Small Sequence‐Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove

Abstract

A series of small diamidines with thiophene and modified N‐alkylbenzimidazole σ‐hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N‐alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3‐amino‐4‐(alkyl‐ or phenyl‐amino) benzonitriles. The final diamidines were synthesized using lithium bis‐trimethylsilylamide (LiN[Si(CH3)3]2) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor‐SPR, fluorescence spectroscopy, DNA thermal melting, ESI‐MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor‐SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.

Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders

“…Intriguingly, extensive medicinal chemistry efforts over the past decades have produced a plethora of high-affinity MGBs with varying specificity profiles that can be explored in future studies. 69,73 Here, the use of combinations of MGBs matching the sequence space of a given DNA-VLP is conceivable. Our initial investigations combining 5 with MGBs 1, 3, or 4 did not result in improved half-lives in 10% MS (Figure S11).…”

“…DNase I preferentially cleaves double-stranded DNA (dsDNA) over ssDNA, with a preference for AT tracts. , Because the endonuclease binds dsDNA via the minor groove, minor groove binders (MGBs) have been previously explored to modulate DNase I-dependent degradation of dsDNA and are commonly used in DNase I footprinting assays. , Three major classes of MGBs have been described: diamidines, benzimidazoles, and pyrrole-imidazole polyamides . MGBs typically display preferential binding to AT tracts, yet their specificity and affinity are readily tunable. − Platin-based phosphate clamps (PCs, hereafter also termed MGBs) interact with the phosphate backbone but have also been shown to restrict access to the minor groove of dsDNA and thereby modulate DNase I activity. − While binding of MGBs to DNA origami has been characterized previously, protection against endonucleases was not evaluated . Upon cellular uptake, DNA-VLPs additionally encounter the intracellular endonuclease DNase II. , Endolysosomal degradation of DNA-based materials is of particular importance for gene therapeutic delivery and has been studied by fluorescence microscopy. , In contrast to DNase I, the dsDNA binding mode of DNase II has not been elucidated, and it remains unknown whether MGBs inhibit its activity …”

Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove

“…The first step in this project involved the design and synthesis of a broad array of heterocyclic diamidines that could recognize a single G·C bp in an AT context ,, (Figure S1). This effort produced several compounds that were selective for the PU.1 promoter target sequence.…”

“…In cases like PU.1, targeting the promoter sequence rather than the transcription factor seems more effective, and our first paper to show this idea in a biological context involved treatment of AML. 39 The first step in this project involved the design and synthesis of a broad array of heterocyclic diamidines that could recognize a single G•C bp in an AT context 7,9,59 (Figure S1). This effort produced several compounds that were selective for the PU.1 promoter target sequence.…”

Facile synthesis of benzobisimidazole and bibenzimidazole‐based bisnitriles as potential precursors for DNA minor groove binders

“…[7][8][9][10][11][12][13] Expanding the DNA sequence recognition ability of DNA minor groove binding diamidines to bind both AT and GC base pairs could also expand their therapeutic targets and have an impact on many indications, such as modulation of transcription factors biological activity. [14,15] Our group has considerable success in the design of mixed sequence binding compounds through making Nalkylbenzimidazole thiophenes which are preorganized to fit the shape of the DNA minor groove and H-bond to the NH of GC base pairs that projects into the minor groove [16][17][18][19][20] (Figure 1). In continuation of our effort to synthesize compounds that can specifically recognize GC base pairs, we report here the facile synthesis of new Nalkyl-benzobisimidazole and N-alkyl-bibenzimidazolebased bisnitrile intermediates to be used in a different investigation to synthesize benzimidazole diamidines that can be used in our drug discovery projects.…”