ArticleMolecular therapy. Nucleic acids2021
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.
Article in Molecular therapy. Nucleic acids, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- Structure-guided development of an electrochemical aptasensor for Salmonella Typhi HlyE antigen detection using in silico and experimental approaches.Scientific reports · 2026Article
- Research Progress on Nucleus-Targeting Carbon Nanoparticles for Tumor Imaging and Therapy.International journal of nanomedicine · 2025Review
- Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics.Molecular therapy. Nucleic acids · 2023Article
- PD-L1 aptamer-functionalized degradable hafnium oxide nanoparticles for near infrared-II diagnostic imaging and radiosensitization.Frontiers in bioengineering and biotechnology · 2023Article
- Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation.Frontiers in chemistry · 2023Article
- Successes and Failures of Static Aptamer-Target 3D Docking Models.International journal of molecular sciences · 2022Review
- The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.International journal of molecular sciences · 2022Article
- Inspirations of Biomimetic Affinity Ligands: A Review.ACS omega · 2022Review
- Liquid biopsy in lung cancer: significance in diagnostics, prediction, and treatment monitoring.Molecular cancer · 2022Review
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood.Sensors (Basel, Switzerland) · 2021Article
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Authors and funding
19 authors at 9 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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