{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T19:23:25Z","timestamp":1776281005345,"version":"3.50.1"},"reference-count":35,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T00:00:00Z","timestamp":1612396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5\u2032-end that are complementary to nucleotides at the 3\u2032-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.<\/jats:p>","DOI":"10.3390\/ph14020121","type":"journal-article","created":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T12:02:10Z","timestamp":1612440130000},"page":"121","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9787-3446","authenticated-orcid":false,"given":"Andr\u00e9","family":"Miranda","sequence":"first","affiliation":[{"name":"CICS-UBI\u2014Centro de Investiga\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4620-0174","authenticated-orcid":false,"given":"Tiago","family":"Santos","sequence":"additional","affiliation":[{"name":"CICS-UBI\u2014Centro de Investiga\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"}]},{"given":"Eric","family":"Largy","sequence":"additional","affiliation":[{"name":"Laboratoire Acides Nucl\u00e9iques: R\u00e9gulations Naturelle et Artificielle, Universit\u00e9 de Bordeaux, INSERM &amp; CNRS, (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6630-1242","authenticated-orcid":false,"given":"Carla","family":"Cruz","sequence":"additional","affiliation":[{"name":"CICS-UBI\u2014Centro de Investiga\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,2,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/346818a0","article-title":"In vitro selection of RNA molecules that bind specific ligands","volume":"346","author":"Ellington","year":"1990","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1126\/science.2200121","article-title":"Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase","volume":"249","author":"Tuerk","year":"1990","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Roxo, C., Kotkowiak, W., and Pasternak, A. (2019). G-Quadruplex-Forming Aptamers\u2014Characteristics, Applications, and Perspectives. Molecules, 24.","DOI":"10.3390\/molecules24203781"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1016\/j.tibtech.2017.06.012","article-title":"G-Quadruplexes: Prediction, Characterization, and Biological Application","volume":"35","author":"Kwok","year":"2017","journal-title":"Trends Biotechnol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1016\/j.molonc.2015.03.012","article-title":"Mechanistic studies of anticancer aptamer AS1411 reveal a novel role for nucleolin in regulating Rac1 activation","volume":"9","author":"Shams","year":"2015","journal-title":"Mol. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1016\/j.bbagen.2016.12.015","article-title":"G-quadruplex oligonucleotide AS1411 as a cancer-targeting agent: Uses and mechanisms","volume":"1861","author":"Bates","year":"2017","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-44388-9","article-title":"Aptamer-based Targeted Delivery of a G-quadruplex Ligand in Cervical Cancer Cells","volume":"9","author":"Carvalho","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.talanta.2015.06.034","article-title":"Aptamer-based microcantilever biosensor for ultrasensitive detection of tumor marker nucleolin","volume":"146","author":"Li","year":"2016","journal-title":"Talanta"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.ejpb.2019.07.017","article-title":"RNA G-quadruplex as supramolecular carrier for cancer-selective delivery","volume":"142","author":"Santos","year":"2019","journal-title":"Eur. J. Pharm. Biopharm."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"4877","DOI":"10.1093\/nar\/gkq166","article-title":"Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence","volume":"38","author":"Dailey","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"7487","DOI":"10.1093\/nar\/gkx274","article-title":"G-quadruplex structure of an anti-proliferative DNA sequence","volume":"45","author":"Do","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1006\/abio.2001.5169","article-title":"Aptamer Beacons for the Direct Detection of Proteins","volume":"294","author":"Hamaguchi","year":"2001","journal-title":"Anal. Biochem."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Wu, C., Yang, C.J., and Tan, W. (2013). Molecular Aptamer Beacons. Molecular Beacons, Springer.","DOI":"10.1007\/978-3-642-39109-5_11"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1093\/nar\/gkp026","article-title":"Circular dichroism and conformational polymorphism of DNA","volume":"37","author":"Kypr","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Vorl\u00ed\u010dkov\u00e1, M., Kejnovsk\u00e1, I., Bedn\u00e1\u0159ov\u00e1, K., Ren\u010diuk, D., and Kypr, J. (2012). Circular dichroism spectroscopy of DNA: From duplexes to quadruplexes. Chirality.","DOI":"10.1002\/chir.22064"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"8566","DOI":"10.1002\/anie.201302995","article-title":"Structural Basis of DNA