DNA, duplex, stabilization

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)...

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.

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. 

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

Figure 2.11 Proposed scheme of the fidelity- and affinityenhancing modulators of DNA duplex stability by trimethoxystilbene[77]. (Reproduced with permission.)...

The wealth of experimental thermodynamic data has been used to develop a powerful predictive capacity. As early as 1986, Breslauer [9] illustrated a useful empirical method to predict DNA duplex stability based on nearest-neighbor interactions in the base sequence. AH and AS of all 10 possible nearest-neighbor interactions were extrapolated from a small library of 28 DNA duplexes. The overall AW and AS " of DNA duplex formation could be predicted from the sum of the appropriate empirical values. This rough but robust method has been verified and further refined by more and more available databases of DNA thermodynamics [10,11]. The predictive power of this empirical methodology is a powerful tool for those interested in using DNA in supramolecular (or other) applications for which specific thermodynamics are an important criterion. 

Venkiteswaran S, Vijayanathan V, Shirahata A, Thomas T, Thranas TJ (2005) Antisense recognition of the HER-2 mRNA effects of phosphorothioate substitution and polyamines on DNA-RNA, RNA-RNA, and DNA-DNA duplex stability. Biochemistry 44 303-312... 

Moreira, B. G. You, Y BehIke, M. A. Owczarzy, R. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun. 2005, 327, 473-484. 

Lawrence, D. P., Wenqiao, C, Zon, G, Stec, W. J., Uznanski, B, and Broido, M. J, (1987) NMR studies of backbone-alkylated DNA. Duplex stability, absolute stereochemistry, and chemical shift anomalies of prototypal isopropyl phospho-triester modified octanucleotides, (Rp Rp)—and (Sp,SpHd-[GGA(iPr)ATTCC] )2 and - flf-[GGAA(iPr)TTCC] 2. L Biochem. Struct Dyn. 4,757-783. 

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