Devices and methods for biochip multiplexing

Abstract

The invention is directed to devices that allow for simultaneous multiple biochip analysis. In particular, the devices are configured to hold multiple cartridges comprising biochips comprising arrays such as nucleic acid arrays, and allow for high throughput analysis of samples.

1 - 14 . (canceled) 
     
     
         15 : A method of analyzing a plurality of biochips comprising:
 a) inserting a first biochip into a first station of an analysis device;   b) inserting a second biochip into a second station of the analysis device;   
       wherein each of said biochips comprises one or more hybridization complexes bearing a detectable label; and
 c) detecting said label as a measure of formation of said one or more hybridization complexes. 
 
     
     
         16 : The method of  claim 15  wherein each of said first and second biochips comprise a substrate comprising: an array of detection electrodes each comprising:
 i) one or more capture binding ligands;   ii) one or more target analytes;   iii) one or more labels that signal binding of said one or more capture binding ligands with said one or more target analytes; and   (iv) a plurality of electrical contacts.   
     
     
         17 : The method of  claim 16 , wherein at least one of said one or more capture binding ligands comprises a nucleic acid capture probe. 
     
     
         18 : A method according to  claim 16  wherein said one or more capture binding ligands comprises a peptide or protein. 
     
     
         19 : The method of  claim 18  wherein said one or more capture binding ligands comprises an antibody or portion thereof. 
     
     
         20 : The method of  claim 15  wherein said detecting step comprises detecting a plurality of different target analytes simultaneously using labels of different electrochemical potential. 
     
     
         21 : The method of  claim 15  wherein said detecting step comprises detecting a plurality of target analytes sequentially. 
     
     
         22 : The method of  claim 19  wherein said one or more capture binding ligands comprises only nucleic acids. 
     
     
         23 : The method of  claim 19  wherein different nucleic acid capture binding ligands are present on different electrodes. 
     
     
         24 : The method of  claim 19  wherein said plurality of target analytes comprises both nucleic acids and non nucleic acids. 
     
     
         25 : The method of  claim 23  wherein said non-nucleic acids comprise a member selected from the group consisting of peptides, proteins, antibodies and portions of antibodies. 
     
     
         26 : The method of  claim 23  wherein said nucleic acid analytes comprise amplified nucleic acids. 
     
     
         27 : The method of  claim 16  wherein said target analytes are nucleic acids. 
     
     
         28 : The method  claim 27  wherein said target analyte is associated with a genetic disease. 
     
     
         29 : The method of  claim 28  wherein genetic disease is selected from the group consisting of cancer, cystic fibrosis, and Alzheimer's disease. 
     
     
         30 : The method of  claim 26  wherein said target analytes are amplified using PCR. 
     
     
         31 : The method of  claim 27  wherein said PCR is reverse transcriptase mediated PCR. 
     
     
         32 : The method of  claim 26  wherein said nucleic acids are bacterial in origin. 
     
     
         33 : The method of  claim 26  wherein said bacteria is  staphylococcus.    
     
     
         34 : The method of  claim 26  wherein said bacteria is associated with a sexually transmittable disease. 
     
     
         35 : The method of  claim 26  wherein said nucleic acids are viral in origin. 
     
     
         36 : The method of  claim 32  wherein said virus is associated with a sexually transmittable disease. 
     
     
         37 : The method of  claim 33  wherein said virus is a retrovirus. 
     
     
         38 : The method of  claim 15  wherein at least one of said one or more labels is covalently attached to a member of a hybridization complex comprising a target analyte and a capture binding ligand. 
     
     
         39 : The method of  claim 35  wherein said capture binding ligand is a nucleic acid or nucleic acid analog. 
     
     
         40 : The method of  claim 35  wherein said nucleic acid analog is a peptide nucleic acid. 
     
     
         41 : The method of  claim 35  wherein said nucleic acid analog has a positively charged backbone. 
     
     
         42 : The method of  claim 35  wherein said hybridization complex further comprises a signal probe and wherein each of said target analyte, ligand and signal probe are independently selected from the group consisting of nucleic acids, amplified nucleic acids, and nucleic acid analogs. 
     
     
         43 : The method of  claim 35  wherein said label is covalently attached to said capture binding ligand. 
     
     
         44 : The method of  claim 38  wherein said label is covalently attached to said signal probe. 
     
     
         45 . The method of  claim 15  wherein said one or more labels are electron transfer moieties (ETMs). 
     
     
         46 : The method of  claim 41  wherein at least one of said one or more ETMs comprises a transition metal complex. 
     
