The over- and under-expression of certain oligonucleotides can be caused by DNA structural conformations, DNA base stacking energies, codon preference, and protein binding sites including transcription/restriction sites, DNA replication and repair, etc. [ 12- 17].
Mutations at other positions on the α4-helix affect the DNA backbone structure by changing the major groove dimensions, as DNA stacks on the α4-helix (Figure 6B and C).
Binding of a base flipping enzyme, MHhaI, to dsDNA greatly decreased the EC signal of DNA labeled with daunomycin, indicating that this binding disturbed the DNA base stacking.
Besides, a hydrogen bond between amino group of HL and DNA and stacking interactions between the nucleotides of nitrogenous GC bases and C60 fullerene appeared.
We have exploited established rules for DNA helical stacking within three-way helical junctions to design and characterize the properties of deoxyribosensors specific for the amino acid derivative, argininamide.
This is due to the presence of an acridine "backbone" that confers a planar structure to the molecules, allowing them to intercalate into DNA by stacking between base pairs.
In the simulation, the TPT-DNA stacking interactions are fully maintained, as well as the Arg362, Gly363 and Lys374 hydrogen bonds with the DNA intact strand, that are present for the 100% of the simulation time.
Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5′-CpG-3′ sequence.
Taken together, these results suggested that APD interacts with G-quadruplex DNA through end stacking.
