Characteristic length scale of electric transport properties of genomes

A tight-binding model together with a statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation parameter $\Omega$ is defined to analyze the relation. For some particular propagation length $w_{\mathit{max}}$, the transport behaviors of the coding and noncoding sequences are very different and the correlation reaches its maximal value ${\Omega }_{\mathit{max}}$. $w_{\mathit{max}}$ and ${\Omega }_{\mathit{max}}$ are characteristic values for each species. A possible reason for the difference between the features of transport properties in the coding and noncoding regions is the mechanism of DNA damage repair processes together with natural selection.

Figure 1

$T_w^{\mathit{av}}$ for Y3 with $t_{\mathit{DNA}}=1.0$ (full circles), 0.9 (open circles), 0.8 (full triangles), 0.7 (open triangles), 0.6 (full squares), 0.5 (open squares), and 0.4 (diamonds). Solid, dotted, dashed, and dash-dotted lines are for a random sequence R3 with $t_{\mathit{DNA}}=1.0$, 0.9, 0.8, and 0.4, respectively. The error bars are smaller than the size of the symbols. (Inset) Localization length $w_0$ of Y3 (full circles) and R3 (open circles) for each $t_{\mathit{DNA}}$ (see text).

Figure 2

Comparison of ${\overline{T}}_{240}\left(i\right)$ (line, $t_{\mathit{DNA}}=1$) and the coding regions (shaded area) of the range from the 5000th to the 30 000th nucleotide of Y3. (Inset) Enlarged plot from the 22 000th to the 24 000th nucleotide.

Figure 3

$\Omega \left(w\right)$ for $t_{\mathit{DNA}}∕t_0=1.0$ (circles), 0.8 (triangles), 0.6 (squares), and 0.4 (diamonds) of Y3. (Inset) ${\Omega }_{\mathit{max}}$ (full circles) and $w_{\mathit{max}}$ (open circles) as functions of $t_{\mathit{DNA}}$.

Figure 4

(Color online) $\Omega \left(w\right)$ for several genomes: chromosomes III (full circles), VIII (open circles), and X (full triangles) of yeast, Ureaplasma parvum serovar 3 str. ATCC 700970 (full diamonds), Acinetobacter sp. ADP1 (full squares), Deinococcus radiodurans R1 chromosome II (open triangles), and Chlamydia trachomatis D/UW-3/CX (open squares). Red circles with error bars are averaged $\Omega \left(w\right)$ for R3, ten randomized sequences of yeast chromosome III (see text). (Inset) Comparison of $\Omega \left(w\right)$ for Y3 and the ten R3’s.