     
         47 : The method of  claim 41  wherein said at least one of said one or more ETMs comprises a ferrocene or a ferrocene derivative. 
     
     
         48 : The method of  claim 41  wherein at least one of said one or more ETMs comprise one or more members selected from the group consisting of redox proteins, riboflavin, xanthene dyes, azine dyes, acridine orange, N,N′-dimethyl-2,7-diazapyrenium dichloride (DAP.sup.2+), methylviologen, ethidium bromide, quinones such as N,N′-dimethylanthra(2,1,9-def 6,5,10-d′e′f′)diisoquinoline dichloride (ADIQ.sup.2+); porphyrins ([meso-tetrakis(N-methyl-x-pyridinium)porphyrin tetrachloride], varlamine blue B hydrochloride, Bindschedler's green; 2,6-dichloroindophenol, 2,6-dibromophenolindophenol; Brilliant crest blue (3-amino-9-dimethyl-amino-10-methylphenoxyazine chloride), methylene blue; Nile blue A (aminoaphthodiethylaminophenoxazine sulfate), indigo-5,5′,7,7′-tetrasulfonic acid, indigo-5,5′,7-trisulfonic acid; phenosafranine, indigo-5-monosulfonic acid; safranine T; bis(dimethylglyoximato)-iron(II) chloride; induline scarlet, neutral red, anthracene, coronene, pyrene, 9-phenylanthracene, rubrene, binaphthyl, DPA, phenothiazene, fluoranthene, phenanthrene, chrysene, 1,8-diphenyl-1,3,5,7-octatetracene, naphthalene, acenaphthalene, peryiene, TMPD and analogs and substituted derivatives thereof. 
     
     
         49 : The method of  claim 41  wherein said one or more ETMs comprise one or more members selected from the group consisting of cobalt, ruthenium and osmium. 
     
     
         50 : The method of  claim 15  wherein at least some of said detection electrodes in said arrays are independently addressable. 
     
     
         51 : The method of  claim 15  wherein said detecting comprises transmission of a signal to a processor and processing of that signal using one or more of a filtering or signal amplification process. 
     
     
         52 : The method of  claim 15  wherein said one or more target analytes comprise one or more members selected from the group consisting of metal ions, heavy metals, and toxic metals. 
     
     
         53 : The method of  claim 15  further comprising adding said one or more target analytes to said biochips in the form of blood, tissue, sputum or saliva samples, and then processing said samples. 
     
     
         54 : The method of  claim 15  wherein said one or more target analytes are present in the form of aqueous samples and wherein said method further comprises mixing said aqueous samples using one or more mixing means selected from the group consisting of piezoelectric mixing, thermal gradients, bubble pump mixers, acoustic streaming, and recirculation of sample. 
     
     
         55 : The method of  claim 15  wherein said one or more capture binding ligands are bound to said electrodes via a self assembling monolayer. 
     
     
         56 : The method of  claim 53  wherein said self assembling monolayer is a mixed self assembling monolayer comprising insulators. 
     
     
         57 : The method of  claim 54  wherein said monolayer comprises species of different lengths. 
     
     
         58 : The method of  claim 41  wherein said ETMs are present in multimers numbering from 2-10 that are covalently attached to the same member of a hybridization complex. 
     
     
         59 : The method of  claim 15  further comprising displaying results of said detection in alphanumeric fashion on a computer screen. 
     
     
         60 : The method of  claim 46  further comprising using digital lock-in to analyze results. 
     
     
         61 : The method of  claim 15  further comprising using one or more of a Fourier transform or joint time-frequency transformation to analyze detection results. 
     
     
         62 : The method of  claim 15  wherein said detecting comprises measuring one or more of a frequency, amplitude, phase shift, DC offset voltage, or faradic impedance response. 
     
     
         63 : The method of  claim 15  wherein said detecting comprises using a combination of AC and DC signals. 
     
     
         64 . The method of  claim 15  wherein said detecting uses a harmonic square wave AC voltammetry or sinusoidal harmonic AC voltammetry. 
     
     
         65 : The method of  claim 46  wherein said filtering is a digital filtering technique selected from the group consisting of match filter, Weiner filtering, Kalman filtering, Finite Impulse Response, infinite impulse response and narrow band filtering. 
     
     
         66 : The method of  claim 15  wherein each detection electrode in said array that contains binding ligand or ligands thereon has at least one duplicate electrode in said array that contains the same binding ligand or combination of binding ligands. 
     
     
         67 : The method of  claim 15  further comprising using multiple ferrocene labels of differing redox potentials and detecting said labels as an indication of the presence or absence of a target analyte of interest.