7XHD

Crystal structure of a dimeric interlocked parallel G-quadruplex

Summary for 7XHD

• Entry DOI: 10.2210/pdb7xhd/pdb
• Descriptor: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3'), POTASSIUM ION (3 entities in total)
• Functional Keywords: g-quadruplex, interlocked, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 10440.06

Authors

Ngo, K.H.,Liew, C.W.,Lattmann, S.,Winnerdy, F.R.,Phan, A.T. (deposition date: 2022-04-08, release date: 2023-02-15, Last modification date: 2023-11-29)

Primary citation

Ngo, K.H.,Liew, C.W.,Lattmann, S.,Winnerdy, F.R.,Phan, A.T.
Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex.
Biochem.Biophys.Res.Commun., 613:153-158, 2022

PubMed Abstract: 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.

PubMed: 35561583
DOI: 10.1016/j.bbrc.2022.04.020

Experimental method

X-RAY DIFFRACTION (1.66 Å)