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Computational selection of RNA aptamer against angiopoietin-2 and experimental evaluation.

Hu WP, Kumar JV, Huang CJ, Chen WY - Biomed Res Int (2015)

Bottom Line: From the best of three aptamers on the basis of ZRANK scores, 189 sequences with two-point mutations were created and simulated with Ang2.We found a selected RNA aptamer has a higher binding affinity and SPR response than a reported sequence with the highest affinity.This is the first study of in silico selection of aptamers against Ang2 by using the ZRANK scoring function, which should help to increase the efficiency of selecting aptamers with high target-binding ability.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Asia University, Taichung City 41354, Taiwan ; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung City 40402, Taiwan.

ABSTRACT
Angiogenesis plays a decisive role in the growth and spread of cancer and angiopoietin-2 (Ang2) is in the spotlight of studies for its unique role in modulating angiogenesis. The aim of this study was to introduce a computational simulation approach to screen aptamers with high binding ability for Ang2. We carried out computational simulations of aptamer-protein interactions by using ZDOCK and ZRANK functions in Discovery Studio 3.5 starting from the available information of aptamers generated through the systematic evolution of ligands by exponential enrichment (SELEX) in the literature. From the best of three aptamers on the basis of ZRANK scores, 189 sequences with two-point mutations were created and simulated with Ang2. Then, we used a surface plasmon resonance (SPR) biosensor to test 3 mutant sequences of high ZRANK scores along with a high and a low affinity binding sequence as reported in the literature. We found a selected RNA aptamer has a higher binding affinity and SPR response than a reported sequence with the highest affinity. This is the first study of in silico selection of aptamers against Ang2 by using the ZRANK scoring function, which should help to increase the efficiency of selecting aptamers with high target-binding ability.

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SPR sensorgrams. Representative SPR sensorgrams for interactions between immobilized Ang2 and different aptamers.
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fig4: SPR sensorgrams. Representative SPR sensorgrams for interactions between immobilized Ang2 and different aptamers.

Mentions: Figure 4 shows the representative SPR sensorgrams of different aptamers. The average and standard deviation values of sensor responses for different aptamers expressed by the surface coverage of biomolecules are listed in Table 3. For Seq1 and Seq16, the final experimental results were consistent with the simulation scores and well-known characteristics. The experimental results indicated that the Seq15_15_38 could generate an SPR signal that was approximate to the SPR response of Seq1 in the end of the experiment. The Seq15_15_38 had a slightly larger average experimental value compared with Seq1. Nevertheless, the ZRANK score of Seq15_15_38 was a little lower than that of Seq1. For other two mutant sequences, Seq15_12_35 and Seq2_12_35, they exhibited a slightly worse performance than Seq1, which were not in agreement with the simulation findings. Actually, a number of factors can influence the kinetics of protein-protein interactions, like viscosity, pH, and ionic strength of a solution [29]. We suggest that the ZRANK scoring function does not take the buffer conditions into the calculation, which is the major reason for the differences in the experimental and computational results.


Computational selection of RNA aptamer against angiopoietin-2 and experimental evaluation.

Hu WP, Kumar JV, Huang CJ, Chen WY - Biomed Res Int (2015)

SPR sensorgrams. Representative SPR sensorgrams for interactions between immobilized Ang2 and different aptamers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383501&req=5

fig4: SPR sensorgrams. Representative SPR sensorgrams for interactions between immobilized Ang2 and different aptamers.
Mentions: Figure 4 shows the representative SPR sensorgrams of different aptamers. The average and standard deviation values of sensor responses for different aptamers expressed by the surface coverage of biomolecules are listed in Table 3. For Seq1 and Seq16, the final experimental results were consistent with the simulation scores and well-known characteristics. The experimental results indicated that the Seq15_15_38 could generate an SPR signal that was approximate to the SPR response of Seq1 in the end of the experiment. The Seq15_15_38 had a slightly larger average experimental value compared with Seq1. Nevertheless, the ZRANK score of Seq15_15_38 was a little lower than that of Seq1. For other two mutant sequences, Seq15_12_35 and Seq2_12_35, they exhibited a slightly worse performance than Seq1, which were not in agreement with the simulation findings. Actually, a number of factors can influence the kinetics of protein-protein interactions, like viscosity, pH, and ionic strength of a solution [29]. We suggest that the ZRANK scoring function does not take the buffer conditions into the calculation, which is the major reason for the differences in the experimental and computational results.

Bottom Line: From the best of three aptamers on the basis of ZRANK scores, 189 sequences with two-point mutations were created and simulated with Ang2.We found a selected RNA aptamer has a higher binding affinity and SPR response than a reported sequence with the highest affinity.This is the first study of in silico selection of aptamers against Ang2 by using the ZRANK scoring function, which should help to increase the efficiency of selecting aptamers with high target-binding ability.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Asia University, Taichung City 41354, Taiwan ; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung City 40402, Taiwan.

ABSTRACT
Angiogenesis plays a decisive role in the growth and spread of cancer and angiopoietin-2 (Ang2) is in the spotlight of studies for its unique role in modulating angiogenesis. The aim of this study was to introduce a computational simulation approach to screen aptamers with high binding ability for Ang2. We carried out computational simulations of aptamer-protein interactions by using ZDOCK and ZRANK functions in Discovery Studio 3.5 starting from the available information of aptamers generated through the systematic evolution of ligands by exponential enrichment (SELEX) in the literature. From the best of three aptamers on the basis of ZRANK scores, 189 sequences with two-point mutations were created and simulated with Ang2. Then, we used a surface plasmon resonance (SPR) biosensor to test 3 mutant sequences of high ZRANK scores along with a high and a low affinity binding sequence as reported in the literature. We found a selected RNA aptamer has a higher binding affinity and SPR response than a reported sequence with the highest affinity. This is the first study of in silico selection of aptamers against Ang2 by using the ZRANK scoring function, which should help to increase the efficiency of selecting aptamers with high target-binding ability.

Show MeSH
Related in: MedlinePlus