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The energetics of DNA tertiary-structure assembly were determined to be driven by the hydrophobic effect, in addition to Watson–Crick base pairing, which is responsible for sequence selectivity, and stacking interactions between the aromatic bases.
A chaotropic agent is a substance which disrupts the structure of, and denatures, macromolecules such as proteins and nucleic acids (e.g. DNA and RNA).Chaotropic solutes increase the entropy of the system by interfering with intermolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic effects.
Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects. [3] [2] Non-covalent interactions [4] are critical in maintaining the three-dimensional structure of large molecules, such as proteins and nucleic acids.
A few research groups have been searching for a third base pair for DNA, including teams led by Steven A. Benner, Philippe Marliere, Floyd E. Romesberg and Ichiro Hirao. [17] Some new base pairs based on alternative hydrogen bonding, hydrophobic interactions and metal coordination have been reported. [18] [19] [20] [21]
Secondary structure is the set of interactions between bases, i.e., which parts of strands are bound to each other. In DNA double helix, the two strands of DNA are held together by hydrogen bonds. The nucleotides on one strand base pairs with the nucleotide on the other strand. The secondary structure is responsible for the shape that the ...
The repeated negative charges of the DNA backbone electrostatically repel each other, preventing interactions both within and between DNA strands. This repulsion promotes specific interactions along the Watson–Crick 'edge' of the nucleobases, promoting Watson–Crick base pairing specificity—A pairs with T and C pairs with G. [2]
The strong hydrophobic interactions between the TOPO and polymer hydrocarbon allow the two layers to "bond" to one another, forming a hydrophobic protection structure. This structure resists degradation via hydrolysis and enzymes, which are common methods of degradation in vivo.
Hydrophobic interaction media are most commonly used to target free carboxyl groups and proteins. ... DNA, rRNA, and other nucleic acids/oligonucleotides. Protein A/G ...