Evolution of Interferon-Gamma Aptamer with Good Affinity and Analytical Utility by a Rational In Silico Base Mutagenesis Post-SELEX Strategy

Abstract

The Systematic Evolution of Ligands by EXponential enrichment (SELEX) is conventionally an effective method to identify aptamers, which are oligonucleotide sequences with desired properties to recognize targets specifically and sensitively. However, there are some inherent limitations, e.g., the loss of potential high-affinity sequences during biased iterative PCR enrichment processes and the limited structural diversity of the initial library, which seriously restrict their real-world applications. To overcome these limitations, the in silico base mutagenesis post-SELEX strategy based on the low Gibbs free energy (ΔG) and genetic algorithm was developed for the optimization of the interferon-gamma aptamer (B1-4). In the process of evolution, new sequences were created and the aptamer candidates with low ΔG values and advanced structures were produced. After five rounds of selection, systematic studies revealed that the affinity of the newly developed evolutionary aptamer (M5-5) was roughly 10-fold higher than that of the parent aptamer (B1-4), and an aptasensor detection system with a limit-of-detection (LOD) value of 3.17 nM was established based on the evolutionary aptamer. The proposed approach provided an efficient strategy to improve the aptamer with low energy and a high binding ability, and the good analytical utility thereof.

Advances in Aptamers-Based Applications in Breast Cancer: Drug Delivery, Therapeutics, and Diagnostics

“…Xie et al [58] adopted carboxylated magnetic beads for HBsAg immobilization by some deoxynucleotide aptamers which can bind with high specificity to the surface antigen of hepatitis B virus (HBV) [59]. In immobilized metal affinity chromatography (IMAC), metal ions such as Zn(II), Cu(II), Ni (II), and Co(II) are immobilized on a support to fractionate and purify proteins in solutions; the IMAC method is used to enrich most of the phosphopeptides from whole cell lysates, and it is reported that titanium dioxide (TiO 2 ) beads have an equivalent ability to enrich phosphopeptides [60,61].…”

Recent Progress in Micro- and Nanotechnology-Enabled Sensors for Biomedical and Environmental Challenges

“…In the biomedical field, these devices have enabled the detection and quantification of biological molecules such as proteins and nucleic acids with high accuracy and in real time [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. They have also enabled the development of point-of-care devices that can rapidly diagnose diseases and monitor treatment outcomes [ 31 , 32 , 33 , 34 , 35 ].…”