Analysis on the in-silico ensemble methods for 3D modelling of ssDNA aptamers

This study identified that the Guanine residues are crucial in the aptamer 3D structure prediction and in algorithms that generate secondary structures. Further, the GC content (<50%), GC bond percentage (<60%), and G:C ratio (<1.12) act as limiting factors in predicting the 2D structures of aptamers. There were variations in the 2D structure predictions by the web applications, even though all these applications were a combination of the MFE, MEA, and McCaskill functions. Processing these structures through the web applications described above produced best-fit 3D structures with the experimental one, thus offering the present ensemble approach to reliably predict the 3D structure of aptamers for various applications.PMID:37774437 | DOI:10.1016/j.bpc.2023.107111

Source: Biophysical Chemistry - September 29, 2023 Category: Chemistry Authors: Vinay Bachu Kangkana Barman Pranab Goswami Source Type: research