Methods and apparatuses for analyzing polynucleotide sequences

1. A method of deriving nucleotide sequence information from polynucleotide molecules, the method comprising the steps of:

immobilizing a plurality of target nucleic acid template molecules on a 2-dimensional substrate, said molecules tagged with a first optically-detectable label attached to each of said molecules;

exposing said molecules to a polymerase and at least one nucleotide comprising a second optically-detectable label under conditions that allow said nucleotide to be incorporated in a primer hybridized to said template molecule if said nucleotide is complementary to a nucleotide in said template immediately 3′ of said primer;

rinsing said substrate to remove unincorporated nucleotides;

positionally locating said second optically-detectable labels appearing in said substrate;

associating each of said positions with a specific polynucleotide in said substrate;

inactivating said second optically-detectable label;

repeating said exposing, rinsing, and locating steps at least once; and

recording a sequence of nucleotides incorporated in said primer at each of said positions in order to determine a sequence of nucleotides in said template,

wherein said substrate is coated with a polyelectrolyte multilayer.

2. The method of claim 1 , wherein said exposing step comprises inhibiting incorporation of more than one nucleotide per primer prior to said determining step.

3. The method of claim 1 , wherein said immobilizing step comprises depositing said target nucleic acid template molecules onto said substrate.

4. The method of claim 1 , wherein said target nucleic acid template molecules are fixed on said substrate by a chemical linkage.

5. The method of claim 1 , wherein said substrate comprises glass.