System, method, and product for generating patterned illumination

Abstract

An embodiment of a method for generating an interference pattern at a probe array is described that comprises directing light at a first waveguide and second waveguide, wherein the first and second waveguides are positioned adjacent to each other and the output from the first and second waveguides produce an interference pattern; and directing the interference pattern at the probe array.

1 . A method for generating an interference pattern at a probe array, comprising:
 directing a light at a first waveguide and second waveguide, wherein the light travels along an optical path, wherein the first and second waveguides are positioned adjacent to each other and the output from the first and second waveguides produce an orientation of an interference pattern;   rotating at least one waveguide about an axis relative to the optical path to alter the orientation of the interference pattern; and   directing the interference pattern at the probe array.   
   
   
       2 . The method according to  claim 1 , wherein the rotating step further comprises rotating the first and second waveguides about a central axis to alter the orientation. 
   
   
       3 . The method according to  claim 1 , further comprising altering a phase relationship between the light in each optical path respective to each other, wherein an optical cladding is applied to at least one of the waveguides. 
   
   
       4 . The method according to  claim 1  wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA. 
   
   
       5 . The method according to  claim 2  wherein the probe array is a nucleic acid or protein probe array. 
   
   
       6 . The method according to  claim 1  further comprising imaging the probe array using a detector. 
   
   
       7 . The method according to  claim 6 , wherein the detector comprises a CCD, EM CCD, EB CCD, CMOS, APS, or PMT. 
   
   
       8 . The method according to  claim 1  further comprising processing the detected image using a computer system. 
   
   
       9 . The method according to  claim 1  wherein the waveguides are optical fibers or rectangular waveguides. 
   
   
       10 . The method for generating an interference pattern to interrogate a surface of a support comprising:
 directing light at a first waveguide, wherein the light travels along a first optical path;   directing light at a second waveguide, wherein the light travels along a second optical path, wherein the first and second waveguides are positioned in an operative relationship so as to produce an orientation of an interference pattern;   rotating at least one waveguide about an axis relative to the optical path to alter the orientation of the interference pattern;   directing the interference pattern at a surface of a support; and   detecting signals from the surface of the support.   
   
   
       11 . The method according to  claim 10 , wherein the rotating step further comprises rotating the first and second waveguides about a central axis to alter the orientation. 
   
   
       12 . The method according to  claim 10 , further comprising altering a phase relationship between the light in each optical path respective to each other, wherein an optical cladding is applied to at least one of the waveguides. 
   
   
       13 . The method according to  claim 10  wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA. 
   
   
       14 . The method according to  claim 10  wherein the detecting step comprises using a detector comprising a CCD, EMCCD, EB CCD, CMOS, APS, or PMT. 
   
   
       15 . The method according to  claim 10 , wherein the waveguides are optical fibers or rectangular waveguides. 
   
   
       16 . The method according to  claim 10  wherein the probe array is a nucleic acid or protein probe array. 
   
   
       17 . A system to image the surface of a support comprising:
 a source of excitation light;   a first waveguide capable of receiving light from the excitation light and transmitting the light out an exit port;   a second waveguide capable of receiving light from an excitation light and producing an orientation of an interference pattern when proximately positioned near the first waveguide, the second waveguide is capable of transmitting the light out an exit port;   a rotating mechanism, wherein the rotating mechanism rotates at least one waveguide about an axis relative to the optical path to alter the orientation of the interference pattern;   a support having probes on a surface of a support facing the exit ports of the first and second waveguides;   a detector capable of receiving reflected signals from the surface of the support; and a processor for analyzing the detected signals.   
   
   
       18 . The system according to  claim 17 , wherein the rotating mechanism further comprises rotating the first and second waveguides about a central axis to alter the orientation. 
   
   
       19 . The system according to  claim 17 , further comprising altering a phase relationship between the light in each optical path respective to each other, wherein an optical cladding is applied to at least one of the waveguides. 
   
   
       20 . The system according to  claim 17  wherein the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and Meta-DNA. 
   
   
       21 . The system according to  claim 17  wherein the probe array is a nucleic acid or protein probe array. 
   
   
       22 . The system according to  claim 17 , wherein the detector images the probe array. 
   
   
       23 . The system in accordance with  claim 22 , wherein the detector comprises a CCD, EMCCD, EB CCD, CMOS, APS, or PMT. 
   
   
       24 . The system according to  claim 17  further comprising a computer system to process the detected image. 
   
   
       25 . The system according to  claim 17  wherein the waveguides are optical fibers or rectangular waveguides. 
   
   
       26 . A system according to  claim 17  further comprising:
 a dispersion cone in an operative relationship with the exit port of the first waveguide for dispersing the exit light from the first waveguide; and   a dispersion cone in an operative relationship with the exit port of the second waveguide for dispersing the exit light from the first waveguide.