Sequence-specific DNA alkylation and transcriptional inhibition by long-chain hairpin pyrrole–imidazole polyamide–chlorambucil conjugates targeting CAG/CTG trinucleotide repeats

Abstract

Introducing novel building blocks to solid-phase peptide synthesis, we readily synthesized long-chain hairpin pyrrole-imidazole (PI) polyamide-chlorambucil conjugates 3 and 4 via the introduction of an amino group into a GABA (γ-turn) contained in 3, to target CAG/CTG repeat sequences, which are associated with various hereditary disorders. A high-resolution denaturing polyacrylamide sequencing gel revealed sequence-specific alkylation both strands at the N3 of adenines or guanines in CAG/CTG repeats by conjugates 3 and 4, with 11bp recognition. In vitro transcription assays using conjugate 4 revealed that specific alkylation inhibited the progression of RNA polymerase at the alkylating sites. Chiral substitution of the γ-turn with an amino group resulted in higher binding affinity observed in SPR assays. These assays suggest that conjugates 4 with 11bp recognition has the potential to cause specific DNA damage and transcriptional inhibition at the alkylating sites.

The Thiophene “Sigma‐Hole” as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove

“…The design and preparation of new types of compounds that recognize mixed base pairs (bps) in nucleic acid sequences is a major goal for the use of DNA as a cellular receptors for therapeutics and biotechnology applications, as well as for the development of gene‐specific probes . Such compounds, for example, are being designed as transcription‐factor inhibitors that bind to a DNA promoter sequence rather than by targeting the transcription factor part of the complex . There are almost unlimited numbers of applications of gene specific probes of this type.…”

“…[1][2][3][4][5][6][7][8] Such compounds, for example,a re being designed as transcription-factor inhibitors that bind to aD NA promoter sequence rather than by targeting the transcription factor part of the complex. [9][10][11][12][13][14] Therea re almostu nlimited numberso fa pplications of gene specific probeso ft his type. The current lack of av ariety of smallm olecules that can bind strongly and sequence specifically to mixed A·Tand G·Cb ps equences of DNA is, however,abarrier to progress in this field.…”

Biotin-Lys-His Blocks Aggregation of RNA-binding Protein TLS, a Cause of Amyotrophic Lateral Sclerosis

“…Automated polyamide synthesis was performed on a PSSM-8 system (Shimadzu) by Fmoc chemistry [43,44]. HPLC purification was performed with a JASCO PU-2080 Plus pump, a UV-2075 Plus detector (254 nm), an MX-2080-32 mixer and a DG-2080-54 degasser.…”

Sequence-specific DNA binding by long hairpin pyrrole–imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit

“…37,38 A biotinylated hairpin DNA was purchased from JBioS and its sequence is shown in Figure 2a. The biotinylated DNA was immobilized to a streptavidin-functionalized SA sensor chip to obtain the desired immobilization level (approximately 900 RU rise).…”