Increased stability and lifetime of the complex formed between DNA and meta -phenyl-substituted hoechst dyes as studied by fluorescence titrations and stopped-flow kinetics 1 1Edited by I. Tinoco

Rapid Communication Cross-linking of Histone Proteins to DNA by UV Illumination of Chromatin Stained with Hoechst 33342¶

“…The histone absorption leads to absorption ratios A 260 :A 280 and A 260 :A 240 for unstained chromatin that are different from those observed in bare DNA: in our samples, the absorbance ratio A 260 :A 280 is 1.5 (17), and the absorbance ratio A 260 :A 240 is 1.3 (14). We note that the absorption of Hoechst dyes depends on the level of staining (20) and that high concentrations can lead to aggregate formation and different binding motifs (21)(22)(23). In all experiments reported in this study, the maximum staining level is 1 dye per 20 base pairs, as determined by the absorption spectrum.…”

Single‐Molecule Approach to DNA Minor‐Groove Association Dynamics

“…This is in agreement with reported results for the binding of the antibiotic distamycin to sequences with different numbers and positions of mismatched sites. [4] Moreover, the absolute values of k + for the AT sequences coincide well with those reported for other minor-groove binders [4][5][6][7] and show the small decrease with increasing Na + ion concentration expected for groove binders, [20] suggesting they might have analogous association mechanisms. Nevertheless, the dissociation rate constants are about four orders of magnitude higher than those of typical minor-groove binders, resulting in much lower binding constants.…”

“…Dynamic data of archetypical minor-groove binders such as distamycin or Hoechst 33258 indicate that the association process is very fast and nearly diffusion limited, which is surprising given the severe geometric constraints imposed upon the inclusion of a binder into the narrow minor groove. [4][5][6][7] Cationic bisbenzamidines are able to target AT-rich sequences preferentially over those containing GC pairs. Prominent examples of this family of molecules, such as pentamidine or furamidine, have found clinical applications and are used for the treatment of several major tropical diseases.…”

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

“…Recognition is known to be a complex process that may involve several steps before formation of the most stable adduct: both noncovalent (17,19,23) and covalent (16,24) binders may exploit mechanisms like one-dimensional sliding within the MG and translocation among different sites (involving binding and dissociation) (10,25–28). In particular, the importance of dissociation for the selectivity and the affinity of different MG binders has been pointed out by several experimental studies (17,18,23,29,30). Such an experimental effort has not been accompanied yet by a thorough theoretical investigation, which would be certainly fundamental to address the mechanism and the energetics of detachment at a molecular level.…”