# Controlling Topology of a Telomeric G‐quadruplex DNA With a Chemical Cross‐link

## TL;DR

Scientists used a chemical cross-link to stabilize a specific DNA structure called a G-quadruplex, which is important for understanding DNA replication and protein interactions.

## Contribution

A chemical cross-link was introduced to stabilize a telomeric G-quadruplex in the presence of complementary DNA.

## Key findings

- A cross-link between G3 and A8 reinforced a stable parallel G4 topology.
- The cross-linked G4 recruited native DNA to form a hybrid G4 even with complementary DNA present.
- This method enables reliable formation of G4s for studying G4-protein interactions.

## Abstract

DNA G‐quadruplexes (G4s) are noncanonical structures formed in guanine‐rich sequences. Within the human genome, they are nonrandomly distributed and influence DNA replication, gene expression, and genome maintenance. Numerous proteins involved in these processes have been identified as G4‐binding proteins. However, the interaction of proteins with G4s in the context of double‐stranded DNA in vitro has been difficult to study due to the transient nature of G4s in the presence of complementary DNA. To overcome this challenge, introducing internal covalent cross‐links between distant nucleotides within the DNA sequence may promote pre‐folding of G4 structures, thereby shifting the thermodynamic equilibrium toward G4‐formation. We used a Cu(I)‐catalyzed azide–alkyne cycloaddition to create a cross‐link between 2′‐O‐propargylguanosine and N
6‐azidoethyl‐2′‐deoxyadenosine in the DNA telomeric sequence (TAG3T)2. A cross‐link between G3 and A8 reinforced the parallel G4 topology that was stable in the presence of complementary DNA. Moreover, even in the presence of its complementary strand, this cross‐linked G4 recruited the parent native DNA (TAG3T)2 to form a hybrid G4. These results suggest that cross‐linking provides a useful tool for stabilizing noncanonical DNA structures in the presence of complementary strands, enabling their study within the context of genomic DNA.

Thermodynamically stable G‐quadruplex (G4) DNA: Chemical cross‐linking between distant nucleotides led to formation of G4‐DNA that is stable in the presence of complementary DNA. This methodology can be used to reliably form G4s within DNA fibers for subsequent structural studies of G4‐protein interactions.