Polymorphism of G4 associates: from stacks to wires via interlocks

Abstract

We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1′,2′-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

“…This configuration contains a planar, tetrameric arrangement of guanines, which in turn can be stacked on top of each other, thanks to π–π interactions, being stabilized by monovalent cations, such as K + and Na + [ 29 , 30 , 31 , 32 ]. These structures may build different types of multimers, such as wires, stacks of intramolecular structures, and interlocked dimers and trimers [ 33 , 34 ]. Therefore, the significant height observed in the case of the TBA–15 probe could correspond to stacks of G-quadruplexes TBA structures.…”

“…In particular, by studying hybridization capacity in time of the Sequence 2 probe, we demonstrate that hybridization with its complementary strand is still efficient after more than one year of storage in air (see Appendix C ). As the Sequence 2 probe is still functional for hybridization after a long period of time, we guess that such a difference between the two oligonucleotides arises from the particular sequence of the TBA–15, which is able to form characteristic G-quadruplex structures and has potential to form complex multimers such as wires [ 33 , 34 ]. As the stability of the multimers increases with dehydration [ 38 ], one can imagine that once stable wires have been formed, it would then be difficult to achieve the hybridization with the DNA complementary strand.…”

Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

“…One noteworthy study used the 1 H 1D NMR of the imino protons quantitatively. Varizhuk et al investigated the polymorphism between G4 monomers and polymers by integrating techniques such as atomic force microscopy, optical and electrophoretic analysis, and molecular modeling with NMR spectroscopy [39]. 2D diffusion ordered spectroscopy was used to estimate the molecular weight from the diffusion coefficients, and the data suggested that parallel G4s without overhangs forms oligomers.…”

ALU non-B-DNA conformations, flipons, binary codes and evolution

“…Triplex [ 3 ] and Z-DNA formation [ 4 ] dynamically change the information read-out from the genome, making different outcomes possible. ALUs can also potentially stack two-layered intramolecular quadruplexes to form G4Q wires [ 5 ]. DNA models are displayed from the following sources: triplex model (PDB:1RX3) with the third strand in blue, Z-DNA (PDB:4LB5), a parallel strand G4Q (PDB: 1NYD), B-DNA (PDB:1BNA).…”

“…The difference between this sequence and the consensus sequence reflects the evolutionary adaptations that improve targeting of RNA strands to specific ALU duplexes [ 8 ]. The lower right logo captures the sequence reported to form an intramolecular quadruplex with the four G quartet forming residues boxed [ 5 ]. …”