A possible explanation for the results is that besides binding to the double-stranded region at the junction, XPA may additionally bind only to one ssDNA sequence without preference for either a 3′- or a 5′-ssDNA overhang.
Duplex invasion through an internal PNA-DNA Watson-Crick duplex has also been observed under certain conditions, and if special modified pseudo-complementary bases, such as the diaminopurine thiouracil base pair, are employed in the PNA oligomers, binding to the target by double duplex invasion is possible.
To test the effect of methylation on factors binding to the CRE site, double stranded 24 bp oligomers of the Ins2 promoter CRE site were synthesized and methylated in vitro or mock methylated.
Strikingly, the mutations of the universally conserved aromatic residues exhibited dramatically decreased binding to the heavy chain; the double mutant Y101A/Y103A exhibited decreased binding to the dynein heavy chain, and the binding appeared to be almost entirely disrupted in the triple mutant Y101A/Y103A/W120A.
On the one hand, the LEF/TCF protein family has the capacity to bend DNA after binding to the minor grove of the double helix.
Upon binding to the enzyme, the DNA double helix conformation changes from a twisted state to a partially untwisted state.
The Mre11/Rad50/Xrs2 complex initiates IR repair by binding to the end of a double-strand break, resulting in 5' to 3' exonuclease degradation creating a single-stranded 3' overhang competent for strand invasion into the unbroken chromosome.
Moreover, PI polyamide can inhibit DNA protein interaction by binding to the minor groove of double-helical DNA with high affinity and sequence specificity.
"They span the whole binding sequence: before binding to the DNA, initial binding to the promoter, subsequent binding after it double checks that this is the right place, and the final state," Nogales said.
A dimeric form of N-methoxycarbonyl-2-amino-1,8-naphthyridine (MCND) connected at the C2 position with a three-atom linker was examined for the binding to mismatches in double stranded RNA.
