MICHAEL ALLEN, PAC
Physician Assistant at Shadow Ln, Las Vegas, NV

6280939, Aug 28, 2001

Sep 1, 1998

9/145352

Michael J. Allen - Santa Barbara CA

Veeco Instruments, Inc. - Plainview NY

C12Q 168

435 6

DNA sequencing is performed in real time using an atomic force microscope (AFM). The AFM's probe detects motions that occur when a polymerase incorporates nucleotides into a growing polynucleotide chain and a newly formed double-stranded polynucleotide helix translocates (or "ratchets") through the polymerase's reaction site. These motions generate a mechanical force that is reflected, either directly or indirectly, by motion of the AFM cantilever. The resulting changes in cantilever motion are detected and can be recorded as an indication that a nucleotide has been incorporated into the DNA template. To determine which nucleotide type has been incorporated, a characteristic of the incorporation of at least one nucleotide type of interest is flagged so as to be distinguishable from the corresponding characteristics of the incorporation of nucleotides of other types. In a preferred embodiment, the average incorporation delay for nucleotides of the nucleotide type of interest are flagged such that the average incorporation delay for nucleotides of the nucleotide type of interest is unique when compared to the average incorporation delay of nucleotides of other nucleotide types.