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Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus.

Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, Li J, Liu N, Cao W, Zhu Y, Shen B, Shao N - Nucleic Acids Res. (2009)

Bottom Line: Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains.In addition, the combined aptamers can probe single S. aureus in pyogenic fluids.Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

View Article: PubMed Central - PubMed

Affiliation: Beijing Institute of Basic Medical Sciences, Beijing, China.

ABSTRACT
In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

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Related in: MedlinePlus

The binding capacity of candidate aptamers to S. aureus by flow cytometry analysis. The FITC-labeled individual aptamer was incubated with 107 target bacteria (S. aureus 8325-4) or non-target bacteria (Streptococcus A5005) at 37°C for 45 min. The selected aptamers with higher ranked specificity and sensitivity were depicted with solid lines, and the GP45 naive library control and candidates with lower ranked specificity and sensitivity were depicted with dot lines. Representative results of three separate experiments.
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Figure 3: The binding capacity of candidate aptamers to S. aureus by flow cytometry analysis. The FITC-labeled individual aptamer was incubated with 107 target bacteria (S. aureus 8325-4) or non-target bacteria (Streptococcus A5005) at 37°C for 45 min. The selected aptamers with higher ranked specificity and sensitivity were depicted with solid lines, and the GP45 naive library control and candidates with lower ranked specificity and sensitivity were depicted with dot lines. Representative results of three separate experiments.

Mentions: Eleven candidate sequences with stable structures and representative motifs out of eight families were chosen for further characterization, with one to two sequences from each family. One family was excluded from characterization because of the least numbers and unstable structure of the members. The binding assays were performed with flow cytometry to screen the specific aptamers for S. aureus 8325-4. Results showed that most of the aptamers could discriminate S. aureus from streptococcus. Five aptamers (SA20, SA23, SA31, SA34 and SA43) with high ranked specificity and sensitivity were selected for further investigation (Figure 3). The five aptamers were determined to be specific to S. aureus with a similar calculated median effective concentration of 8325-4 binding in the nanomolar (nM) range (Table 1) and were not cross-reactive to Streptococcus A5005, S. epidermidis 26069 and E. coli DH5α (Figure 4A and B). The sequences and the representative structures of the strong binders were shown as Supplementary Data (Supplementary Figure 1).Table 1.


Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus.

Cao X, Li S, Chen L, Ding H, Xu H, Huang Y, Li J, Liu N, Cao W, Zhu Y, Shen B, Shao N - Nucleic Acids Res. (2009)

The binding capacity of candidate aptamers to S. aureus by flow cytometry analysis. The FITC-labeled individual aptamer was incubated with 107 target bacteria (S. aureus 8325-4) or non-target bacteria (Streptococcus A5005) at 37°C for 45 min. The selected aptamers with higher ranked specificity and sensitivity were depicted with solid lines, and the GP45 naive library control and candidates with lower ranked specificity and sensitivity were depicted with dot lines. Representative results of three separate experiments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724295&req=5

Figure 3: The binding capacity of candidate aptamers to S. aureus by flow cytometry analysis. The FITC-labeled individual aptamer was incubated with 107 target bacteria (S. aureus 8325-4) or non-target bacteria (Streptococcus A5005) at 37°C for 45 min. The selected aptamers with higher ranked specificity and sensitivity were depicted with solid lines, and the GP45 naive library control and candidates with lower ranked specificity and sensitivity were depicted with dot lines. Representative results of three separate experiments.
Mentions: Eleven candidate sequences with stable structures and representative motifs out of eight families were chosen for further characterization, with one to two sequences from each family. One family was excluded from characterization because of the least numbers and unstable structure of the members. The binding assays were performed with flow cytometry to screen the specific aptamers for S. aureus 8325-4. Results showed that most of the aptamers could discriminate S. aureus from streptococcus. Five aptamers (SA20, SA23, SA31, SA34 and SA43) with high ranked specificity and sensitivity were selected for further investigation (Figure 3). The five aptamers were determined to be specific to S. aureus with a similar calculated median effective concentration of 8325-4 binding in the nanomolar (nM) range (Table 1) and were not cross-reactive to Streptococcus A5005, S. epidermidis 26069 and E. coli DH5α (Figure 4A and B). The sequences and the representative structures of the strong binders were shown as Supplementary Data (Supplementary Figure 1).Table 1.

Bottom Line: Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains.In addition, the combined aptamers can probe single S. aureus in pyogenic fluids.Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

View Article: PubMed Central - PubMed

Affiliation: Beijing Institute of Basic Medical Sciences, Beijing, China.

ABSTRACT
In this article, a panel of ssDNA aptamers specific to Staphylococcus aureus was obtained by a whole bacterium-based SELEX procedure and applied to probing S. aureus. After several rounds of selection with S. aureus as the target and Streptococcus and S. epidermidis as counter targets, the highly enriched oligonucleic acid pool was sequenced and then grouped under different families on the basis of the homology of the primary sequence and the similarity of the secondary structure. Eleven sequences from different families were selected for further characterization by confocal imaging and flow cytometry analysis. Results showed that five aptamers demonstrated high specificity and affinity to S. aureus individually. The five aptamers recognize different molecular targets by competitive experiment. Combining these five aptamers had a much better effect than the individual aptamer in the recognition of different S. aureus strains. In addition, the combined aptamers can probe single S. aureus in pyogenic fluids. Our work demonstrates that a set of aptamers specific to one bacterium can be used in combination for the identification of the bacterium instead of a single aptamer.

Show MeSH
Related in: MedlinePlus