Polymorphic pair thermodynamic stability

Properties such as thermodynamic values, sequence asymmetry, and polymorphisms that contribute to RNA duplex stability are taken into account by these databases (Pei and Tuschl 2006). In addition, artificial neural networks have been utilized to train algorithms based on the analysis of randomly selected siRNAs (Huesken et al. 2005). These programs siphon significant trends from large sets of RNA sequences whose efficacies are known and validated. Certain base pair (bp) positions have a tendency to possess distinct nucleotides (Figure 9.2). In effective nucleotides, position 1 is preferentially an adenosine (A) or uracil (U), and many strands are enriched with these nucleotides along the first 6 to 7 bps of sequence (Pei and Tuschl 2006). The conserved RISC cleavage site at nucleotide position 10 favors an adenosine, which may be important, while other nucleotides are... 

Similar data obtained for other pairs of polymorphic modifications are presented in Fig. 5.13. The thermodynamic data and enantiotropic or monotropic relationship between modifications are given in Table 5.2, summarizing the relative stability of the phases from room temperature to the melting points (save the difficult to obtain ORP form). 

Stability of polymorphs in general. As noted in Section 2.2.2 the relative stability of polymorphs depends on the free energy (AG = AH — TAS) between them. The relative importance of the two terms on the right can be measured by the ratio between them (say TAS/AH). As seen in Fig. 2.5 at absolute zero T = 0, AG = AH and TAS/AH = 0. At a transition temperature between two polymorphic phases, AG = 0 so the ratio TAS/AH = 1. Above a transition temperature this ratio will be > 1. Applied to some of the polymorphs of 5-Xn, for example, for the pair Y-R at the melting point of R the ratio is 0.85, which means that while Y is the more stable form at that temperature, the entropy is an important contributor to the free energy. Other similar comparisons based on the data in Table 5.2 strengthen the notion of the importance of entropy in the consideration of thermodynamic relationships among polymorphs. 

This Structural feature has been shown to be a necessary condition for electrical conductivity in these materials, although the mixed mode of stacking is generally considered to be the thermodynamically preferred one (Shaik 1982). Proof of the relative stability of the mixed and segregated stack motifs, and a recipe for obtaining crystals of the latter, came with the discovery of a pair of polymorphic 1 1 complexes of 6-II with 6-III (Bechgaard etal. 1977 Kistenmacher etal. 1982). The red, transparent, mixed-stack form of the complex is a semiconductor, while the black, opaque structure with segregated stacks is a conductor (Fig. 6.2). 

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