Binding Site Size

Recall that for a 2 1 polyamide DNA complex a subsef of pairing mles Im//9 or Py//9 pairs can substitute, in certain cases, for Im/Py or Py/Py pairs, respectively [36]. The incorporation of y9-alanine allows a broader set of sequences to be targeted with high affinity. However, the extra flexibility of polyamides containing internal y9-alanines allows both 2 1 and 1 1 hgand DNA stoichiometries in the mi- 

A high-resolution 1 1 solution NMR structure of lmPy-y9-lm-y9-lmPy-y9-Dp elucidated the role of /9-alanine in minor groove recognition (Fig. 3.7 b) [47]. The p residues allow both Im rings in the /9-lm-/9-lm subunit to adapt to the relatively large 

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Fig. 3.6 Polyamide-DNA binding motifs targeting longer DNA sequences. Overlapped and slipped homodimers depending on the sequence context, six-ring polyamides with central p-Ma residues can bind to DNA as fully overlapped homodimers, recognizing 11 bp, or as slipped homodimers, recognizing 13 bp. Extended hairpin extended conformation increases binding site size (to 9 bp) and enhances binding affinity. Cooperative dimer a cooperatively binding hairpin polyamide can...

Kelly, J.J., E.E. Baird, and P.B. Dervan. Binding site size limit of the 2 1 pyrrole-imidazole polyamide-DNA motif. Proc. 

In the presence of DNA reactions (17) and (18) that generate the excited complex directly or indirectly via reaction (19), become much slower or do not take place, and therefore the ECL disappears. This is due to the fact that the Ru(II) and Ru(III) complexes, physically bound to DNA, are protected by the negatively charged phosphate backbone from the reduction by C02. Thus the ECL titration of the metal complex in the presence of DNA has allowed the determination of the equilibrium constant and binding-site size for association of Ru(phen)3 to DNA [82]. 

Tab. 2.5.1. Binding constants and binding-site size of acridizinium bromides 5a and 5b as determined from spectrophotometric titrations with st DNA, (poly[dA-dT -poly[dA-dT ), and (po ly[d G-d C]-po ly[d G -d C]).

Luminescence titrations further demonstrate that the ruthenated duplex behaves as a 15 mer bearing one intercalator (76). As free [Ru(phen)2(dppz)]2+ is added to a solution of unmetallated 15 mer duplex, the luminescence increases linearly until the emission reaches saturation at about three equivalents of ruthenium(II) per duplex, consistent with competitive binding of [Ru(phen)2(dppz)]2+ to the 15-mer duplex and an average binding site size of a little more than four base pairs. When the analogous experiment is conducted with the ruthenated duplex, saturation of luminescence occurs after almost two equivalents of [Ru(phen)2(dppz)]2+ are added. This comparison indicates that the covalently bound ruthenium(II) complex is not displaced by additional intercalators. 

The calcium-dependent C-type lectins include the E-, L- and P-selectins, while the ga-lectins are calcium-independent S-type lectins. The latter have a binding site sized for tight interaction with di- or trisaccharides. The former bind their ligand mainly through co-ordination of two vicinal hydroxyl groups of a single sugar moiety to a bound calcium... 

The DNA-binding affinities of metallo-MPE were obtained with inert metal ions. The affinity constants of Ni -MPE and Mg -MPE are 2.4 X 10 and 1.5 X 10 M, respectively, similar to the affinity constant of ethidium bromide (125). As expected for an intercalator, Mg -MPE unwinds DNA (11 3° per bound molecule), and the binding site size is two base pairs. 

K is the binding affinity, n is the binding site size (in nucleotide bases), and v is the binding density given by... 

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