Methods and applications of in silico aptamer design and modeling

AA Buglak, AV Samokhvalov, AV Zherdev… - International journal of …, 2020 - mdpi.com
Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such
as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow …

Computational tools for aptamer identification and optimization

D Sun, M Sun, J Zhang, X Lin, Y Zhang, F Lin… - TrAC Trends in …, 2022 - Elsevier
Aptamers are single-stranded DNA or RNA oligonucleotides that can selectively bind to a
specific target. They are generally obtained by SELEX, but the procedure is challenging and …

Systematic evaluation of error rates and causes in short samples in next-generation sequencing

F Pfeiffer, C Gröber, M Blank, K Händler, M Beyer… - Scientific reports, 2018 - nature.com
Next-generation sequencing (NGS) is the method of choice when large numbers of
sequences have to be obtained. While the technique is widely applied, varying error rates …

Design and prediction of aptamers assisted by in silico methods

SJ Lee, J Cho, BH Lee, D Hwang, JW Park - Biomedicines, 2023 - mdpi.com
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding
affinity. Aptamers are developed through the process of systematic evolution of ligands by …

Implementation of high-throughput sequencing (HTS) in aptamer selection technology

N Komarova, D Barkova, A Kuznetsov - International journal of molecular …, 2020 - mdpi.com
Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have
gained in popularity due to their high potential for different applications in analysis …

AptaSUITE: a full-featured bioinformatics framework for the comprehensive analysis of aptamers from HT-SELEX experiments

J Hoinka, R Backofen, TM Przytycka - Molecular Therapy-Nucleic Acids, 2018 - cell.com
The capability of producing and efficiently processing big data has revolutionized virtually
every field of science and technology and has enabled the analysis of experimental results …

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display

DE Hacker, J Hoinka, ES Iqbal, TM Przytycka… - ACS chemical …, 2017 - ACS Publications
Highly constrained peptides such as the knotted peptide natural products are promising
medicinal agents because of their impressive biostability and potent activity. Yet, libraries of …

Aptamers as an approach to targeted cancer therapy

F Mahmoudian, A Ahmari, S Shabani, B Sadeghi… - Cancer Cell …, 2024 - Springer
Conventional cancer treatments can cause serious side effects because they are not specific
to cancer cells and can damage healthy cells. Aptamers often are single-stranded …

A 2′ FY-RNA motif defines an aptamer for Ebolavirus secreted protein

S Shubham, J Hoinka, S Banerjee, E Swanson… - Scientific reports, 2018 - nature.com
With properties such as stability to long-term storage and amenability to repetitive use,
nucleic acid aptamers are compatible with many sensing/transducing platforms intended for …

Hybrid-Type SELEX for the selection of artificial nucleic acid aptamers exhibiting cell internalization activity

H Uemachi, Y Kasahara, K Tanaka, T Okuda… - Pharmaceutics, 2021 - mdpi.com
Nucleic acid aptamers have attracted considerable attention as next-generation
pharmaceutical agents and delivery vehicles for small molecule drugs and therapeutic …