor Stephen P. A. (Palo Alto CA) Stryer Lubert (Stanford CA), Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof.
Backman Keith C. (Bedford MA) Carrino John J. (Gurnee IL) Shimer George H. (Boston MA) Yocum Robert R. (Lexington MA), Ligase chain reaction with endonuclease IV correction and contamination control.
Matson Robert S. (Orange CA) Coassin Peter J. (San Juan Capistrano CA) Rampal Jang B. (Yorba Linda CA) Southern Edwin M. (Kidlington GB2), Method and apparatus for creating biopolymer arrays on a solid support surface.
Davis Ronald W. (Palo Alto CA) Myles Arthur (Hopedale MA), Method for detecting a nucleotide at a specific location within a nucleic acid using exonuclease activity.
Drmanac Radoje T. (Zvecanska 46 Beograd 11000) Crkvenjakov Radomir B. (Bulevar JNA 118 Beograd YUX 11000), Method of sequencing of genomes by hybridization of oligonucleotide probes.
Grossman Paul D. (Burlingame CA) Fung Steven (Palo Alto CA) Menchen Steven M. (Fremont CA) Woo Sam L. (Redwood City CA) Winn-Deen Emily S. (Foster City CA), Probe composition containing a binding domain and polymer chain and methods of use.
Gelfand David H. (Oakland CA) Kwok Shirley Y. (San Ramon CA) Sninsky John J. (El Sobrante CA), Reduction of non-specific amplification glycosylase using DUTP and DNA uracil.
McGall Glenn H. (Mountain View CA) Fodor Stephen P. A. (Palo Alto CA) Sheldon Edward L. (Menlo Park CA), Spatially-addressable immobilization of oligonucleotides and other biological polymers on surfaces.
Fodor Stephen P. A. (Palo Alto CA) Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Stryer Lubert (Stanford CA), Synthesis and screening of immobilized oligonucleotide arrays.
Barany Francis ; Zebala John ; Nickerson Deborah ; Kaiser ; Jr. Robert J. ; Hood Leroy, Thermostable ligase mediated DNA amplification system for the detection of genetic diseases.
Barany Francis (New York NY) Zebala John (New York NY) Nickerson Deborah (Seattle WA) Kaiser ; Jr. Robert J. (Seattle WA) Hood Leroy (Seattle WA), Thermostable ligase-mediated DNA amplifications system for the detection of genetic disease.
Fodor Stephen P. A. (Palo Alto CA) Stryer Lubert (Stanford CA) Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA), Very large scale immobilized polymer synthesis.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.