Nucleotide base stacks

Ladik, J., A. Sutjianto, and P. Otto. 1991. Improved Band Structures of Some Homopolypeptides with Aliphatic Side Chains and of the Four Nucleotide Base Stacks Estimation of Their Fundamental Gap. J. Mol. Struct. (Theochem) 228, 271-276. 

Table 9 Limits and widths of the valence and conduction bands of the four nucleotide base stacks (in eV). For comparison the table also contains the locations of the corresponding MOs... 

Finally, we point out that CT from the sugar-phosphate (SP) unit to the cytosine (C) molecule cannot be explained by the naive HOMO (D)-LEMO (A) picture, because the valence band of polySP (see Table 10) lies below the valence band of polyC by about 0.8 eV. The same is true if one compares the upper limits of the valence bands of the three other nucleotide base stacks (see Table 9) with the upper limits of the valence band of polySP. 

Application to Proteins and Nucleotide Base Stacks. - The NFC method described above (in its matrix block form17,18) has been applied for different proteins and nucleotide base stacks. In these calculations the DOSs of active and inactive pig insulin24,25 were first computed. 

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... 

Figure 3 The DOS of a single aperiodic nucleotide base stack using (a) a STO-3G basis, (b) a 6-31G basis and (c) 6-31G + MP2...

In this section we should like to point out the possibility of two different kinds of solitons (non-linear quasi particles) in a nucleotide base stack. They quite probably play an important role in long-range effects of chemical carcinogens and direct hits of ionizing radiations along a DNA double helix. In this way they may play an important role in the activation of oncogenes or in the inactivation of antioncogenes. 

Figure 5 Binding of a bulky carcinogen to a nucleotide base stack (1) causes a geometrical distortion of the stack and (2) the electron-electron interaction in the stack (indicated by overlapping ellipsoids) will be changed also. Therefore, two effects occur simultaneously (non-linearity)...

Figure 8 Formation of a solitary wave in a nucleotide base stack by the simultaneous effect of the increased perimeter of the excited molecule (zig-zag line) and of the changed electron-electron interaction of the excited molecule with its neighbor (shaded orbital lobes)...

The second chapter examines applications of crystal-orbital theory presented earlier. These applications include polymers widely used in the production of plastics, primarily polyethylene and its fluorine derivatives. Other examples are from the field of highly conducting polymers, such as the different polyacetylenes, (SN) , and TCNQ and TTF stacks. Applications to nucleotide base stacks and to periodic polynucleotides and periodic polypeptides conclude this part of the book. 

Results (1.65) and (1.66) enable the ab initio SCF LCAO CO program for linear chains to be modified and hence applicable also in the case of a combined symmetry operation. This modified program has been applied for the nucleotide base stacks (see Section 2.3 in the next chapter). 

TABLE 2.6. Limits and Widths of the Highest Filled and Lowest Unfilled Bands of the Four Nucleotide Base Stacks (in eV ... 

If the gap of the nucleotide base stacks is really about 5 eV, the question of whether periodic (homo)polynucleotides could become intrinsic conductors because of the 0.2e charge shift between the sugar and base molecules seems to be legitimate, and will only be answered through even more accurate computations than are now possible. 

Periodic single-stranded DNA helices have been represented by the four homopoly (nucleotide bases stacks), with either cytosine, thymine. 

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. 

In Section 6 a larger number of applications will be presented for different polyacetylenes, for polyethylenes and different halogenated polyethylenes, for different homopolypeptides (where in the polypeptide chain always one amino acid is repeated), for polyparaphenylene (PPP) and polyperinaph-thalene, and for the four nucleotide base stacks. 

In a very recent calculation we have computed the QP band structure of the four nucleotide base stacks using the geometry of DNA S and that of the bases." dementi s... 

It should be pointed out here that in the case of polymers with a larger molecule as unit cell (like TCNQ and TTF stacks, nucleotide base stacks or homopolypeptides with a larger amino acid residue as unit cell) it is necessary to localize further the WF s or Bloch orbitals into different parts of the molecule which is repeated in the periodic polymer. For that purpose one has to investigate how is possible to combine the Fourier transformation leading to WF s with the usual localization... 

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