Polyanion backbone

FIGURE 4.3 The repeating charges in the backbone force interstrand interactions away from the backbone, causing the strands to make contact at the Watson-Crick edge of the heterocycles. Without the polyanionic backbone, interstrand contacts can be anywhere. X is H in DNA and OH in RNA. 

In DNA, the polyanionic backbone dominates the physical properties of DNA. Replacing one nucleobase with another, therefore, has only a second-order effect on the physical behavior of the molecule. That allows nucleobases to be replaced during Darwinian evolution without losing properties essential for replication. Therefore, a repeating charge may be a universal structural feature of any genetic molecule that supports Darwinian evolution in water. Polycationic backbones may be as satisfactory as polyanionic backbones, however. Thus, if NASA missions detect life in water on other planets, its genetic system is likely to be based on polyanionic or polycationic backbones even if its nucleobases differ from those found on Earth. That structural feature can be easily detected with simple analytical devices. 

Evidence supporting this theory first came from Tom Cech and Sidney Altman s groups, which showed that extant RNAs can function as enzymes, termed ribozymes [8, 9]. Both synthetic and naturally-occurring ribozymes have been shown to make (ligate) and break phosphodiester bonds (the polyanionic backbone of nucleic acids) [10-12], and a derivative of the Class I ligase ribozyme [13] can polymerize up to 95 nucleotides on an RNA primer [14], In addition, RNAs can fold into structures that bind to specific targets. Such RNAs are known as aptamers (from the Latin aptus, meaning to fit ). Many people believe that RNA should be able to direct its own replication. 

As with other analytical platforms, there are some drawbacks associated with the use of MALDI-TOF MS for DNA analysis. Nucleic acids are susceptible to adduct formation and fragmentation. Their negatively charged backbone makes them behave as polyanions in aqueous solutions. In the presence of cations they tend to form adducts. Most enzymes used in biochemical assays require cations as co-factors, and the predominant ones are sodium (23 Da), magnesium (24 Da), and potassium (39 Da). For example, a sodium ion would add 22 Da to the mass of the analyte, since it would replace a proton (1 Da). Therefore, if adducts are not removed prior to analysis, a distribution of several signals may be obtained, resulting in lower... 

Irrespective of its biological function, the DNA double helix may be described as a prototype 7r-stacked column and therefore a novel medium through which to examine electron-transfer reactions. The double helix is a polymer containing a relatively rigid, electronically coupled column of stacked base pairs within a water-soluble polyanion, the sugar-phosphate backbone. The electronic coupling within the column is reflected in the extensive hypochromicity of the stacked double helix compared to the random coil, and it is this stacking interaction that accounts substantially for the stabilization of the helical form (23). 

The new ternary compound SrMgSi2 shows a considerable disproportionation of the silicon atoms into terminal (lb)Si , bridging (2b)Si, and branching (3b)Si" species (Fig. 2b, [31]). As shown in figure 2b the whole polyanion contains a one dimensional planar chain of silicon atoms with syndiotactically arranged side chains [Si(Si3)] . The Si-Si distances vary somewhat between 235 and 249 pm, with the shortest distances between the side chain bridging atoms and those of the main backbone. 

---