Quadruplex-Duplex Junction Formation","volume":"52","author":"Lim","year":"2013","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e138","DOI":"10.1093\/nar\/gni134","article-title":"Thermal difference spectra: A specific signature for nucleic acid structures","volume":"33","author":"Mergny","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"10645","DOI":"10.1002\/anie.201105193","article-title":"Topological Characterization of Nucleic Acid G-Quadruplexes by UV Absorption and Circular Dichroism","volume":"50","author":"Karsisiotis","year":"2011","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S0014-5793(98)01043-6","article-title":"Following G-quartet formation by UV-spectroscopy","volume":"435","author":"Mergny","year":"1998","journal-title":"FEBS Lett."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1093\/nar\/gkw006","article-title":"Re-evaluation of G-quadruplex propensity with G4Hunter","volume":"44","author":"Bedrat","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1021\/jacs.5b13130","article-title":"Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches","volume":"138","author":"Largy","year":"2016","journal-title":"J. Am. Chem. Soc."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-11104-0","article-title":"Involvement of G-quadruplex regions in mammalian replication origin activity","volume":"10","author":"Prorok","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3693","DOI":"10.1039\/c3sc50474c","article-title":"A \u201csugar-deficient\u201d G-quadruplex: Incorporation of aTNA in G4 structures","volume":"4","author":"Zhou","year":"2013","journal-title":"Chem. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e65","DOI":"10.1093\/nar\/gku111","article-title":"Thioflavin T as a fluorescence light-up probe for G4 formation","volume":"42","author":"Bedrat","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2992","DOI":"10.1039\/C9OB00318E","article-title":"Aptamer-guided acridine derivatives for cervical cancer","volume":"17","author":"Carvalho","year":"2019","journal-title":"Org. Biomol. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Zhu, L.-N., Zhao, S.-J., Wu, B., Li, X.-Z., and Kong, D.-M. (2012). A New Cationic Porphyrin Derivative (TMPipEOPP) with Large Side Arm Substituents: A Highly Selective G-Quadruplex Optical Probe. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0035586"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3419","DOI":"10.1007\/s00216-011-5018-z","article-title":"Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures","volume":"400","author":"Largy","year":"2011","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1021\/ja5099403","article-title":"Ligand-Induced Conformational Changes with Cation Ejection upon Binding to Human Telomeric DNA G-Quadruplexes","volume":"137","author":"Marchand","year":"2015","journal-title":"J. Am. Chem. Soc."},{"key":"ref_29","first-page":"10376","article-title":"Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes","volume":"43","author":"Podlipnik","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.biochi.2015.06.002","article-title":"Assessment of selectivity of G-quadruplex ligands via an optimised FRET melting assay","volume":"115","author":"Mergny","year":"2015","journal-title":"Biochimie"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1093\/nar\/gkm098","article-title":"Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation","volume":"35","author":"Mergny","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_32","first-page":"1","article-title":"Solution structures of multiple G-quadruplex complexes induced by a platinum(II)-based tripod reveal dynamic binding","volume":"9","author":"Liu","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Santos, T., Miranda, A., Campello, M.P., Paulo, A., Salgado, G., Cabrita, E.J., and Cruz, C. (2020). Recognition of nucleolin through interaction with RNA G-quadruplex. Biochem. Pharmacol., 114208.","DOI":"10.1016\/j.bcp.2020.114208"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.omtn.2018.06.003","article-title":"Gemcitabine-Incorporated G-Quadruplex Aptamer for Targeted Drug Delivery into Pancreas Cancer","volume":"12","author":"Park","year":"2018","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1021\/acs.biochem.9b01094","article-title":"Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes","volume":"59","author":"Saha","year":"2020","journal-title":"Biochemistry"}],"container-title":["Pharmaceuticals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8247\/14\/2\/121\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:20:20Z","timestamp":1760160020000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8247\/14\/2\/121"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,4]]},"references-count":35,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["ph14020121"],"URL":"https:\/\/doi.org\/10.3390\/ph14020121","relation":{},"ISSN":["1424-8247"],"issn-type":[{"value":"1424-8247","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,4]]}}}