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Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature (T m) is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA) state. T m depends on the length of the DNA molecule and its specific ...
Melting curve analysis is an assessment of the dissociation characteristics of double-stranded DNA during heating. As the temperature is raised, the double strand begins to dissociate leading to a rise in the absorbance intensity, hyperchromicity .
This region that is amplified is known as the amplicon. After the PCR process the HRM analysis begins. The process is simply a precise warming of the amplicon DNA from around 50 ˚C up to around 95 ˚C. At some point during this process, the melting temperature of the amplicon is reached and the two strands of DNA separate or "melt" apart.
GC-content alone can also be used to estimate the free energy and melting temperature of a nucleic acid duplex. This is less accurate but also much less computationally costly. [5] Software for thermodynamic modeling of nucleic acids includes Nupack, [6] [7] mfold/UNAFold, [8] and Vienna. [9]
Phase transitions play many important roles in biological systems. Examples include the lipid bilayer formation, the coil-globule transition in the process of protein folding and DNA melting, liquid crystal-like transitions in the process of DNA condensation, and cooperative ligand binding to DNA and proteins with the character of phase ...
An example is they separate when heated at a higher temperature than dissimilar sequences, a process known as "DNA melting". [2] [3] [4] To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column or filter and the mixture is heated in small steps.
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The area of partially separated DNA is known as the denaturation bubble, which can be more specifically defined as the opening of a DNA double helix through the coordinated separation of base pairs. [19] The first model that attempted to describe the thermodynamics of the denaturation bubble was introduced in 1966 and called the Poland-Scheraga ...