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Related Experiment Video

Updated: Nov 20, 2025

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol.

Xu Shang1, Zhen Guan, Shuai Zhang

  • 1State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China. youhaihang@ict.ac.cn.

Physical Chemistry Chemical Physics : PCCP
|January 26, 2021
PubMed
Summary
This summary is machine-generated.

Researchers developed a new computational method to predict the 3D structures of aptamers and their protein complexes. This advancement overcomes limitations in current methods, paving the way for enhanced diagnostic and therapeutic applications of aptamers in cancer research.

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Related Experiment Videos

Last Updated: Nov 20, 2025

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08:09

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Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Aptamers, like SYL3C, are promising alternatives to antibodies in cancer research due to their specificity and stability.
  • Predicting the 3D structures of aptamers and their complexes is challenging due to experimental costs and unreliable computational methods, limiting their applications.
  • Accurate structural information is crucial for understanding aptamer function and optimizing their use in diagnostics and therapeutics.

Purpose of the Study:

  • To develop a robust computational protocol for predicting the 3D structures of aptamer-protein complexes.
  • To address the scarcity of reliable 3D structure prediction methods for aptamers.
  • To enable more accurate modeling for aptamer-based diagnostics and therapeutics.

Main Methods:

  • Proposed a Martini-based computational protocol integrating base-base contact maps from simulations with secondary structure predictions.
  • Introduced a soft elastic network to maintain canonical structures in hairpin regions of single-stranded DNA (ssDNA) aptamers.
  • Validated the protocol by predicting the 3D structure of the aptamer SYL3C and its complex with EpCAM.

Main Results:

  • Achieved improved secondary structure predictions by combining simulation-derived contact maps and diverse prediction tools, reducing errors in base pairing.
  • Successfully predicted the first 3D structure of the aptamer SYL3C and its complex with the EpCAM protein.
  • Demonstrated the reliability of the developed protocol for modeling aptamer-protein interactions.

Conclusions:

  • The proposed Martini-based protocol offers a reliable method for predicting aptamer and aptamer-protein complex structures.
  • This advancement can significantly reduce the limitations imposed by inaccurate structural predictions.
  • The findings are expected to accelerate aptamer-related research and facilitate medical applications in cancer diagnostics and therapeutics.