Data stream determination

Abstract

A sequencing methodology is disclosed that allows a single DNA or RNA molecule or portion thereof to be sequenced directly and in substantially real time. The methodology involves engineering a polymerase and/or dNTPs with atomic and/or molecular tags that have a detectable property that is monitored by a detection system.

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         29 . A system for retrieving stored information comprising: 
 a nucleotide sequence comprising a data stream;    a single-molecule sequencer including a polymerase having a tag associated therewith a primer adapted to form a duplex with a portion of the nucleotide sequence and monomers for the polymerase, each monomer type including at least one monomer tag;    an excitation source adapted to excite the at least one of the tags; and    a detector adapted to detect a response from at least one of the tags,    where the response changes during polymerization of a complementary sequence and the changes in response represent a content of the data stream.    
     
     
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         35 . The system of  claim 29 , wherein the monomer tags are the same or different.  
     
     
         36 . The system of  claim 29 , wherein the monomer tags are different.  
     
     
         37 . The system of  claim 29 , wherein the monomers are deoxynucleotide triphosphates (dNTPs) and the monomer tags are the same or different.  
     
     
         38 . The system of  claim 37 , wherein the monomer tags are covalently bonded to an α-phosphate, a β-phosphate, a γ-phosphate, a sugar or a base of each dNTP type.  
     
     
         39 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent donor and one of the monomer tags is an fluorescent acceptor tag and the response is a fluorescent property of the donor and/or acceptor tag.  
     
     
         40 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent tag and one of the monomer tags is a quencher and the response is a fluorescent property of the fluorescent tag.  
     
     
         41 . The system of  claim 37 , wherein a first monomer tag is covalently bonded to an α-phosphate, a sugar and/or a base of each dNTP type, and a second monomer tag is covalently bonded to a β-phosphate and/or a γ-phosphate of each dNTP type.  
     
     
         42 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent donor and the second monomer tags is an fluorescent acceptor tag and the response is a fluorescent property of the donor and/or acceptor tag.  
     
     
         43 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent tag and the second monomer tags is a quencher and the response is a fluorescent property of the fluorescent tag.  
     
     
         44 . The system of  claim 29 , wherein the monomers are deoxynucleotide triphosphates and the monomer tags are different.  
     
     
         45 . The system of  claim 37 , wherein the monomer tags are covalently bonded to an α-phosphate, a β-phosphate, a γ-phosphate, a sugar or a base of each dNTP type.  
     
     
         46 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent donor and one of the monomer tags is an fluorescent acceptor tag and the response is a fluorescent property of the donor and/or acceptor tag.  
     
     
         47 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent tag and one of the monomer tags is a quencher and the response is a fluorescent property of the fluorescent tag.  
     
     
         48 . The system of  claim 37 , wherein a first monomer tag is covalently bonded to an α-phosphate, a sugar and/or a base of each dNTP type, and a second monomer tag is covalently bonded to a β-phosphate and/or a γ-phosphate of each dNTP type.  
     
     
         49 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent donor and the second monomer tags is an fluorescent acceptor tag and the response is a fluorescent property of the donor and/or acceptor tag.  
     
     
         50 . The system of  claim 37 , wherein one of the polymerase tags is a fluorescent tag and the second monomer tags is a quencher and the response is a fluorescent property of the fluorescent tag.  
     
     
         51 . A system for retrieving stored information comprising: 
 a molecule having a sequence of known elements comprising a data stream,    a single-molecule sequencer comprising a polymerase having at least one tag associated therewith,    an excitation source adapted to excite at least one tag on the polymerase, and    a detector adapted to detect a response from the excited tag on the polymerase,    where the response from the at least one tag changes during polymerization of a complementary sequence of elements and the change in response represents a content of the data stream.    
     
     
         52 . A system for determining sequence information from a single-molecule comprising: 
 a molecule comprising a sequence of nucleotides or nucleotide analogs,    a single-molecule sequencer comprising a polymerase including at least one polymerase fluorescent tag, a primer adapted to form a duplex with a portion of the molecule and monomers for the polymerase, each monomer type having a fluorescent tag associated therewith,    an excitation light source adapted to excite at least one fluorescent tag on the polymerase and/or monomer and    a fluorescent light detector adapted to detect at least an intensity of emitted fluorescent light from at least one fluorescent tag on the polymerase and/or monomer, where the signal intensity changes each time a new nucleotide or nucleotide analog is polymerized into a complementary sequence and either the duration of the emission or lack of emission or the wavelength range of the emitted light evidences the particular nucleotide or nucleotide analog polymerized into the sequence so that at the completion of the sequencing the data stream is retrieved.    
     
     
         53 . A system for storing and retrieving data comprising a sequence of nucleotides or nucleotide analogs representing a given data stream; a single-molecule sequencer comprising a polymerase having at least one fluorescent tag covalently attached thereto; an excitation light source adapted to excite the at least one fluorescent tag on the polymerase and/or monomer; and a fluorescent light detector adapted to detect emitted fluorescent light from at least one fluorescent tag on the polymerase and/or monomer, where at least one fluorescent tag emits or fails to emit fluorescent light each time a new nucleotide or nucleotide analog is polymerized into a complementary sequence and either the duration of the emission or lack of emission or the wavelength range of the emitted light evidences the particular nucleotide or nucleotide analog polymerized into the sequence so that at the completion of the sequencing the data stream is retrieved.