Solid phase detection of nucleic acid molecules

A method for detecting a target nucleic acid molecule in a sample, said method comprising:

• providing a first oligonucleotide primer coupled by a linking agent to a solid substrate, wherein said first oligonucleotide primer is complementary to at least 18 contiguous nucleic acid residues of a first strand of a target nucleic acid molecule;
• contacting the first oligonucleotide primer with the sample under conditions effective to permit any of the first strand of the target nucleic acid molecule present in the sample to hybridize to the first oligonucleotide primer;
• extending the first oligonucleotide primer hybridized to the first strand of the target nucleic acid molecule under conditions effective to yield a double stranded extension product coupled by the linking agent to the solid substrate, wherein the linking agent is configured to position the first oligonucleotide primer sufficiently apart from the solid substrate to permit said extending;
• denaturing the extension product under conditions effective to yield an immobilized extension portion complementary to the target nucleic acid molecule;
• contacting the immobilized extension portion with a detection probe, having a nucleotide sequence like that of the target nucleic acid molecule and a label, under conditions effective to permit the detection probe to hybridize specifically to the immobilized extension portion;
• and
• detecting the label immobilized on the solid substrate, thereby indicating a presence or absence of the target nucleic acid molecule in the sample.