Duplex stability

The quantum yield for the formation of 8-oxodGuo 44 from guanine in relation to the formation of products arising from the oxidation of other nucle-obases may be considered as a marker of charge transfer efficiency. This parameter was therefore used to study the influence of duplex stability on... 

Fig. 4 Effect of DNA duplex stability on the formation of DNA lesions. Samples (75 pg/ ml of calf thymus DNA) were solubilized in pure water. The different conditions were heated (the solution was heated at 100°C prior to irradiation) control (irradiations were performed at room temperature) compacted (irradiations were performed in the presence of 0.1 mM spermidine)...

Douki T, Ravanat J-L, Angelov D, Wagner JR, Cadet J (2004) Effects of Duplex Stability on Charge-Transfer Efficiency within DNA. 236 1-25 Drabowicz J, Mikolajczyk M (2000) Selenium at Higher Oxidation States. 208 143-176 Dutasta J-P (2003) New Phosphorylated Hosts for the Design of New Supramolecular Assemblies. 232 55-91... 

Figure 3.16 Dynamic combinatorial modification of 2 -amino-2-deoxyuridine (U-NH ) containing DNA by aldehydes Ra-Rc. The nalidixic aldehyde was selectively appended to both U-NH positions resulting in DNA duplex stabilization.

Petri S, Dueck A, Lehmann G et al (2011) Increased siRNA duplex stability correlates with reduced off-target and elevated on-target effects. RNA 17 737-749... 

Effects of Duplex Stability on Charge-Transfer Efficiency within DNA... 

One implication of the ability of the database to make reasonable predictions about the thermodynamics of duplex melting is that base sequence, rather than total base composition, determines duplex stability. This conclusion is supported by the observation that the second and third entries in Table 16.6, which involve only A and T, have the same base composition but yield significantly different melting thermodynamics. 

Why would the mole fraction of C and G influence duplex stability (Tm) differently than A and T ... 

Freier, S., Kierzek, R., et al. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83(24), 9373—9377. 

Nakano, S.-I., Fujimoto, M., Hari, H., and Sugimoto, N. (1999). Nucleic acid duplex stability Influence of base composition on cation effects. Nucleic Acids Res. 27, 2957-2965. 

Breslauer KJ, Frank R, Blocker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986 83 3746-3750. 

SantaLucia J, Allawi HT Jr, Seneviratne PA. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996 35 3555-3562. 

The thermal stability of a short DNA duplex can be estimated by the simple 4 + 2 rule each GC pair contributes 4° and each AT pair contributes 2° to the duplex melting temperature in 0.9 M NaCl solution.50 Although more rigorous estimates of duplex stability are possible,51 this simple method is reasonably accurate, and, in any event, we find it useful... 

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... 

SantaLucia, J., Allawi, H.T., Seneviratne, P.A. (1996) Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability, Biochemistry 35, 3555-3562. 

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