The Effect of DNA Sequence Directionality on G‐Quadruplex Folding

Abstract

Sequence inversion in G-rich DNA from 5'→3' to 3'→5' exerts a substantial effect on the number of structures formed, while the type of G-quadruplex fold is in fact determined by the presence of K(+) or Na(+) ions. The melting temperatures of G-quadruplexes adopted by oligonucleotides with sequences in the 5'→3' direction are higher than those of their 3'→5' counterparts with both KCl and NaCl. CD, UV, and NMR spectroscopy demonstrates the importance of primary sequence for the structural diversity of G-quadruplexes. The changes introduced by mere sequence reversal of the G-rich DNA segment have a substantial impact on the polymorphic nature of the resulting G-quadruplexes and their potential physiological roles. The insights resulting from this study should enable extension of the empirical rules for the prediction of G-quadruplex topology.

Sugar Puckering Drives G‐Quadruplex Refolding: Implications for V‐Shaped Loops

“…A V‐shaped loop was first reported for a two‐layered G‐quadruplex forming an interlocked dimer . In the past years, a growing number of such V‐shaped loops have been found in various three‐layered bi‐ or monomolecular G4s, making the V‐loop a more recurrent structural motif in G‐quadruplexes . It links two adjacent antiparallel G‐columns through residues located on opposite outer faces of the G‐core.…”

“…Interestingly, HPV52 and ODN are derived from the same sequence encompassing five G‐runs. Whereas HPV52 comprises G‐tracts I‐IV, the ODN sequence includes G‐tracts II‐V with additional inversion of the 5′‐3′ orientation . ODN(14,15), HPV52 , and CHL1 differ in the length and sequence of loops, but they all feature a lateral loop adenosine directly preceding the V‐loop.…”

“…[18] In the past years, a growing number of such V-shaped loops have been found in various three-layered bi-or monomolecular G4s, making the Vloop a more recurrent structural motif in G-quadruplexes. [11,15,[19][20][21][22][23][24] It links two adjacent antiparallel G-columns through residues located on opposite outer faces of the Gcore. Starting with a guanosine in the bottom tetrad of a broken G-tract it is easily distinguished from a propeller-type loop by the upward orientation of this G nucleotide at the Vloop 5'-end ( Figure S18).…”

“…Depending on the relative strand orientation as fixed by the type of loops in case of monomolecular G4s, topologies can be of a parallel, antiparallel, or hybrid type. Additional features such as bulges, [8][9][10] capping structures like base triplets, [11][12][13][14][15][16][17] interrupted G-tracts and V-loops, [11,15,[18][19][20][21][22][23][24] as well as interlocked G4s [18,25,26] further expand the topological landscape of these highly polymorphic structures. Notably, despite an ever-growing number of available high-resolution structures our understanding of the factors driving G4 folding to a particular topology remains limited.…”

Encoding canonical DNA quadruplex structure

“…Many principles of design are already established that make it possible to engineer the architectures described. For example, in canonical quadruplex architectures, positioning of loops (as first, second, and third) is fundamental in sequence design, that is, reversing the loop-length sequence in the combination of loops does not result in the same topology ( 36 ). The nature of residues able to realize the desired loop combinations is equally significant.…”