biostudies-literatureShin WRKorea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and FisheriesNational Research Foundation of Korea204https://www.ebi.ac.uk/biostudies/studies/S-EPMC9044640biostudies-literatureUnknown20(1)<h4>Background</h4>Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, is a biomarker of hepatocellular carcinoma (HCC) progression. Aptamers specifically binding to target biomolecules have recently emerged as clinical disease diagnosis targets. Here, we describe 3D structure-based aptaprobe platforms for detecting GPC3, such as aptablotting, aptaprobe-based sandwich assay (ALISA), and aptaprobe-based imaging analysis.<h4>Results</h4>For preparing the aptaprobe-GPC3 platforms, we obtained 12 high affinity aptamer candidates (GPC3_1 to GPC3_12) that specifically bind to target GPC3 molecules. Structure-based molecular interactions identified distinct aptatopic residues responsible for binding to the paratopic nucleotide sequences (nt-paratope) of GPC3 aptaprobes. Sandwichable and overlapped aptaprobes were selected through structural analysis. The aptaprobe specificity for using in HCC diagnostics were verified through Aptablotting and ALISA. Moreover, aptaprobe-based imaging showed that the binding property of GPC3_3 and their GPC3 specificity were maintained in HCC xenograft models, which may indicate a new HCC imaging diagnosis.<h4>Conclusion</h4>Aptaprobe has the potential to be used as an affinity reagent to detect the target in vivo and in vitro diagnosing system.Journal of nanobiotechnologyStructure based innovative approach to analyze aptaprobe-GPC3 complexes in hepatocellular carcinoma.PMC90446402020R1A6A1A06046235NRF-2020R1A2C1009463MAFRA_321108-04Kim SYThai NQOh IHMin JChoi WKim SCKim YHShin WRLee JPKim JHSekhon SSPark DYCho BKAhn JYfalseStructure based innovative approach to analyze aptaprobe-GPC3 complexes in hepatocellular carcinoma.<h4>Background</h4>Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, is a biomarker of hepatocellular carcinoma (HCC) progression. Aptamers specifically binding to target biomolecules have recently emerged as clinical disease diagnosis targets. Here, we describe 3D structure-based aptaprobe platforms for detecting GPC3, such as aptablotting, aptaprobe-based sandwich assay (ALISA), and aptaprobe-based imaging analysis.<h4>Results</h4>For preparing the aptaprobe-GPC3 platforms, we obtained 12 high affinity aptamer candidates (GPC3_1 to GPC3_12) that specifically bind to target GPC3 molecules. Structure-based molecular interactions identified distinct aptatopic residues responsible for binding to the paratopic nucleotide sequences (nt-paratope) of GPC3 aptaprobes. Sandwichable and overlapped aptaprobes were selected through structural analysis. The aptaprobe specificity for using in HCC diagnostics were verified through Aptablotting and ALISA. Moreover, aptaprobe-based imaging showed that the binding property of GPC3_3 and their GPC3 specificity were maintained in HCC xenograft models, which may indicate a new HCC imaging diagnosis.<h4>Conclusion</h4>Aptaprobe has the potential to be used as an affinity reagent to detect the target in vivo and in vitro diagnosing system.2022-01-01T00:00:00Z2022 Apr2022-07-23T19:10:32.499Z2022-07-23T19:10:32.499ZS-EPMC90446403547750110.1186/s12951-022-01391-z