An In Silico Study of the Differential Effect of Oxidation on Two Biologically Relevant G-Quadruplexes: Possible Implications in Oncogene Expression

A quadruplex sequence from the promoter region of the c-KIT gene forms a stable quadruplex, as characterized by crystallographic and NMR methods. Two new crystal structures are reported here, together with molecular dynamics simulation studies on these quadruplex crystal structures and an NMR structure. The new crystal structures, each in a distinct space group and lattice packing arrangement, together with the existing structures, demonstrate that the c-KIT quadruplex fold does not change with differing environments, suggesting that quadruplex topological dynamism is not a general phenomenon. The single and dinucleotide loops in these structures show a high degree of conformational flexibility within the three crystal forms and the NMR ensemble, with no evidence of clustering to particular conformers. This is in accord with the findings of high loop flexibility from the molecular dynamics studies. It is suggested that intramolecular quadruplexes can be grouped into two broad classes (i) those with at least one single-nucleotide loop, often showing singular topologies even though loops are highly flexible, and (ii) with all loops comprising at least two nucleotides, leading to topological dynamism. The loops can have more stable and less dynamic base-stacked secondary structures.

Section: Discussionsupporting

confidence: 89%

Flexibility and structural conservation in a c-KIT G-quadruplex

Wei

Husby

Neidle

2014

“…in 10–20 base pairs. As natural base lesions also form in non-canonical nucleic acids, such as the G-quadruplexes ( 39 – 41 ) the original definition needs to be formulated to fit quadruplexes as well. We define it here as two or more lesions within a four-stranded core quadruplex unit assembling from 21 to 25 nucleotides.…”

Section: Discussionmentioning

confidence: 99%

“…The present study highlights the fact that clustered AP lesions in the human telomere quadruplex of d[TAG 3 (TTAG 3 ) 3 TT] can change the folding and stability and can even prevent its formation. Even if the chromosomes’ capping telomere DNA–protein complexes (Shelterin) render the telomere DNA inaccessible to recognition and attack by various cellular enzymes, spontaneous depurination as well as other oxidative base damage of the DNA do occur in these tight complexes too ( 39 – 41 ). As the clustered damages are relatively inaccessible for repair even in double-stranded DNAs ( 4 , 57 , 58 ), these can be fateful for the telomere quadruplex.…”

Section: Discussionmentioning

confidence: 99%

Clustered abasic lesions profoundly change the structure and stability of human telomeric G-quadruplexes

Kejnovská

Bednářová

Renčiuk

et al. 2017

Ionizing radiation produces clustered damage to DNA which is difficult to repair and thus more harmful than single lesions. Clustered lesions have only been investigated in dsDNA models. Introducing the term ‘clustered damage to G-quadruplexes’ we report here on the structural effects of multiple tetrahydrofuranyl abasic sites replacing loop adenines (A/AP) and tetrad guanines (G/AP) in quadruplexes formed by the human telomere d[AG3(TTAG3)3] (htel-22) and d[TAG3(TTAG3)3TT] (htel-25) in K+ solutions. Single to triple A/APs increased the population of parallel strands in their structures by stabilizing propeller type loops, shifting the antiparallel htel-22 into hybrid or parallel quadruplexes. In htel-25, the G/APs inhibited the formation of parallel strands and these adopted antiparallel topologies. Clustered G/AP and A/APs reduced the thermal stability of the wild-type htel-25. Depending on position, A/APs diminished or intensified the damaging effect of the G/APs. Taken together, clustered lesions can disrupt the topology and stability of the htel quadruplexes and restrict their conformational space. These in vitro results suggest that formation of clustered lesions in the chromosome capping structure can result in the unfolding of existing G-quadruplexes which can lead to telomere shortening.

“…Indeed, G4DNA loops and 5′ core guanines are primary targets for oxidation ( 18 ). Damage within G4DNA folds is inefficiently repaired by glycosylases and lesions alter G4DNA stability ( 16 , 19 , 20 ). Such occurrences at regulatory sites in the genome would appear to foster deleterious outcomes for the cell.…”

Section: Introductionmentioning

confidence: 99%

G-Quadruplex loops regulate PARP-1 enzymatic activation

Edwards

Marecki

Byrd

et al. 2020

G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.