The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes

Abstract

G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.

Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex

“…Previously, ultra-stable 4-layer parallel G4s which exhibit an even higher stability were constructed [47,48]. Therefore, it would be possible to build an 8-layer G4 structure consisting of two interlocked 4-layer monomers, effectively extending the 93del structure with one extra G-tetrad on each side.…”

On Water Arrangements in Right- and Left-Handed DNA Structures

“…No hydrogen bonds with O4′ oxygen atoms are formed. Analogous to the RH B-DNA spine, waters also contact guanine base edge hydrogen bond donors/acceptors at the floor of the groove, although the pattern is less regular than that in the B-DNA arrangement [ 64 , 66 ]. Waters can also frequently bridge between strands ( Figure 3 b), and the groove is (or becomes) especially narrow in these regions [ 64 ].…”

“…Several “deep spine” (W D ) and “outer spine” waters (W O ) are highlighted. ( c ) The seven waters in the narrow groove of PDB id 6XT7 [ 66 ], by contrast, form a continuous and regular spine, with hydrogen bonding to phosphates, alternating from one strand to the other.…”