DNA-based molecules

Kneipp K, Kneipp H, Kartha VB, Manoharan R, Deinum G, Itzkan I, Dasari RR, Feld MS (1998) Detection and identification of a single DNA base molecule using surface-enhanced Raman scattering (SERS). Phys Rev E 57 R6281-R6284... 

High-resolution in situ STM as well as phase transition dynamics of nucleobases on Au(lll) and other low-index electrode surfaces supported by infrared spectroscopy have been reviewed recently by Nichols and coworkers [142] and Wandlowski and coworkers [143]. We refer to these reviews for details and note instead another aspect of single-molecule dynamics of DNA-based molecules. The observed electronic conductivity of oligonucleotides of variable length and variable base composition has opened almost a Pandora s box of novel DNA-based electronic properties. These include particularly photochemical and interfacial electrochemical ET. We refer to other recent reviews [144, 145] for this, still far from settled, issue but note the following STM-based studies that illuminate the conductivity issue at the single-molecule level (Figure 2.4). 

The chapter by Hill and Kelley addresses the interfacial electronic conductivity of DNA-based molecules controlled by the electrochemical potential. Binding of redox probes is a probe for electronic communication between the probe and the electrode through the DNA-molecular frame and therefore of the tunneling conductivity of the latter. This remains an intriguing issue as the redox-based electronic energies of the nucleobases are strongly off-rcsonance with the electrode Fermi energy and the redox level of the probe molecule. 

High-energy radical states are also likely to be involved in onedimensional single-molecule (or a few molecules) conductivity of DNA-based molecules in solid state configurations where the molecules are immobilized... 

In comparison, DNA-based molecules functionalized by suitable redox groups display efficient long-range interfacial electrochemical electron (or hole) transmission between the electrode and oligonucleotide-tethered redox groups under mild conditions, i.e. close to reversible electrochemical conditions in aqueous buffers, cf Chapter 5 and below. This remains as one of the puzzles of DNA-based electronic transmission behaviour. 

Charge delocalization and h q)ersensitivity of the conductivity to packing and lateral order may hold other clues to the observed remarkable insensitivity of interfacial ET of DNA-based molecules. Other notions such as columnar aggregation and cationic condensation " can be other crucial factors in these intriguing observations. 

In addition to the fundamental importance of electronic conductivity of molecules as intriguing as DNA and proteins, electronic conductivity of DNA-based molecules holds other perspectives. Charge transfer along the DNA double-strand has been forwarded as an in vivo mechanism for radiation and chemical damage of the DNA-based genetic system, and for... 

The double-strand structure of an oligonucleotide is shown schematically in Fig. 6-1. Anticipating discussion in later Sections, the molecule is shown in a upright orientation attached to an atomically planar metallic electrode surface (Au(lll), cf below) by chemisorption via a hexamethylenethiol group. Fig. 6-1 shows the four nucleobases presently in focus. We discuss first concepts and formalism of electron and hole transport of DNA-based molecules in homogeneous solution and at electrochemical interfaces. We then focus on DNA-based molecules in electrochemical nanogaps and STM in electrochemical environments in situ STM). Some case examples illustrate accordance and limitations of current theoretical views of DNA-conductivity. This adds to the comprehensive overview of interfacial electrochemical ET of DNA-based molecules by O Kelly and Hill in Chapter 5. 

Concepts and formalism of interfacial ET of DNA-based molecules at electrochemical interfaces and in nanogap systems rest on data and theory of... 

A Primer of Electron and Hole Transfer Formalism for DNA-Based Molecules... 

Excess charge hopping has been formalized by Bixon and Jortner, and later by Ratner and others.We provide elements of such a formalism in Section 5, explicitly in the novel context where DNA-based molecules are immobilized in well-defined configurations between enclosing electrochemical in situ STM substrate and tip electrodes or similarly... 

The photo-induced charge conduction mechanism in double-strand guanine-rich DNA-based molecules, and AT pairs attenuating the conductivity by off-resonance superexchange steps is broadly supported. Mechanistic mapping has been based on both direct charge transfer kinetics in the nano-, pico- and femtosecond ranges... 

INTERFACIAL ELECTROCHEMICAL ELECTRON TRANSFER THROUGH DNA-BASED MOLECULES... 

Interfacial electrochemistry and electronic conductivity of double-strand oligonucleotides is discussed in detail in Chapter 5. The overview below summarizes some additional observations of interfacial electrochemical adsorption, organization, and charge transfer, of importance to approaches towards single-molecule electrochemical conductivity and in situ STM of DNA-based molecules to follow in Sections 4 and 5. 

Interfacial electrochemical ET between metallic electrodes and redox molecules through variable-length and variable-composition DNA-based molecules has disclosed important information about the molecular conduction mechanisms, based on monolayers of molecular thickness but averaged over two-dimensional macroscopic assemblies. Important conclusions are that the molecular contact can be a controlling factor and that the conductivity is hypersensitive to base pair order and stacking. The conductivity is effectively turned off when base pair mismatches or kinks invoked by external molecular structure-modifier binding (say cis-platinum ). This view carries over in part to DNA-based conductivity at the single-molecule level but here some other modification is needed. 

Conductivity of Pure and Redox-Modified DNA-Based Molecules in Dense Monolayers... 

DNA-based molecules in their natural enviromnent. We offer briefly in Section 5 some further concepts and implications of such observations. 

The hopping conductivity scheme above represents formally the data for in situ STM imaging and up to a point single-molecule conductivity of DNA-based molecules as observed. The issues of the energetics and the nature of the charge (electron or hope) transmitting states are, however, left open. 

Once a note of caution is expressed, novel DNA-based molecular design and architectures have, however, reached levels where the emerging supramolecular structures can perhaps become robust to different electronically working environments. Redox- and fluorophor-labeled molecules offer steps towards device-like function where both structural organization and, as noted, additional sophisticated electronic function can be added to the DNA-based molecules. " " " New electronic conductivity mechanisms based on hopping via a chain of well-defined redox probes bound in the DNA-backbone were noted above." Such... 

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