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Publication Abstract from PubMed

93del is a 16-nucleotide G-quadruplex-forming aptamer which can inhibit the activity of the HIV-1 integrase enzyme at nanomolar concentration. Previous structural analyses of 93del using NMR spectroscopy have shown that the aptamer forms an interlocked G-quadruplex structure in K(+) solution. Due to its exceptional stability and unique topology, 93del has been used in many different studies involving DNA G-quadruplexes, such as DNA aptamer and multimer design, as well as DNA fluorescence research. To gain further insights on the structure of this unique aptamer, we have determined several high-resolution crystal structures of 93del and its variants. While confirming the overall dimeric interlocked G-quadruplex folding topology previously determined by NMR, our results reveal important detailed structural information, particularly the formation of a water-mediated A*G*G*G*G pentad. These insights allow us to better understand the formation of various structural elements in G-quadruplexes and should be useful for designing and manipulating G-quadruplex scaffolds with desired properties.

Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A*G*G*G*G pentad in an interlocked G-quadruplex.,Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT Biochem Biophys Res Commun. 2022 Jul 12;613:153-158. doi: , 10.1016/j.bbrc.2022.04.020. Epub 2022 Apr 10. PMID:35561583^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.