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, 100 (7), 3960-4

Sequence Information Can Be Obtained From Single DNA Molecules

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Sequence Information Can Be Obtained From Single DNA Molecules

Ido Braslavsky et al. Proc Natl Acad Sci U S A.

Abstract

The completion of the human genome draft has taken several years and is only the beginning of a period in which large amounts of DNA and RNA sequence information will be required from many individuals and species. Conventional sequencing technology has limitations in cost, speed, and sensitivity, with the result that the demand for sequence information far outstrips current capacity. There have been several proposals to address these issues by developing the ability to sequence single DNA molecules, but none have been experimentally demonstrated. Here we report the use of DNA polymerase to obtain sequence information from single DNA molecules by using fluorescence microscopy. We monitored repeated incorporation of fluorescently labeled nucleotides into individual DNA strands with single base resolution, allowing the determination of sequence fingerprints up to 5 bp in length. These experiments show that one can study the activity of DNA polymerase at the single molecule level with single base resolution and a high degree of parallelization, thus providing the foundation for a practical single molecule sequencing technology.

Figures

Figure 1
Figure 1
The experimental system. (a) Schematic drawing of the optical setup. The green laser illuminates the surface in total internal reflection mode while the red laser is blocked. Both Cy3 and Cy5 fluorescence spectra are recorded independently by the intensified charge-coupled device. (b) Single-molecule images obtained by the system. The two images show colocation of Cy3- and Cy5-labeled nucleotides in the same template. (Scale bar = 10 μm.) (c) Schematic of primed DNA template attached to the surface of a microscope slide via streptavidin-biotin.
Figure 2
Figure 2
The polymerase is active on anchored single DNA templates. (a) Correlation between the locations of the DNA templates and the labeled nucleotides. (a1) Image of the Cy3-labeled template locations. (Scale bar = 10 μm.) (a2) Positions of each molecule in a1, found by software. (a3) Image of the surface after the template fluorophores are photobleached and an incorporation reaction is performed. (a4) Positions of the molecules in a3, found by software. (a5) Overlay of the template positions with the labeled nucleotide positions. (a6) There is a high degree of correlation between template and nucleotide positions. (b) The polymerase maintains selectivity and fidelity in these experiments. In consecutive incorporations (b1), the polymerase correctly refused to incorporate C-Cy3. (b2) The next reaction correctly incorporated U-Cy3. (b3) After filling the gap with unlabeled A and G and by using FRET from the first incorporation, the polymerase correctly refused to incorporate U-Cy5. (b4) The next reaction correctly incorporated C-Cy5.
Figure 3
Figure 3
Sequencing single molecules with FRET. (a) Schematic illustrating extension of the template through the first few steps of sequencing. (b) Intensity trace from a single template molecule through the entire session. The green and red lines represent the intensity of the Cy3 and Cy5 channels, respectively. The label at each column indicates the last nucleotide to be incubated, and successful incorporation events are marked with an arrow. (c) FRET efficiency as a function of the experimental epoch.
Figure 4
Figure 4
Histogram of sequence space for 4-mers composed of A and G. All traces that reached at least four incorporations are included. (a) Results for template 1 (actual sequence fingerprint: AAGA). (b) Results for template 2 (actual sequence fingerprint: AGAA).
Figure 5
Figure 5
Consecutively labeled bases. (a) Schematic illustrating extension of template 3, which includes adjacent incorporations of labeled dCTP and dUTP. (b) Sequence trace from an experiment with template 3 (see Fig. 3b for graph details). (c) FRET efficiency as a function of the experimental epoch.

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