The upper band has a mobility of approximately 68 kDa corresponding to M.SssI (42 kDa) bound to the duplex (26 kDa).
Yokochi et al. [50] have already performed gel shift analysis with hDNMT1 and mDNMT3a on 21 pb long duplexes, revealing multiple protein-DNA complexes, with 1, 2, 3 or 4 proteins bound to the duplex.
At higher concentration of either RAD52 or RAD52Y104pCMF, we observed decrease in EFRET, which is likely due to the stretching of dsDNA by multiple RAD52 rings bound to the duplex or the ends that are not completely paired.
A single molecule of bleomycin can also produce dsbs via a mechanism in which the iron-containing antibiotic is reactivated following oxidation of one DNA strand while it remains bound to the duplex.
Genetic epistasis data suggest that some aspect of MRX/Tel1 function is directly inhibited in cis by the action of Rap1/Rif complexes bound to the duplex portion of the TG repeat tracts (Craven and Petes, 1999; Ray and Runge, 1999; Chan et al, 2001).
Furthermore, cellular RNases are able to bind to the DNA RNA duplex and hydrolyze the mRNA, resulting in increased mRNA transcript degradation [12], [13], [14].
In this case, however, N was close to 0.5, suggesting that two copies of PhoP could bind to the DNA duplex.
(ii) We have shown that both prokaryotic and mammalian DNMTs bind to the three duplexes by non denaturing gel analysis.
Close inspection of the data reveals that while IHF binds to the nonspecific duplex (R3, black) in a monotonic manner, the binding curve for the specific duplex (I1, red) appears to be biphasic.
These experimentally resolved values are in good agreement with hydrodynamic modeling of both the specific complex (ssp = 2.36 S, based on the IHF·DNA crystal structure) and nonspecific complex [ sns = 3.52 S, based on a structural model of IHF bound to the R3 duplex (Table 1)].
