SEQUENCE DETERMINATION IN CONFINED REGIONS

1 . A method of sequencing nucleic acid molecules at the single molecule level, comprising:

immobilizing a member of a replication complex comprising a polymerizing agent, an oligonucleotide primer and a nucleic acid template on or in a substrate;

contacting the immobilized member with the non-immobilized members of the replication complex to form an immobilized replication complex;

incubating the immobilized replication complex with monomers for the polymerizing agent, where at least one of the monomer types includes a monomer tag covalently bonded to a site on the monomer that is not incorporated into a growing complementary nucleic acid sequence, where the monomer tag has a detectable property capable of being detected by a detector;

detecting a change in the detectable property of each monomer tag as a tagged monomer is incorporated by the polymerizing agent into the growing complementary nucleic acid sequence; and

converting the detected changes in the detectable property of the monomer tags to an identity of one monomer or a plurality of monomers corresponding to one nucleotide or a plurality of nucleotides of the template.

2 . A method of sequencing nucleic acid molecules comprising the steps of:

confining a plurality of polymerizing agents on or in a substrate to form a plurality of confined polymerizing agents;

contacting the confined polymerizing agents with a solution including a nucleic acid template and oligonucleotide primers, where the primers are adapted to duplex with a portion of the templates to form extendable nucleic acid duplexes and the duplexes are adapted to complex with some or all of the confined polymerizing agents to form confined replication complexes;

incubating the confined replication complexes with monomer types for the polymerizing agent, where at least two of the monomer types include unique monomer tags covalently bonded to monomer sites on the monomer types that are not incorporated into a growing complementary nucleic acid sequence and where the monomer tags have a detectable property capable of being detected by a detector;

detecting a change in the detectable property of each monomer tag as a tagged monomer is incorporated by the polymerizing agent into the growing complementary nucleic acid sequence; and

converting the detected changes in the detectable property of the incorporated tagged monomer to an identity of one nucleotide or a plurality of nucleotides of the template

3 . A method of sequencing nucleic acid molecules comprising the steps of:

confining a plurality of polymerizing agents on or in a substrate to form a plurality of confined polymerizing agents, where each polymerizing agent includes a polymerizing agent donor fluorescent tag covalently bonded to a site on the polymerizing agent or associated with a molecule associated with the polymerizing agent;

contacting the confined polymerizing agents with a solution including a nucleic acid template and oligonucleotide primers, where the primers are adapted to duplex with a portion of the template to form extendable nucleic acid duplexes and the duplexes are adapted to complex with some or all of the confined polymerizing agents to form confined replication complexes;

incubating the confined replication complex with four nucleotide types for the polymerizing agent, where a first nucleotide type includes a first acceptor fluorescent tag covalently bonded to a site thereof and a second nucleotide type includes a second acceptor fluorescent tag covalently bonded to a site thereof and where the nucleotide tags are not incorporated by the polymerizing agent into a growing complementary nucleic acid sequence and where the nucleotide tags are capable of undergoing fluorescence resonance energy transfer (FRET) with the donor tag and where the acceptor tags are the same or different;

detecting fluorescent light emitted by each monomer tag as a tagged nucleotide is incorporated by a polymerizing agent into a growing complementary nucleic acid sequence via an FRET interaction between the incorporating acceptor tag on the tagged nucleotide and the donor tag on the polymerizing agent incorporating the tagged monomer to produce data evidencing a sequence of tagged monomer incorporation events; and

converting the FRET data into an identity of one nucleotide or a plurality of nucleotides of the template.

4 . A method of sequencing nucleic acid molecules comprising:

confining a plurality of polymerizing agents on or in a substrate to form a plurality of confined polymerizing agents, where each polymerizing agent includes a polymerizing agent donor fluorescent tag covalently bonded to a site on the polymerizing agent or associated with a molecule associated with the polymerizing agent;

contacting the confined polymerizing agents with a solution including a nucleic acid template and oligonucleotide primers, where the primers are adapted to duplex with a portion of the template to form extendable nucleic acid duplexes and the duplexes are adapted to complex with some or all of the confined polymerizing agents to form confined replication complexes;

