Search results
Search for "DNA minor groove" in Full Text gives 6 result(s) in Beilstein Journal of Organic Chemistry.
Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator
Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185
- -DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over
- NDI into ds-DNA. Also, we showed previously that positioning of the GCP-unit into the DNA minor groove resulted in a strong positive ICD band at 300–320 nm [13][18][19]. At pH 7 the CD spectrum of ct-DNA upon titration with compound 4 (Figure 2a) showed significant changes. The intensity of the
- ][18][19]. Thus, all mentioned changes supported binding of the whole molecule of 4 in the DNA minor groove. The saturation of ICD band intensity (Figure 2b) at r = 0.2–0.3 nicely agreed with the obtained value of ratio n[bound 4]/[polynucleotide] from the Scatchard fitting results (Table 2). The
Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides
Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8
- promising strategy to obtain photoswitchable Im/Py hairpin polyamides capable of interacting with the dsDNA minor groove only in the Z-configuration. Keywords: azobenzene; DNA minor groove; N-methylimidazole; N-methylpyrrole; photoswitches; polyamide; Introduction The development of small chemical agents
- was proven amenable for the light-induced triggering of transcription [24], photoswitchable polyamides that can act as selective DNA minor groove binders displaying tunable affinity have not yet been reported [29][30]. We envisaged that control of the geometry and functionality could be achieved upon
- % P1; 67% P2; after 1 d: 76% P3). Analysis of polyamide–DNA interaction by induced circular dichroism CD spectroscopic analysis is suitable for the characterization of DNA minor groove binders, providing semiquantitative information about binding affinity and thermal stability of the target dsDNA [47
An overview of recent advances in duplex DNA recognition by small molecules
Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93
- recognize the minor groove by sufficiently distorting the DNA structures leading to the opening of the minor groove [2]. In addition to the conventional direct and indirect readout mechanism, proteins have also been proposed to recognize the DNA minor groove by sensing variations in the shape and
- particular, we cover the advances made in DNA minor groove recognition using new analogues and derivatives of classical minor groove binders such as distamycin, netropsin, polyamides, bisbenzimidazoles and organic cations. We have also included new intercalating agents as well as major groove binding ligands
- successful class of synthetic DNA (minor groove) binders that can be designed to bind chosen DNA sequences via directed H-bonds, shape complementarity, and can compete with specific protein–DNA binding interactions in the minor or major grooves [67][68]. A variety of sequence-specific Py/Im polyamides were
Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial
Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5
- ligand aggregates binding to polynucleotides (Figure 2). Many naturally occurring small molecules owe different biological activities due to aggregation, for instance, the close analogs netropsin (the single molecule in the DNA minor groove) and distamycin (the dimer in DNA minor groove) [13]. In
- aggregation types which could take place upon DNA/RNA binding. For instance, at an excess of ligand over dominant DNA binding site (minor groove), surplus ligand molecules can form simple dimers within the DNA minor groove [28], which at even higher excesses over DNA can change to different, larger aggregates
Come-back of phenanthridine and phenanthridinium derivatives in the 21st century
Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312
- mutagenic activities) compared with ethidium bromide. A recent study showed that substitution of both ethidium bromide (EB) and exocyclic amines by guanidines converted the classical intercalator (EB) into a DNA minor groove binder [57]. The most intriguingly, binding mode change did not weaken the DNA
- affinity, thus the affinity of guanidine derivative 2 (Figure 2) towards AT-rich DNA sequences was significantly stronger compared to ethidium and comparable to that of the known DNA minor groove binder furamidine. The above mentioned guanidine-induced switch of the DNA- and RNA-binding mode [57] inspired
Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives
Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225
- (EC) ICD band of the AP3 (also AP3am) dimer inside the ds-DNA minor groove. On the other hand, AP3 binds to poly dT as a single molecule (not stacked with other DBTAA) and, therefore, it is lacking the characteristic bisignate ICD band at 350 nm. Interestingly, the negative ICD band at 350 nm is also
- stacked dimers within the DNA minor groove similar to the crystal structure of close analogue (Figure 4, right). Conversely, the AP5 and AP6 aliphatic linkers are long enough to allow self-folding and easy intramolecular π–π stacking of adenine with DBTAA (Figure 4, upper right). During the binding event
- to ds-DNA (AT minor groove) AP5 and AP6 have to combine intramolecular (self-folded) and intermolecular (with DNA) interactions, whereby the best compromise could be the binding of self-folded molecules within a DNA minor groove (see schematic presentation in Figure 5). The reference compound APH has
Other Beilstein-Institut Open Science Activities
