Methods, Systems and Compositions for Nucleic Acid Analysis Using Back-Scattering Interferometry

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

• a) providing a substrate having a channel formed therein for reception of a fluid sample to be analyzed;
• b) introducing a target nucleic acid in a sample into the channel;
• c) providing at least one nucleic acid polymer probe with a known sequence;
• d) providing hybridization conditions in the channel;
• e) directing a coherent light beam onto the substrate such that the light beam is incident on the channel to generate backscattered light through reflective and refractive interaction of the light beam with a substrate/channel interface and the sample, the backscattered light comprising interference fringe patterns including a plurality of spaced light bands whose positions shift in response to changes in the refractive index of the fluid sample;
• and
• f) detecting positional shifts in the light bands.

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

• a) providing a substrate having a channel formed therein for reception of a fluid sample to be analyzed;
• b) introducing a sample comprising a target nucleic acid polymer;
• c) providing one or more oligonucleotide probes with sequences that have from 1 to ten nucleotide bases different from the target nucleic acid and that hybridize to the target nucleic acid polymer;
• d) directing a coherent light beam onto the substrate such that the light beam is incident on the channel to generate backscattered light through reflective and refractive interaction of the light beam with a substrate/channel interface and the sample, the backscattered light comprising interference fringe patterns including a plurality of spaced light bands whose positions shift in response to changes in the refractive index of the fluid sample;
• and
• e) detecting positional shifts in the light bands;
• wherein the positional shifts in the light bands detect the extent of hybridization of the one or more probes to the target nucleic acid polymer.

A method for detecting the location of a sequence mutation in a target nucleic acid sequence, comprising providing a BSI device having at least a first nucleic acid polymer probe immobilized in the channel, wherein the probe sequence is known;

• introducing a composition comprising a non-immobilized nucleic acid polymer composition comprising target sequence nucleic acid polymers into the channel, wherein the immobilized nucleic acid polymers interact under hybridization conditions with the non-immobilized nucleic acid polymers;
• directing a coherent light beam to generate backscattered light comprising interference fringe patterns including a plurality of spaced light bands which positions shift in response to changes in the refractive index of the compositions and hybridization products in the channel;
• detecting positional shifts in the light bands relative to a baseline;
• and determining the formation of one or more hybridization products of the immobilized nucleic acid polymer with the non-immobilized nucleic acid polymer from the positional shifts of the light bands in the interference patterns.