DNA duplex structures

The choice of metal ion in this work is interesting since it has been known for a considerable time that Ag+ is a rare example of a d-block metal ion that does not disrupt the duplex DNA structure (172,173). Rationalization of this effect has tended to focus on the possible base-pair crosslinking due to the preferred linear coordination geometry of Ag1 ions (174). The importance of Ag+ DNA coordination chemistry to the procedure described is not clear. However, reports that other metal ions, e.g., Pdri (175), can be plated to DNA to fabricate metallic wires (Fig. 51) suggests that this may not be essential. 

The intercalation of polycyclic aromatic compounds into duplex DNA structures was used to develop nucleic acid-based electrochemical sensors.66 For example, the bis-ferrocene-tethered naphthalene diimide (16) was used as a redox-active intercalator to probe DNA hybridization.67 The thiolated probe was assembled on a Au electrode, and the formation of the duplex DNA with the complementary analyte nucleic acid was probed by the intercalation of (16) into the double-stranded nucleic acid structure and by following the voltammetric response of the ferrocene units (Fig. 12.17a). The method enabled the analysis of the target DNA with a sensitivity that corresponded to ca. 1 x 10-20mol. 

A form. A duplex DNA structure with right-handed twisting in which the planes of the base pairs are tilted about 70° with respect to the helix axis. 

Z form. A duplex DNA structure in which the usual type of hydrogen bonding occurs between the base pairs but in which the helix formed by the two polynucleotide chains is left-handed rather than right-handed. 

Modulation of DNA structure and dynamics is also possible using base-pair mismatches. Mismatches exert little influence on the global structure of B-DNA duplexes. Locally, the extent of base stacking perturbation depends sensitively on the nature of the mismatch [139-141]. Therefore, while a CA mismatch introduces a significant distortion in local stacking, the well-stacked GA mismatch is, by many criteria, barely perceptible. The dynamics of mismatched base-pairs may also be significantly distinct from matched Watson-Crick base pairs [9]. We exploit these features of DNA mismatches to probe the sensitivity of DNA-mediated CT to base structure and dynamics. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

Fig. 2 Structures of the anthraquinone-linked sensitizers. AQ is covalently attached to the 5 -end of one strand. UAQ can be placed at any position, and the attached anthraquinone intercalates in duplex DNA at the 3 -side of its linked nucleotide...

From a structural point of view, there are two possible orientations for the externally bound adduct in duplex DNA. They are easiest to discuss for BPDE-N2(g) adduct formation. The first results from an anti - syn rotation of G about its glycosidic bond. The BPDE-N2(G) adduct is transferred to the major groove and the DNA... 

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