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. 2011 Sep 5;12(13):2021-4.
doi: 10.1002/cbic.201100046. Epub 2011 Jul 27.

Identifying protein variants with cross-reactive aptamer arrays

Sara Stewart  1 , Angel Syrett, Arti Pothukuchy, Sancheeta Bhadra, Andrew Ellington, Eric Anslyn
Affiliations

Identifying protein variants with cross-reactive aptamer arrays

Sara Stewart et al. Chembiochem. .
No abstract available

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Figures

Figure 1
Figure 1
A biotinylated LNA anchor complementary to the 5′ end of the aptamer, securing the aptamer to the Nutravidin coated slide. A second LNA conjugated to the 3′ end of the aptamer acts as a probe for detection of bound aptamer.
Figure 2
Figure 2
Slide treatment. Each small square represents a single reaction well, 16 per slide. Each well was identical and consisted of 30 aptamers printed in replicates of 6. The aptamer’s position is a representation of where each aptamer was positioned relative to the others; each name represents a set of six replicates. Each slide was separated into three groups of wells. The top eight wells correspond to the treatment group; where one of the four HIV-RT variants were applied. The next four wells correspond to negative controls and the final four correspond to the positive controls.
Figure 3
Figure 3
GenePix scan of the 30 aptamer set. Red corresponds to the Cy5 channel and the signal intensity is proportional to the amount of aptamer bound to the slide. “Black” spots indicated locations where little or no aptamer was deposited. If the background intensity exceeded the foreground intensity in either channel the spots were excluded. Green corresponds to the Cy3 channel where the signal intensity is proportional to the amount of protein bound to the aptamer. a) Wild-type b) M3 c) M5 d) M9 e) negative control.
Figure 4
Figure 4
a)“ within-slide” normalized LDA of 30 aptamers set 91.2% explained. Ellipses represent 95% confidence intervals b) LDA of 30 aptamer set including 3 components “within slide normalized”, 98.33% captured. c) Leave-one out cross validation
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