Nucleic Acids in Chemistry and Biology

two or more six-membered rings that form a platform of approximately the same size as a DNA base pair. Intercalators are an impo ...

Reversible Small Molecule–Nucleic Acid Interactions 349 Figure 9.4 Structures of some DNA-intercalating compounds Figure 9.5 Two ...

separatedby approximately 3.4Å(the van der Waals thickness of a phenyl ring) to accommodate the lig- and. This base pair separat ...

9.6.2.1 Structure. The first X-ray crystal structure of a monointercalator–DNA complex was obtained by Wang and Rich in 1987 for ...

9.6.2.2 Thermodynamics of Daunomycin: DNA Interactions. The details of the energetics of anthracycline–DNA interactions have bee ...

interactions are equivalent, with only subtle differences in hydration and ion binding. However, adri- amycin has a binding affi ...

all sites, i.e.any sequence dependence for drug binding is ignored, and nthe binding site size, i.e.the number of base pairs occ ...

Ghydby using algorithms derived from semi-empirical relationships based on heats of solvent transfer of small molecules and prot ...

bind at adjacent base pair sites in violation of neighbour exclusion, whereas molecules with longer linkers would bind with at l ...

a distortion is not possible in the sequence used for NMR under those specific solution conditions, then the disparity between N ...

because the bisintercalator imposes a greater amount of rigidity in the DNA helix compared to dauno- mycin. There is considerabl ...

substituent groups must be threaded through the base pair stack to the opposite side of the helix. This more complicated binding ...

same direction in the intercalation complex and they overlap the G C base pair in the binding site. The nogalamycin–DNA contacts ...

(1) the polar side chain must go from aqueous solvent through the hydrophobic region in between two adja- cent base pairs, (2) t ...

pyrrole–amidine antibiotics(Figure 9.13) that have antibacterial and antiviral activity, presumably as a result of their interac ...

grooveand forms van der Waals contacts with the atoms of DNA that constitute the sugar–phosphate walls of the groove. These cont ...

complex is that it requires the minor groove to widen two-fold compared to drug-free DNA or to the 1:1 com- plex (Figure 9.14). ...

of aromatic rings is pyrrole–pyrrole (PyPy) for netropsin and pyrrole–pyrrole–pyrrole (PyPyPy) for dis- tamycin. Dickerson and L ...

sequence of the type 5 -XGXCX, (again X can be either A or T). An NMR structure of the complex showed that ImPyPy binds as an an ...

9.7.5.1 Structures of Hoechst 33258–DNA Complexes. Hoechst 33258–DNA structures are extremely well studied. NMR analysis has rev ...