Backbone nucleic acids

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

This approach was the first application of non-enediyne carbon centered radical mediated DNA cleavage agents that were not only capable of binding to DNA but could also be sequence specific. Further work is still needed to elucidate and confirm the sites of cleavage, nature of binding of these molecules and the mechanism of hydrogen abstraction from the nucleic acid backbone. 

The above potential energy method provides a convenient way to identify directly those conformations of the nucleic acid backbone and base that can participate in double helix formation. 

Figure 2.5. Catalytic RNA. (A) The base-pairing pattern of a "hammerhead" ribozyme and its substrate. (B) The folded conformation of the complex. The ribozyme cleaves the bond at the cleavage site. The paths of the nucleic acid backbones are highlighted in red and blue. 

Figure 38 Peptide nucleic acid backbones (a) glycine-ethylenediamine, (b) / -alanine-ethylenediamine and (c) glycine-propylene diamine. All have bases (B) linked by acetyl groups, except for (d) which has a propionyl linker...

Both mechanical means and transfection reagents, among others, have been used to facilitate the cellular uptake of oligonucleotides. The application of intraluminal pressure enhances the uptake of particular oligonucleotides in vascular tissues such as carotid arteries or venous bypass grafts [14, 15]. Other approaches use chemical modifications in order to secondarily modify the nucleic acid backbone [16, 17]. In general, these modifications increase uptake through the cell membrane based on the classical receptor-mediated endocytosis pathway. However, once inside the cell, most nucleic acid compounds taken up by endocytosis are ultimately trapped in the lysosomal compartment... 

A11 Tni values have been measured in phosphate buffer unless otherwise noted. If present during measurement, transition metal ions are specihed in parentheses. Ligands are shown including the linkers used to connect them to the nucleic acid backbone (e.g., the Cl of DNA and C8 of PNA) (see Fig. 4 for atom numbering information). Concentration is of duplex. 

The Conformation of the Nucleic Acid Backbone. The saturated six-mem-bered ring is conformationally more rigid and clearly defined than the corresponding five-membered ring. This is also true for nucleic acid analogs in... 

Figure 11.5 The structure of ACGT, a tetranucleotide segment of DNA. The nucleic acid backbone is in color. 

Nucleic acid (Introduction) Nucleic acid backbone (11.2) Nucleotide (11.1)... 

Hydrolysis of the phosphodiester hnkage would break the nucleic acid backbone and allow the removal of intron segments. Esterification (ester formation) of the 5 — PO/ group of one exon segment to the 3 —OH group of another exon segment would be used to join exons. 

Fig. 24. Biomesogenic backbone geometries providing structural prerequisites for dynamic order-disorder patterns (left to right and top to bottom) phospholipid and helical protein, nucleic acid strand and protein helix, protein-nucleic acid backbone interplays, presumably engaged in the induction of in terferon. ...

---