Synthetic Receptors for CG Base Pairs

Abstract

Hydrogen-bond-mediated complexation of a CG base pair by a hexylureido phthalimide and a hexylureido isoindolin-1-one was studied by (1)H NMR spectroscopy in an organic solvent. Chemical shift data indicate that both receptors effectively bind the CG base pair from the major groove side.

Towards the Sequence‐Selective Recognition of Double‐Stranded DNA Containing Pyrimidine‐Purine Interruptions by Triplex‐Forming Oligonucleotides

“…[19] The capabilities of carbocyclic nucleosides L1 or L2 (Figure 5) as partners for a CG base pair in triplex formation were also evaluated. [20] With the aid of 1 H NMR studies in organic solvent with nucleoside monomers, [22] Zimmerman's group designed a [6-(3-ethylureido)-1-oxoisoindolin-2-yl]methyl nucleobase for a CG base pair. In addition, imidazolo[4,5-h] quinoline nucleobases (e.g., NH 2 Q, Figure 5) or the debutylated analogue (Z) of the nucleobase developed by Zimmerman's group [21] as a receptor for a CG base pair at the nucleoside level showed low affinities with slight preferences for a GC base pair.…”

“…[20] Through quantitative DNase I footprinting analysis, it was concluded that L1 and L2, like D3, acted as intercalators in order to show affinities towards pyrimidine-purine base pairs. [23] However, UV melting experiments indicated that the nucleobase showed little affinity for any base pairs. [20] With the aid of 1 H NMR studies in organic solvent with nucleoside monomers, [22] Zimmerman's group designed a [6-(3-ethylureido)-1-oxoisoindolin-2-yl]methyl nucleobase for a CG base pair.…”

“…In addition, imidazolo[4,5-h] quinoline nucleobases (e.g., NH 2 Q, Figure 5) or the debutylated analogue (Z) of the nucleobase developed by Zimmerman's group [21] as a receptor for a CG base pair at the nucleoside level showed low affinities with slight preferences for a GC base pair. [20] With the aid of 1 H NMR studies in organic solvent with nucleoside monomers, [22] Zimmerman's group designed a [6-(3-ethylureido)-1-oxoisoindolin-2-yl]methyl nucleobase for a CG base pair. [23] However, UV melting experiments indicated that the nucleobase showed little affinity for any base pairs.…”

Nucleobases as supramolecular motifs

“…8) was designed to interact with a CG base pair through two hydrogen bonds with the 4-amino group of C and the 6-carbonyl oxygen of G. 18 NMR titrations measured an association constant of 37 M 21 in CD 2 Cl 2 . A receptor (10) which is also capable of interacting with the CG base pair has been designed by Zimmerman et al 19 10 can interact with the CG base pair through three hydrogen bonds and this extra hydrogen bond results in a much stronger binding interaction (ca. 10 3 M 21 in CDCl 3 ).…”

Unnatural Nucleosides with Unusual Base Pairing Properties

“…For comparison, four compounds that can associate with both bases of a CG base pair through hydrogen bonding in the major groove are illustrated in Figure 1.4.33. The ureido derivatives S.132 (Mertz et al, 2000(Mertz et al, , 2004 and S.134 (Wang et al, 2004), which…”