Loop Lengths of G-Quadruplex Structures Affect the G-Quadruplex DNA Binding Selectivity of the RGG Motif in Ewing’s Sarcoma

Abstract

The G-quadruplex nucleic acid structural motif is a target for designing molecules with potential anticancer properties. To achieve therapeutic selectivity by targeting the G-quadruplex, the molecules must be able to differentiate between the DNA of different G-quadruplexes. We recently reported that the Arg-Gly-Gly repeat (RGG) of the C-terminus in Ewing's sarcoma protein (EWS), which is a group of dominant oncogenes that arise due to chromosomal translocations, is capable of binding to G-quadruplex telomere DNA and RNA via arginine residues and stabilize the G-quadruplex DNA form in vitro. Here, we show that the RGG of EWS binds preferentially to G-quadruplexes with longer loops, which is not related to the topology of the G-quadruplex structure. Moreover, the G-quadruplex DNA binding of the RGG in EWS depends on the phosphate backbone of the loops in the G-quadruplex DNA. We also investigated the G-quadruplex DNA binding activity of the N- and C-terminally truncated RGG to assess the role of the regions in the RGG in G-quadruplex DNA binding. Our findings indicate that the RGG and the other arginine-rich motif of residues 617-656 of the RGG in EWS are important for the specific binding to G-quadruplex DNA. These findings will contribute to the development of molecules that selectively target different G-quadruplex DNA.

The cellular protein nucleolin preferentially binds long-looped G-quadruplex nucleic acids

“…By extending the results from the telomeric sequences to cellular oncogene and HIV-1 promoter G4s, we were able to show that loop length is the major determinant in the enhancement of NCL binding to G4s even in more variable and complex sequences. This observation is in line with the reported recognition of G4s by the cellular protein EWS: EWS shares with NCL the RGG domain which mediates recognition of G4s [82] and binds to G4s independently of base composition in long loops [64].…”

“…To investigate the determinants required for efficient NCL binding, we initially tested the human telomeric sequence, formed by GGGTTA repeats, and a simplified sequence formed by GGGTTT repeats, which is found in telomeres of ciliates of the genus Paramecium [62]. The interaction of NCL and its four RNA binding domains (RBD) and the Arg-Gly-Gly (RGG) domain to telomeric G4s has been previously reported [41,63,64]. Telomeric sequences are rather simple compared to the G4 sequences in oncogene and HIV-1 promoters and were thus chosen to allow assessment of oligonucleotide length, loops, repeats, conformation and sequence contribution to NCL binding.…”

Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines

“…Noticeably, only longer loop length combinations exhibited higher representation in the PhenDC3 and 360A-up-regulated genes. One possible explanation might be that longer loops provide more surface for recognition by interaction partners as also concluded recently [52]. In the presence of G4-binding small molecules these interactions may be hindered leading to differential expression of the corresponding genes.…”

Allelic Dropout During Polymerase Chain Reaction due to G-Quadruplex Structures and DNA Methylation Is Widespread at Imprinted Human Loci

“…The structural profiles obtained in the presence and absence of potassium demonstrated a cationic dependence for structure formation, a property which is characteristic of G4 (Neidle 2009; Sun and Hurley 2010; Takahama et al 2011; Yang and Hurley 2006). This observation was most pronounced at 95°, where the only structural signatures in the presence of potassium were representative of parallel-stranded G4.…”