Duplex formation, thermodynamics

In the thermodynamic study of duplex formation, a variety of complementary pairs of relatively simple, well-defined oligonucleotides are employed, " while the intercalation thermodynamics was examined with more complex or natural DNA duplexes. " Typical intercalating agents examined are acridine orange, acriflabine, actinomycin, daunomycin, ethidium bro-... 

Forman, J.E., et al. Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays. ACS Symposium Series, 1998, 682, p. 206-228. 

Figure 25. Left Base stacking in double-stranded DNA (only one strand shown) Right Determination of thermodynamic parameters of duplex formation Oligonucleotides 3 -dA(U]-A(MEQ1-5 and T 12) were diluted starting from 9 pM to 4.5 pM in 0.15 M NaCl, 0.01 M Tris-HCl, pH 7.0,25 °C and hybridization data were collected. From [149],...

Thermodynamics of Duplex Formation and Mismatch Discrimination on Photolithographically Synthesized Oligonucleotide Arrays... 

Duplex formation in solution has been extensively studied, and the kinetics and thermodynamics of such interactions for short oligonucleotides can be described by a model involving nucleation followed by helix zipping (Figure 2a). a In immobilized... 

Duplex formation in DNA or RNA is dependent on mnlti-ple thermodynamic variables innate to the biopolymers and the environment in which they reside. The combination of intermolecular forces of varying strengths canses hybridization to be favored in aqueous solution. The forces that inflnence dnplex creation include electrostatic factors, van der Waals interactions, hydrophobic effects, and hydrogen bonding (see Self-Assembly of Nucleic Acids, Self-Processes). 

The higher thermodynamic stability of Homo - DNA versus DNA duplexes is due not to greater binding energy, but rather to a less negative entropy of duplex formation. 

As described in the following sections, supramolecular polymerizations of DNA will reflect the thermodynamics and kinetics of duplex formation. There are generally two major methods... 

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. 

Additional data in ref. cs vs. temperature profiles of base proton resonances of both sequences NH proton exchange lifetimes (inversion recovery experiment) Arrhenius plots for NH exchange thermodynamic parameters of duplex formation. ... 

For example, the thermodynamic properties for duplex formation by GKjCC can be predicted as follows. The predicted free energy change at 37 C,... 

Data 3.6.5.1 Thermodynamic parameters for duplex formation by RNA oligonucleotides Table 1. Thermodynamic parameters for duplex formation by RNA oligonucleotides in 1 MNaCl, pH 7. (T atlO- M) ... 

Table 4. Thermodynamic parameters for duplex formation by DNA oligonucleotides in 1 M NaCl. All Watson-Crick base pairs. (T at 10 ...

Three types of data are presented (1) experimental thermodynamic parameters for particular transitions, (2) parameters for prediction of thermodynamic parameters from sequence, and (3) experimental kinetic parameters for particular transitions. All parameters are for the transition from a less ordered to a more ordered state. For example, for single strand stacking and duplex formation, parameters listed are for the reactions ... 

A. P. Williams, C. E. Longfellow, S. M. Freier, R. Kierzek, and D. H. Turner, Biochemistry, 28, 4283 (1989). Laser Temperature-Jump, Spectroscopic, and Thermodynamic Study of Salt Effects on Duplex Formation by dGCATGC. 

Table 19.1 Thermodynamic parameters for duplex formation and activation enthalpies for imino proton exchange of base pair 2. Tm is the melting temperature, HSf the activation enthalpy for the exchange of the G-NIH of base pair 2 with water, and (f the Gibbs free energy for duplex formation at 37 °C. Typical experimental errors are +0.5 °C for T, +2% for AG°, and +5% ioruf . Single-strand concentrations in the melting curve analyses were always 3 pM.

It is sometimes more convenient to analyze the melting process in reverse, that is, the association of monomers to form the duplex. If the process is truly an equilibrium one, then either direction should give an equivalent analysis. We will switch back and forth in our discussion if one direction is more convenient, although most experimental measurements have been of the melting process (rather than the formation reaction), and all thermodynamic properties will be reported for melting. 

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