Computational biochemistry ferenc Bogár György Ferency
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| 4. DNA and PNA Structures
The primary structure of a linear sequence of nucleotides linked with phoshodiester bonds. The nucleic acid sequence is the primary structure (Figure 1.10.). The secondary structure depends on the H-bonds and stacking interactions between the basis (Figure 1.11.). The two rings in adenine and the 5-membered ring in guanine is aromatic. Neither cytosine and thymine are aromatic (http://en.wikipedia.org/wiki/Nucleic_acid_structure). The tertiary structure can be in DNA’s double helix B-DNA, A-DNA and Z-DNA. The quatarnary structure of DNA is similar to that of protein: the interactions with proteins and other DNAs (Figure 1.12. and 1.13.). PNAs were developed int he early 90s. In DNA, RNA the backbone is sensitive to pH because of the charged phosphate backbone. In PNA the backbone was changed to a neutral, geometrically almost the same backbone. This bacbone is not sensitive to pH. It is a good possibility to develope DNA-chips to recognize the basis in DNA. It is also a good possibility for the personal therepeautic procedure (see e.g. Figure 1.15.). 
Figure 1.10. The nucleinbasis, deoxyriboze-nucleosides, deoxyriboze-nucleotides (A, G, C, T, U basis. 
Figure 1.11. The Watson-Crick duplexes with H-bonds of AMP::TMP and GMP::CMP 
Figure 1.12. Sequence of duplex DNA (PDB Id.: 2m2c) 
Figure 1.13. Animation of duplex DNA Chain A: (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP* TP*AP*CP*GP*CP*G)-3'); Chain B: (5'-D(*CP*GP*CP*GP*TP*AP*GP*CP*AP*TP* GP*CP*GP*C)-3'). (blue: G,C, red:A, T) (PDB Id.: 2m2c, NMR structure) 
Figure 1.14. The sequence of triplex DNA and its junction with a duplex DNA (XRD result) (PDB Id.: 1d3r) 
Figure 1.15. The animation of triplex DNA and its junction with a duplex DNA (blue: G, C, red:A, T) (XRD result) (PDB Id.: 1d3r) 
Figure 1.16. The sequence of PNA duplexes (Hexamer, Chains A, B, C, D, E, F, G, H) (XRD result) (PDB Id.: 1qpy) 
Figure 1.17. The animation of PNA duplex (Chain A and B) without H-atoms (Double stranded helix, P-form, right and left handed helix) (XRD result) (PDB Id.: 1qpy) 
Figure 1.18. The sequence of hairpin PNA/DNA triplex (XRD result) (PDB Id.: 1pnn) The H-bonds based on Watson-Crick and Hoogsten type interactions. 
Figure 1.19. The animation of PNA/DNA triplex without H-atoms (blue: G, red:A) (XRD result) (PDB Id.: 1pnn)
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