System and methods for selective molecular analysis

A method for selectively amplifying a target DNA sequence in the presence of non-target DNA sequence in a sample, the method comprising:

• contacting an oligonucleotide system with the sample under hybridization conditions to form a reaction mixture, said oligonucleotide system including a forward primer and a reverse primer, wherein one of said forward or reverse primer is modified to preferentially increase hybridization between said primer and said target sequence, said modification comprising:
• (i) a modified 3′ terminal nucleotide, and (ii) one or more additional modified nucleotides;
• cycling said oligonucleotide system so that, if the target DNA sequence is present in the sample, said forward primer and said reverse primer hybridize to the target DNA sequence and the reaction mixture results in a first amplified product;
• providing a microarray comprising a set of features including at least a target DNA probe component for detecting said target DNA sequence, and further including a component intended to serve as a positive control and a component intended to serve as a negative control, wherein said target DNA probe component comprises a first modification, wherein said first modification preferentially increase hybridization between said target DNA probe component and said first amplified product;
• contacting the microarray with said cycled reaction mixture to enable the first amplified product to bind to said target DNA probe component, wherein such binding results in the feature emitting the detectable signal;
• and
• detecting said emitted detectable signal;
• wherein said target DNA probe component comprises a first modification, wherein said first modification preferentially increases hybridization between said target DNA probe component and said first amplified product.

A system for selectively amplifying a target DNA sequence, the system comprising:

• a sample comprising a non-target DNA sequence and potentially comprising said target DNA sequence;
• an oligonucleotide system comprising a forward primer and a reverse primer under hybridization conditions to form a reaction mixture, wherein one of said forward or reverse primer is modified to preferentially increase hybridization between said primer and said target sequence, said modification comprising a modified 3′ terminal nucleotide;
• a thermocycler adapted to cycle the oligonucleotide system so that, if the target DNA sequence is present in the sample, said forward primer and said reverse primer hybridize to the target DNA sequence and the reaction mixture results in a first amplified product;
• a target DNA probe component for detecting said target DNA sequence, said target DNA probe component comprising a first modification, wherein said first modification preferentially increases hybridization between said target DNA probe component and said first amplified product;
• and
• a detector adapted to detect the first amplified product.