Loop permutation affects the topology and stability of G-quadruplexes

Abstract

G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on Tm as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.

The diverse structural landscape of quadruplexes

“…6A) increasing overall stability of the parent quadruplex structure [181]. Beyond single-looped quadruplexes, RNA G 3 -quadruplexes differing in loop positions or compositions but possessing the same TLLs did not reveal any differences in thermodynamic stability [62,64], which is in contrast to findings for DNA G 3 -quadruplexes [68,90]. However, variations in the thermodynamic stability of RNA G 3quadruplexes were observed when TLL ≥ 7 and loop compositions were different [62], suggesting the formation of alterative secondary structures in longer looped RNA sequences or the presence of loop-tetrad interactions.…”

“…Long loops in antiparallel topologies enhance DNA‐quadruplex stability, possibly due to secondary interactions in the loops or interactions between loops and the G‐tetrads . In addition, not all loops contribute equally to the stability of the G‐quadruplex . Parallel DNA G‐quadruplexes with a central variable loop and flanking one‐nucleotide loops (three propeller loops) are most common among G‐quadruplexes in promoters .…”

Effects of Length and Loop Composition on Structural Diversity and Similarity of (G3TG3NmG3TG3) G-Quadruplexes

“…Thus, loop sequence plays a major role on their folding topology and thermal stability [4,5]. To deduce rules for predicting the folding pattern and stability of G4s, the effects of loop length and base composition on G4 stability have been extensively studied [6][7][8][9][10][11][12]. Most of studies used CD spectra to identify different types of G4 structures and melting to measure melting temperature for characterizing G4 stability [6,7].…”

“…A large number of guanine (G)-rich sequences are found in the human genome [1][2][3]. In general, G-rich sequences may adopt into various G-quadruplex (G4) structures, which depend on their sequences and lengths, loop composition, and flanking nucleotides in K + solution [4][5][6][7][8][9][10][11][12]. Accumulating evidence on the biological functions of G4 structures in regulating multiple cellular processes [13][14][15][16][17][18] and imaging-based studies on G4 antibodies and G4 ligands for visualizing the presence of G4s in cells [19][20][21][22][23] support the existence of G4 structure in vivo.…”

Structures and stability of simple DNA repeats from bacteria

“…Within any particular sequence that can form G-quadruplexes the bases that separate the G-tracts may be different in type and number and, thus, they represent a complicated type of interrupted repeat tract (see Figure 1). A wide array of sequences have been shown to form quadruplexes, but longer G-tracts and shorter interruptions form more stable G-quadruplexes, although the size of the loop also impacts on the type of folding seen in stable quadruplexes [44]. Importantly, the likelihood of G-quadruplexes forming in genomes varies dramatically in different locations of DNA molecules [45].…”