3D Structure Modeling Services for Aptamer Characterization

Three-dimensional (3D) aptamer structures provide invaluable insights into the molecular basis of aptamer functions. Powered by cutting-edge technologies and the rich expertise in 3D modeling, we offer the best aptamer structural 3D modeling services, helping our clients investigate the mechanisms of functions of aptamers.

Introduction of 3D Structure Modeling

3D structure modeling is a powerful technology that is used to model 3D structure of aptamers in silico, which helps to understand the mechanisms of functions and aptamer-target interactions. In a study, scientists revealed the molecular interactions of anti-HER2 ssDNA aptamers (H1-H7) that specifically bind to the extracellular domain of HER2 protein. Molecular docking and molecular dynamics (MD) simulations showed the stable HER2 binding nature of H1, H2, and H6 aptamers and the amino acid residues (Asn37, Gln59, Arg81-Gln84, Asp88, and Lys128) of Site 2a were found to be crucial for high-affinity binding. In another study, the authors used computational RNA structure and RNA/protein docking modeling to guide the truncation of the A9 prostate-specific membrane antigen (PSMA) RNA aptamer. Furthermore, the modeled RNA 3D structure and protein/RNA docking modeling also indicated key nucleotides within the aptamer that are essential for binding to PSMA and inhibiting its enzymatic activity.

Fig. 1 3D structure for THF riboswitch aptamer predicted by using RNAComposer program online.^{1, 2}

3D Structure Modeling Services at Creative Biolabs

Equipped with solid professional knowledge in aptamer 3D structure modeling and state-of-the-art technologies, Creative Biolabs provides a variety of solutions for aptamer 3D modeling for studying the mechanism of aptamer-target binding. There are two strategies for aptamer 3D modeling at Creative Biolabs:

1. Template-based modeling, also called homology modeling or comparative modeling. The procedure of template-based modeling generally consists of the following steps: (1) identification of a template structure associated with the target sequence; (2) alignment of the sequences of the target and templates; (3) constructing a 3D model of the aptamer from the alignment; (4) optimization of the models.
2. Free-based modeling, also called abinitio modeling. The strategy is used in the case of a lack of structural analogs in the reference libraries. The modeling mechanism is based on biophysical rules that simulate the process of folding using minimum free energy.

Table 1. Methods that have been used for modeling 3D structure for aptamers.¹

Based on a variety of well-established 3D modeling methods such as RNA Composer, Rosetta, JAR3D, and iFoldRNA, we provide the best and affordable 3D modeling services for aptamers to support their functional research.

Advantages

1. Extensive experience in 3D modeling of aptamers
2. Strong project management
3. All-around services from the first concept to the final result
4. Short turnaround time

If you are interested in our aptamer 3D modeling services, please contact us for more details.

References

1. Gong, Sha, et al. "Computational methods for modeling aptamers and designing riboswitches." International journal of molecular sciences 18.11 (2017): 2442.
2. under Open Access license CC BY 4.0, without modification

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