Processes for detecting or quantifying nucleic acids using an array of fixed or immobilized nucleic acids
4 Assignments
0 Petitions
Accused Products
Abstract
This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.
-
Citations
558 Claims
-
1-437. -437. (canceled)
-
438. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:
-
a) providing;
(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;
(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and
(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said second set of primers comprises at least two segments, the first segment at the 3′
end comprising random sequences, and the second segment comprising at least one production center;
(iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions;
b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;
c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;
d) contacting said extended first copies with said second set of primers to form more than one second bound entity;
e) extending said bound second set of primers by means of template sequences provided by said extended first copies to form more than one complex comprising extended first copies and extended second set of primers;
f) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;
g) hybridizing said nucleic acid copies formed in step f) to said array of nucleic acids provided in step a) (i); and
h) detecting or quantifying any of said hybridized copies obtained in step g). - View Dependent Claims (439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466)
-
-
467. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:
-
a) providing;
(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;
(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;
(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said first set of primers comprise at least one production center; and
(iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions;
b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;
c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;
d) extending said first copies by means of at least four (4) or more non-inherent homopolymeric nucleotides;
e) contacting said extended first copies with said second set of primers to form more than one second bound entity;
f) extending said bound second set of primers by means of template sequences provided by said extended first copies to form more than one complex comprising extended first copies and extended second set of primers;
g) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;
h) hybridizing said nucleic acid copies formed in step g) to said array of nucleic acids provided in step a) (i); and
i) detecting or quantifying any of said hybridized copies obtained in step h). - View Dependent Claims (468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496)
-
-
497. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:
-
a) providing;
(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;
(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;
(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said first set comprises at least one production center;
(iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of said second set of primers; and
(v) means for ligating said set of oligonucleotides or polynucleotides (iv);
b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;
c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;
d) ligating said set of oligonucleotides or polynucleotides a) (iv) to the 3′
end of said first copies formed in step c) to form more than one ligated product;
e) contacting said ligated product with said second set of primers to form more than one second bound entity;
f) extending said bound second set of primers by means of template sequences provided by said ligated products formed in step d) to form more than one complex comprising said ligated products and said extended second set of primers;
g) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;
h) hybridizing said nucleic acid copies formed in step g) to said array of nucleic acids provided in step a) (i); and
i) detecting or quantifying any of said hybridized copies obtained in step h). - View Dependent Claims (498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526)
-
-
527. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:
-
a) providing;
(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;
(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;
(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said second set comprises at least one production center;
(iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of said second set of primers; and
(v) means for ligating said set of oligonucleotides or polynucleotides (iv);
b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;
c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;
d) ligating said set of oligonucleotides or polynucleotides a) (iv) to the 3′
end of said first copies formed in step c) to form more than one ligated product;
e) contacting said ligated product with said second set of primers to form more than one second bound entity;
f) extending said bound second set of primers by means of template sequences provided by said ligated products formed in step d) to form more than one complex comprising said ligated products and said extended second set of primers;
g) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;
h) hybridizing said nucleic acid copies formed in step g) to said array of nucleic acids provided in step a) (i); and
i) detecting or quantifying any of said hybridized copies obtained in step h). - View Dependent Claims (528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557)
-
-
558-952. -952. (canceled)
Specification