Method of performing PCR amplification on a microarray

1. A method of amplifying a target DNA sequence on a microarray, the method comprising:

(a) synthesizing first and second 5′ end immobilized array probes in a common area on the microarray using a maskless array synthesizer, the first array probe having a first universal primer linked to a first sequence-specific probe complementary to a region flanking the target DNA sequence, the second array probe having a second universal primer linked to a second sequence-specific probe identical to a region flanking the opposite end of the target DNA sequence;

(b) adding to the common area a sample non-array target DNA sequence and a sufficient amount of amplification reagents comprising a non-array first universal primer and a non-array second universal primer;

(c) annealing the complementary region of the non-array target DNA sequence to the first sequence-specific probe;

(d) extending the first sequence-specific probe to form a first array strand of a first intermediate, whereby the first array strand comprises a region complementary to the second sequence-specific probe;

(e) denaturing the first intermediate to release the sample non-array target DNA sequence into the common area;

(f) annealing the complementary region of the first array strand to the second sequence-specific probe such that the first array strand immobilized to the microarray is annealed to the second sequence-specific robe;

(g) extending the second sequence-specific probe to form a second array strand of a second intermediate, whereby the second array strand comprises a region complementary to the entire first array probe, including the first universal primer;

(h) denaturing the second intermediate to form two single-stranded array-immobilized strands such that one of the two single-stranded array-immobilized strands is the first array strand and the other is the second array strand;

(i) annealing the non-array first universal primer to the region of the second array strand complementary to the first universal primer;

(j) extending the non-array first universal primer annealed to the second array strand to form a third intermediate that comprises the second array strand and a complementary non-array strand that comprises the first and second array probes on opposite ends of the target DNA sequence;

(k) denaturing the third intermediate to yield the non-array strand;

(l) subjecting the non-array strand to multiple rounds of thermal cycling under suitable PCR reaction conditions to amplify the target DNA sequence; and

(m) optionally, detecting the amplified target DNA sequence.

2. The method of claim 1 wherein a calibration probe sequence is optionally synthesized between the first universal primer and the first sequence-specific probe or between the second universal primer and the second sequence-specific probe.