Narrow Results

The mechanism of DNA damage caused by the isomerization of purine base is studied with density functional theory calculations at the B3LYP/6-311+G(d,p) level. The transition states of all the isomerizations are obtained, and the intrinsic reaction coordinate (IRC) analyses are performed to identify these transition states further. The isomerizations of purine bases can be classified into two types. The first is the hydrogen transfer between atoms, whose transition state includes a four-member ring. The second is the bond N–H rotation about the double bond N=C, and the plane CNH is perpendicular to the molecular plane in its transition state. The hydrogen transfer has higher reaction potential barrier, larger tunnel effect, and smaller equilibrium constant and rate constant than that of the N–H rotation. Effects of the hydration are considered in the framework of the polarizable continuum model (PCM) in SCRF method at the B3LYP/6-311+G(d,p) level. The isomerizations which result in the configuration changes of purine base and bring directly the DNA damage are endothermic and thermodynamic nonspontaneous processes. The probability of DNA damage caused by the guanine isomerization is larger than that by adenine.

The G3MP2B3 and P3 methods have been used to calculate the adiabatic and vertical ionization potentials (IPs) of the eight most stable tautomers of guanine. The calculated energy discrepancy between adiabatic and vertical IPs are in good agreement with the changes in geometry from neutral ground state to stable cation radicals. The geometries of imino-oxo form tautomers have no obvious change in the ionization process, which results in less energy discrepancy between vertical and adiabatic IPs. In the ionization process, the geometries of the amino-oxo and amino-hydroxy form tautomers change from nonplanar to planar structures. Hence the amino-oxo and amino-hydroxy form tautomers have larger energy discrepancy between vertical and adiabatic IPs. Further studies on the interconversion of the cation radicals shed further light on the transition process between the cation radicals and the main pathways are the hydrogen migrations and internal rotations of hydroxy (OH) and imino (NH) groups. The barriers of hydrogen rotations are lower than those of hydrogen migrations. Furthermore, the barriers for the hydrogen migrations between two rings are higher, which are about 3.0 eV.

The interaction of the free nucleic acid bases adenine, cytosine, and thymidine with meso-tri(4-sulfonatophenyl) meso 4-phenyl porphyrin cytosine amide (TPSC) trisodium salt at pH 5.9, 7.4, and 9.3 results is a decrease in the absorbance of the Soret (B-band) at 413 nm of TPSC. A decrease in Soret band absorbance is observed with guanine below pH 8; at higher pH values a new absorbance band at 424 nm is observed. The appearance of the band is consistent with hydrogen bonding between the cytosine-functionalized porphyrin and guanine and the resulting perturbation of the electron orbitals of the porphyrin.

Nature offers an astonishing array of complex structures and functional devices. The most sophisticated examples of functional systems with multiple interconnected nano-scale components can be found in biology. Biology uses a limited number of building blocks to create complexity and to extend the size and the functional range of basic nano-scale structures to new domains. Three main groups of molecular tools used by biology include oligonucleotides (linear chains of nucleotides), proteins (folded chains of amino acids), and polysaccharides (chains of sugar molecules). Nature uses these tools to store information, to create structures, and to build nano-scale machines.

Recent advances in understanding the structure and function of these building blocks has enabled a number of novel uses for them outside the biological domain. Of particular interest to us is the use of these building blocks to self-assemble nano-scale electronic, photonics, or nanomechanical systems. In this chapter we will look at two groups of building blocks (oligonucleotides and proteins) and review how they have been used to self-assemble engineered structures and build functional devices in the nano-scale.

We will begin by a review of the basic structure and properties (both physical and chemical) of oligonucleotides and proteins. This section is meant to be used as a self-contained reference for the readers from the engineering community that may be less familiar with the symbols and jargon of biochemistry. The most salient properties of the biomolecules are emphasized and listed here to facilitate future research in the area. We continue by a review of recent advances in designing artificial nano-scale DNA structures that can be constructed entirely via engineered self-assembly. Rapid advances in the design and construction of self-assembled DNA structures has resulted in an impressive level of understanding and control over this type of nano-scale manufacturing. Polypeptides and proteins are decidedly less understood and their use in engineered self-assembly has been relatively limited. Nevertheless, as we discuss in the concluding sections of the chapter, both genetically engineered polypeptides and proteins can be used to guide self-assembly processes in nano-scale and help in interfacing nano-scale objects with micron-scale components and templates.