Nucleotide base pair stacks

The 7i TC interactions occur in all areas of chemistry and for chemically diverse molecules. The stacking of 7t-delocalized molecules favors cooperative phenomena. such as electron conduction. The n-stacking motifs are key components of the design of molecular materials with ensemble properties. Nucleotide base-pair stacking is fundamental to molecular biology, and aromatic interactions between amino-acid side chains influence protein structure. 

In order to understand the effects of radiation damage to DNA it is necessary to consider larger model systems such as nucleotides, base pairs, and stacked bases. The question then becomes whether or not it is possible to do reliable calculations on such large systems. The literature is full of various attempts to study these complex systems. Some attempts have been more successful than others. 

Computations were performed also for the nucleotide base stacks and base pair stacks.31-34 In the case of the cytosine (C) stack we have investigated the DOS and hopping conductivity as a function of the basis set and correlation corrections (inverse Dyson equation with MP2 self energy see above). In Figure 3 we show how the DOS changes if one uses instead of an STO-3G a... 

TABLE 9.11. Characteristic Quantities of Charge Carrier Transport in Periodic DNA Nucleotide Base and Base Pair Stacks (after Suhai )... 

If a periodic polymer chain has a very narrow bandwidth [like the so-called narrow-band (widths of order 10" eV) periodic nucleotide base stacks or base pair stacks in Table 9.11) or a polymer consists of a nonperiodic sequence of different types of units, then the electronic states become localized molecular states and coherent Bloch-type conduction is no longer possible. 

Due to the central role of DNA and proteins in biochemistry and biophysics the computation of the electronic structure of periodic polymers built from nucleotide bases, base pairs, nucleotides and amino acids, respectively, had been of high interest since about twenty years. Early calculations of the band structure of DNA related periodic polymers have been performed with the crystal orbital (CO) method on the basis of different semiempirical levels (1). Recently the results of ab initio Hartree-Fock CO (2, 3) band structure calculations for the four nucleotide base stacks (4-6), the two Watson-Crick base pair stacks (6), the sugar-phosphate chain (4,5) and the three nucleotides cytidine (4,5), adenylic acid and th3nnidine (6) have been reported. These computations represent a significant progress but the following improvements are required for a more accurate description of the electronic structure of real DNA and its transport properties ... 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

The nucleotide bases are flat molecules. Each base pair is parallel to the one below it, with 340 picometers separating the two. There is a rotation of 36° between pairs, giving ten base pairs per complete turn of the helix. The two sugar-phosphate backbone strands wind around these stacked pairs, as shown in Figure 13-29. The two strands of DNA run in opposite directions, with the terminal phosphate end of one polynucleotide matched with the free hydroxyl end of the other. 

Consequently, the electrochemistry of the Fc marker can be observed, allowing for highly sensitive detection of complementary DNA (cDNA). The presence of single-nucleotide mismatch in the duplex causes, presumably, a blockage of the -conduction pathway through the base stack at the position of the base-pair... 

Among the new RNA structures are those of RNA-antisense RNA pairs in "kissing" hairpin complexes 87,319 Another interesting complex folding pattern in RNA is the pseudoknot, a structural feature that has been identified in many RNA sequences.85,320 327 A pseudoknot can be formed if nucleotide sequences favorable to formation of two short RNA stems are overlapped as shown in Fig. 5-29. After stem 2 in this drawing is formed (step a) additional base pairing can lead to formation of stem 1 (step b). The base pairs of the two stems can stack coaxially to form the pseudoknot (step c). 

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