The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

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.

Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood

“…The tertiary structure of the aptamer LC-18, capable of binding to lung cancer biomarkers [ 41 ], was identified using small-angle X-ray scattering and molecular simulations [ 59 ]. The thiolated group was attached at the part of this aptamer that is not involved tertiary structure formation, so the aptamer’s active site appeared to be on the top of the attached molecule.…”

Inspirations of Biomimetic Affinity Ligands: A Review

“…Aptamer LC-18 is composed of 80 nucleotides containing two constant 20 nucleotide primers on each side and shows good binding affinity toward the lung carcinoma cells, blood plasma, and tissues. 72 Morozov et al 72 designed a new truncated LC-18 (LC-18t) aptamer with the aid of computational approaches to reduce its size to increase the binding affinity of the new aptamer, and the molecular structure of LC-18t was compared with small-angle X-ray scattering (SAXS). After that, the selectivity of the new aptamer was investigated against the lung carcinoma cells.…”

Liquid biopsy in lung cancer: significance in diagnostics, prediction, and treatment monitoring

“…After NGS analysis of CTCs from lung cancer patients, more than 50% of patients were found to carry four common mutant genes (Notch1, IGF2, EGFR, and PTCH1) [ 8 ]. In addition, when analyzed by LC-MS, 100 differential metabolites were found, in which 10 different metabolites were identified to have potential clinical value in the diagnosis of CTC-positive early lung cancer, suggesting that NGS and metabonomics of CTCs may provide new tumor markers for the early diagnosis of lung cancer [ 9 ]. Additionally, CTCs were isolated from people that had a high risk of developing lung cancer (i.e., smokers with chronic obstructive pulmonary disease) who did not find nodules on a chest CT scan.…”