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Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration
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10.1063/1.2787618
/content/aip/journal/jcp/127/14/10.1063/1.2787618
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/14/10.1063/1.2787618

Figures

Image of FIG. 1.
FIG. 1.

A schematic of a target molecule binding to an -segment long “end-type” probe molecule tethered to the surface.

Image of FIG. 2.
FIG. 2.

vs probe length for 0.000 278 (square), 0.000 625 (diamond), 0.00 111 (upward triangle), 0.0025 (downward triangle), and 0.0044 (rightsided triangle) probe on the surface for spacer length four segments and .

Image of FIG. 3.
FIG. 3.

vs probe length for 0.000 278 (square), 0.000 625 (diamond), 0.00 111 (upward triangle), 0.0025 (downward triangle), and 0.0044 (rightsided triangle) probe on the surface for spacer length 4 segments and .

Image of FIG. 4.
FIG. 4.

Probability of a contiguous stretch of segments along target binding to segments along end-type probes of length 12 segments with spacer at for 0.000 017 4 (cross), 0.000 069 4 (triangle), 0.000 278 (square), 0.000 625 (circle), 0.001 11 (inverted triangle), 0.0025 (diamond), and 0.0044 (right triangle) probe surface area.

Image of FIG. 5.
FIG. 5.

Probability (contours) of a contiguous stretch of segments along target (-axis) simultaneously binding to probe 1 , probe 2 , probe 3 , and so on, at surface , probe , spacer , and .

Image of FIG. 6.
FIG. 6.

Probability of a contiguous stretch of segments along target binding to segments along end-type probes of length 8, 12, 16, 20, and 24 and spacer at at (a) low surface density (1 probe), (b) intermediate surface density (16 probes), and (c) high surface density (144 probes).

Image of FIG. 7.
FIG. 7.

(a) Fraction of targets in the system that are bound to probes by at least one segment vs probe length, and (b) fraction of targets in the system that are bound to the probes completely at varying target concentrations of (circle), (square), (upward triangle), and (downward triangle) at intermediate surface density of and .

Tables

Generic image for table
Table I.

Surface density for varying number of probes on the surface.

Generic image for table
Table II.

Target concentration for varying number of target molecules in the system.

Generic image for table
Table III.

Overlap surface density for varying probe lengths.

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/content/aip/journal/jcp/127/14/10.1063/1.2787618
2007-10-12
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Computer simulation study of probe-target hybridization in model DNA microarrays: Effect of probe surface density and target concentration
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/14/10.1063/1.2787618
10.1063/1.2787618
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