In silico designed RNA aptamer against epithelial cell adhesion molecule for cancer cell imaging

被引：31

作者：

Bavi, Rohit ^{[1
]}

Liu, Zicun ^{[1
]}

Han, Zhihao ^{[1
]}

Zhang, Hang ^{[1
]}

Gu, Yueqing ^{[1
]}

机构：

[1] China Pharmaceut Univ, State Key Lab Nat Med, Dept Biomed Engn, Sch Engn, 24 Tongjia Xiang, Nanjing 210009, Gulou District, Peoples R China

来源：

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS | 2019年 / 509卷 / 04期

基金：

中国国家自然科学基金;

关键词：

EpCAM; RNA aptamer; Virtual screening; MD simulation; Flow cytometry assays; Inhibition of endocytosis; CIRCULATING TUMOR-CELLS; IDENTIFICATION; CD326;

D O I：

10.1016/j.bbrc.2019.01.028

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Aptamers are short, single-stranded oligonucleotides that bind to their targets with high affinity and specificity. Usually, aptamers are selected experimentally using SELEX approach. Here, we describe a computational approach for selection of aptamers for proteins, which involves generation of a virtual library of sequences, modeling of their 3D-structures and selection of perspective aptamers through docking, molecular dynamics simulation, binding free energy calculations and finally estimating the experimental affinity. Using this method, a 15-mer RNA aptamer was designed for epithelial cell adhesion molecule. Flow cytometry and fluorescence microscopy results reviled that RNA1 aptamer interacts specifically with human cancer cells that express EpCAM, but not with the EpCAM negative cells. The binding affinity of the RNA1 aptamer to MCF-7 and MDA-MB-231 is approximately 21.8 and 96.9 nM respectively. This novel RNA aptamer will help in the future development of targeted therapeutics and molecular imaging. (C) 2019 Elsevier Inc. All rights reserved.

引用

页码：937 / 942

页数：6

共 30 条

[1] Prospective identification of tumorigenic breast cancer cells [J].