In Silico Selection of Gp120 ssDNA Aptamer to HIV-1

Abstract

Nucleic acid aptamers that specifically bind to other molecules are mostly obtained through the systematic evolution of ligands by exponential enrichment (SELEX). Because SELEX is a time-consuming procedure, the in silico design of specific aptamers has recently become a progressive approach. HIV-1 surface glycoprotein gp120, which is involved in the early stages of HIV-1 infection, is an attractive target for RNA and DNA aptamer selection. In this study, four single-stranded DNA aptamers, referred to as HD2, HD3, HD4, and HD5, that had the ability of HIV-1 inhibition were designed in silico. In a proposed non-SELEX approach, some parts of the B40 aptamer sequence, which interacted with gp120, were isolated and considered as a separate aptamer sequence. Then, to obtain the best docking scores of the HDOCK server and Hex software, some modifications, insertions, and deletions were applied to each selected sequence. Finally, the cytotoxicity and HIV inhibition of the selected aptamers were evaluated experimentally. Results demonstrated that the selected aptamers could inhibit HIV-1 infection by up to 80%, without any cytotoxicity. Therefore, this new non-SELEX approach could be considered a simple, fast, and efficient method for aptamer selection.

Aptamer-Linked Photonic Crystal Assay for High-Throughput Screening of HIV and SARS-CoV-2

“…The SARS-CoV-2 S1-protein of omicron (B.1.1.529), HIV gp120, and human serum albumin (HSA) were purchased from SinoBiological and Sigma-Aldrich. The NH 2 -modified S1-protein ssDNA aptamer (5′-NH 2 AAA­GCCACA­ACGAGCT­CGGGTG­AAAGC­AGTCC­GTTGA­GTAGG­CTTGCG­GCTGCGT­GGCATA­TCGATT-3′) and (5′-NH 2‑ GATT­TGTTTT­CCCGATT­TTGCCC­AGGGT­TAATT-3′) were synthesized by Sangon Biotech, China. The inactivated SARS-CoV-2 (B.1.1.529) and HIV and adenovirus were obtained from YEASEN Co., Ltd. Carboxy-modified polystyrene nanoparticles (230 nm diameter) were obtained from Aladin.…”

“…31 Here, we present a robust and simple PC-based new microplate testing platform equipped with DNA aptamers: (i) We preadsorbed carboxy-modified polystyrene microspheres to the 96-well microplate by self-assembly in a confined environment resulting in the formation of photonic crystals colloidal array (PCCA). (ii) Amino-modified ssDNA aptamers specific for S1-protein recently selected by our research group 31 and gp120 32 were cross-linked to the polystyrene microspheres by EDC/NHS cross-linking resulting in the fabrication of the aptamer-linked photonic crystals array (ALPA). (iii) ALPA was utilized as a detection platform for S1-protein and the SARS-CoV-2 whole virus, gp120, and HIV whole virus.…”

“… 15 − 17 They can bind to many targets such as small molecules, proteins, viruses, or bacteria with high affinity and specificity. 18 , 19 Only a few aptamers have been selected for S1-protein 20 and gp120, 21 which have been used in sensors as the major recognition elements. These sensors include a RNA aptamer-based liquid crystal sensor for the detection of gp120 22 and aptamer-based sandwich assay, 23 electrochemical sensor, 24 and aptamer-based immunosorbent assay (ALISA) for S1-protein.…”

“…Their advantages such as production independent of the living host, stability at room temperature, and rare batch-to-batch variation make them even superior to antibodies . Aptamers are oligonucleotides that are selected by systematic evolution of ligands by an exponential enrichment (SELEX) process. − They can bind to many targets such as small molecules, proteins, viruses, or bacteria with high affinity and specificity. , Only a few aptamers have been selected for S1-protein and gp120, which have been used in sensors as the major recognition elements. These sensors include a RNA aptamer-based liquid crystal sensor for the detection of gp120 and aptamer-based sandwich assay, electrochemical sensor, and aptamer-based immunosorbent assay (ALISA) for S1-protein .…”

A Photonic Resonator Interferometric Scattering Microscope for Label-free Detection of Nanometer-Scale Objects with Digital Precision in Point-of-Use Environments

“…Complementary thiol-modified single-strand DNAs are conjugated to commercially available pre-activated AuNPs (10-40 nm, Cytodiagnostics) so that the nanoparticles will bind to the surface of the PCs. Pseudovirus capture follows a similar method; modified HD4 DNA aptamers (Integrated DNA Technologies) are fixed to the silanized PC surfaces by amine bonds, and these aptamers capture the HIV viruses via interactions with the GP120 protein on the outer shell of the virus [34]. The process for the capture of SARS-CoV-2 viruses resembles that of the HIV viruses, except AR-10 aptamers that selectively bind with the SARS-CoV-2 spike protein (Integrated DNA Technologies) are used [27].…”