incubating the confined replication complex with four dNTP types for the polymerizing agent, where a first monomer type includes a first acceptor fluorescent tag covalently bonded to a site thereof, a second monomer type includes a second acceptor fluorescent tag covalently bonded to a site thereof, and a third monomer type includes a third acceptor fluorescent tag covalently bonded to a site thereof, and where the monomer tags are not incorporated by the polymerizing agent into a growing complementary nucleic acid sequence, and where the monomer tags are capable of undergoing fluorescence resonance energy transfer (FRET) with the donor tag and where the acceptor tags are the same or different;

detecting fluorescent light emitted by each monomer tag as a tagged monomer is incorporated by a polymerizing agent into a growing complementary nucleic acid sequence via an FRET interaction between the incorporating acceptor tag on the monomer and the donor tag on the polymerizing agent incorporating the tagged monomer to produce data evidencing a sequence of monomer incorporation events; and

converting the FRET data into an identity of one nucleotide or a plurality of nucleotides of the template.

5 . A method of sequencing nucleic acid molecules comprising:

confining a plurality of polymerizing agents on or in a substrate to form a plurality of immobilized polymerizing agents, where each polymerizing agent includes a polymerizing agent donor fluorescent tag covalently bonded to a site on the polymerizing agent or associated with a molecule associated with the polymerizing agent;

contacting the confined polymerizing agents with a solution including a nucleic acid template and oligonucleotide primers, where the primers are adapted to duplex with a portion of the template to form extendable nucleic acid duplexes and the duplexes are adapted to complex with some or all of the confined polymerizing agents to form confined replication complexes;

incubating the confined replication complex with four dNTP types for the polymerizing agent, where a first monomer type includes a first acceptor fluorescent tag covalently bonded to a site thereof, a second monomer type includes a second acceptor fluorescent tag covalently bonded to a site thereof, a third monomer type includes a third acceptor fluorescent tag covalently bonded to a site thereof, and a fourth monomer type includes a fourth acceptor fluorescent tag covalently bonded to a site thereof, and where the monomer tags are not incorporated by the polymerizing agent into a growing complementary nucleic acid sequence, and where the monomer tags are capable of undergoing fluorescence resonance energy transfer (FRET) with the donor tag and where the acceptor tags are the same or different;

detecting fluorescent light emitted by each monomer tag as a tagged monomer is incorporated by a polymerizing agent into a growing complementary nucleic acid sequence via an FRET interaction between the incorporating acceptor tag on the monomer and the donor tag on the polymerizing agent incorporating the tagged monomer to produce data evidencing a sequence of monomer incorporation events; and

converting the FRET data into an identity of one nucleotide or a plurality of nucleotides of the template.

6 . A method comprising the steps of:

confining a polymerizing agent on or in a substrate;

incubating the polymerizing agent in the presence of a template polymer comprising a sequence of the monomers, optionally primers adapted to duplex with a portion of the template polymer, and monomers for the polymerizing agent, where each monomer type includes an unique monomer tag covalently bonded to a site of the monomer that is not incorporated by the polymerizing agent into a growing complementary polymer comprising a sequence of the monomers complementary to the template polymer and each monomer tag has a detectably property capable of being detected by a detector;

detecting a change in the detectable property as each monomer is incorporated by the polymerizing agent into the growing complementary polymer; and

converting the detected changes in the detectable property of the monomer tag of each incorporated monomer to a sequence of monomers in the template polymer.

7 . A method of sequencing nucleic acid molecules at the single molecule level, comprising the steps of:

confining a member of a replication complex comprising a polymerizing agent, a primer and a template in a region, area, well, groove, channel or other similar structure on the substrate capable of being filled with an appropriate polymerizing medium;

contacting the confined member with the other members of the replication complex to form a confined replication complex;

incubating the confined replication complex with monomers for the polymerizing agent in the presence of the medium, where at least one of the monomer types includes monomer tag attached to a site on the monomer that is not incorporated into a growing complementary sequence of monomers, where the monomer tag has a detectably property capable of being detected by a detector;

detecting a change in the detectable property of each monomer tag as a tagged monomer is incorporated by the polymerizing agent into the growing complementary sequence; and

converting the detected changes in the detectable property to an identity of one monomer or a plurality of monomers corresponding to one nucleotide or a plurality of nucleotides of the template.