G-quadruplex conformation and dynamics are determined by loop length and sequence

Abstract

The quadruplex forming G-rich sequences are unevenly distributed throughout the human genome. Their enrichment in oncogenic promoters and telomeres has generated interest in targeting G-quadruplex (GQ) for an anticancer therapy. Here, we present a quantitative analysis on the conformations and dynamics of GQ forming sequences measured by single molecule fluorescence. Additionally, we relate these properties to GQ targeting ligands and G4 resolvase 1 (G4R1) protein binding. Our result shows that both the loop (non-G components) length and sequence contribute to the conformation of the GQ. Real time single molecule traces reveal that the folding dynamics also depend on the loop composition. We demonstrate that GQ-stabilizing small molecules, N-methyl mesoporphyrin IX (NMM), its analog, NMP and the G4R1 protein bind selectively to the parallel GQ conformation. Our findings point to the complexity of GQ folding governed by the loop length and sequence and how the GQ conformation determines the small molecule and protein binding propensity.

Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin

“…3). The loop length and sequence contribute to the conformation of the G-quadruplex [15]. Replacement of the central G by A or I also alter the overall structure (Supporting information S2), particularly the lower G-quartet.…”

“…These monovalent cationic ions interact with the carbonyl group of the G bases. A variety of structures depending on the number of G-quartet, nature of loops and central cation have been reported [8][9][10][11][12][13][14][15]. For example, an early NMR study of a thrombin-binding aptamer, 5′G 2 T 2 G 2 TGTG 2 T 2 G 2 , showed that this DNA adopts a highly compact, high symmetrical structure that consist of tetrads of G base pairs and three loops ( Fig.…”

“…The loops linking the G quartets on the top or bottom of the Gquadruplex can have various sequences and lengths. The nature of the loops is related to the direction of the G-quartet runs [10,[15][16][17][18]. For example, a recent single molecule fluorescence technique showed that both the loop length and sequence contribute to the conformation of the G-quadruplex.…”

“…For example, a recent single molecule fluorescence technique showed that both the loop length and sequence contribute to the conformation of the G-quadruplex. The folding dynamics also depends on the loop composition [15]. On the other hand, the interaction and the role of the nucleo-bases at the central loop in the stabilization of the Gquadruplex are unclear.…”

Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex

“…Much less is known however about the effect on the quadruplex structure of such lesions of the loops [40e42]. Current knowledge is that the sequence and length of loop determine primarily the quadruplex folding, which of course, influences its stability [43,44]. A recent study on single-molecule mechanical unfolding of a three-tetrad telomeric G-quadruplex however concluded that the loop interactions contributed more to G-quadruplex stability than the stacking of G-tetrads [45].…”