Template‐Mediated Stabilization of a DNA G‐Quadruplex formed in the HIV‐1 Promoter and Comparative Binding Studies

Abstract

G-rich DNA oligonucleotides derived from the promoter region of the HIV-1 long terminal repeat (LTR) were assembled onto an addressable cyclopeptide platform through sequential oxime ligation, a thiol-iodoacetamide SN2 reaction, and copper-catalyzed azide-alkyne cycloaddition reactions. The resulting conjugate was shown to fold into a highly stable antiparallel G4 architecture as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. The binding affinities of six state-of-the-art G4-binding ligands toward the HIV-G4 structure were compared to those obtained with a telomeric G4 structure and a hairpin structure. Surface plasmon resonance binding analysis provides new insights into the binding mode of broadly exploited G4 chemical probes and further suggests that potent and selective recognition of viral G4 structures of functional significance might be achieved.

Scaffold stabilization of a G-triplex and study of its interactions with G-quadruplex targeting ligands

“…The dissociation constants obtained for the interactions of those three ligands with the G4 structure 2 were consistent with reported values of three-digit nanomolar for BRACO-19, two-digit nanomolar for PDS and low nanomolar for PhenDC3. 16 Yet in all cases, the dissociation constant obtained for the interactions with the G3 structure 1 were found to be similar or somewhat lower to that obtained with the G4 structure.…”

“…Cyclopeptide scaffold 3 was assembled using standard Fmoc/tBu solid phase peptide synthesis (SPPS) on a 2-chlorotrityl resin and cyclized in solution according to reported procedures as described in Scheme S1. 16 Briefly, a biotin was anchored onto the lower domain of the peptide using a biotin-functionalized lysine building block during SPPS. The azido and aminooxy moieties were introduced during SPPS using a L-azidonorleucine building block and a previously reported lysine building block modified with a protected aminooxyacetic acid (Scheme S1).…”

“…14 To do so, we have assembled DNA and RNA conjugates capable of mimic naturally occurring G4 structures from the telomeric region of the human genome 15 and from the HIV genome. 16 Those conjugates are formed by the covalent association of G4 forming DNA or RNA strands with a rigid and addressable cyclopeptide platform.…”

Towards the Development of Photo‐Reactive Ruthenium(II) Complexes Targeting Telomeric G‐Quadruplex DNA

“…It allows the determination of kinetic parameters of an interaction (such as SPR) and has been used to study biomolecular interactions between large biomolecules, such as protein–membrane interactions . We have hitherto employed an SPR analysis method based on the use of a template‐assembled synthetic G‐quadruplex (TASQ) that allows precise control of G‐quadruplex topology through the assembly of constrained structures on a template . We have now adapted this SPR method for BLI.…”

Cover Feature: Towards the Development of Photo‐Reactive Ruthenium(II) Complexes Targeting Telomeric G‐Quadruplex DNA (Chem. Eur. J. 72/2018)

“…[56] We have hitherto employed an SPR analysis method based on the use of at emplate-assembled syntheticG -quadruplex (TASQ) that allows precise control of G-quadruplex topology through the assembly of constrained structures on at emplate. [57][58][59][60][61] We have now adapted this SPR method for BLI. Different G-quadruplex features were used:i ntermolecular-like G-quadruplex motif A constrained in ap arallel G-quadruplext opology,i ntramolecular G-quadruplex B (HTelo sequence in equilibrium between different topologies), human telomeric sequence (HTelo) C constrained in antiparallel topology, and hairpin DNA D (Figure 3).…”