The stability of intramolecular DNA quadruplexes with extended loops forming inter- and intra-loop duplexes

Abstract

We have examined the formation of intramolecular quadruplex DNA structures in which the loops have been extended so as to generate short DNA duplexes. Fluorescence melting and DNase I cleavage studies show that duplexes can be formed within each loop, but that duplexes between the loops are not stable.

Combination of i‐Motif and G‐Quadruplex Structures within the Same Strand: Formation and Application

“…[5][6][7] Herein, we demonstrate the formation of a "doublequadruplex" structure with i-motif and G4 domains on the same strand. Previous studies have demonstrated that duplexes can be combined with quadruplexes; [8][9][10] however, to the best of our knowledge, the coexistence of G4 and i-motif structures on the same strand has not been reported previously. G-quadruplex formation requires the presence of a G4-compatible cation, whereas the i-motif demands acidic conditions ( Figure 1).…”

Novel Insight into Proximal DNA Domain Interactions from Temperature‐Controlled Electrospray Ionization Mass Spectrometry

“…[5] Factors that have as ignificant impact on GQ stability are the number of guanines involved, [6] then umber of stacked G-quartets,l oop length, [7,8] and the type of intercalated cations. [8] GQ structures are highly abundant in the genome and are typically localized in gene promoters,t elomeres or minisatellites. [9] Functions of GQs have been extensively studied, primarily for their regulatory roles especially in gene expression and telomere shortening.Remarkably,GQs that are stable in vivo can both down-and up-regulate gene expression, depending on their location in the gene promoters.…”

“…[2] G-quartets,f our guanine bases arranged in ap lanar structure,a re stabilized by Hoogsteen hydrogen-bonding interactions, [3] p-p stacking, [4] and hydrophobic interactions. [5] Factors that have as ignificant impact on GQ stability are the number of guanines involved, [6] then umber of stacked G-quartets,l oop length, [7,8] and the type of intercalated cations. [8] GQ structures are highly abundant in the genome and are typically localized in gene promoters,t elomeres or minisatellites.…”

Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study

“…Interspersing duplex SL motifs within quadruplex-forming motifs could lead to the generation of intramolecular quadruplex–duplex hybrids (QDH) (Figure 1c ), which combine the structural traits of both conformations. The facile formation of such hybrid structures have been demonstrated ( 44 ) and they were shown to exhibit excellent stability ( 45 , 46 ). We have previously shown that such structures can arise in a diverse arrays of arrangement between the duplex and quadruplex segments ( 44 ).…”