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For DNA oligonucleotides, i.e. short sequences of DNA, the thermodynamics of hybridization can be accurately described as a two-state process. In this approximation one neglects the possibility of intermediate partial binding states in the formation of a double strand state from two single stranded oligonucleotides.
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 nucleic acid assumes. The bases in the DNA are classified as purines and pyrimidines. The purines are adenine and guanine ...
In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to the adenine-thymine bond of DNA. Base stacking interactions, which align the pi bonds of the bases' aromatic rings in a favorable orientation, also promote helix formation. The stability of the loop also influences the formation of the stem-loop structure.
DNA ends refer to the properties of the ends of linear DNA molecules, which in molecular biology are described as "sticky" or "blunt" based on the shape of the complementary strands at the terminus. In sticky ends , one strand is longer than the other (typically by at least a few nucleotides), such that the longer strand has bases which are ...
Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove. [6] Many double-helical forms are possible; for DNA the three biologically relevant forms are A-DNA, B-DNA, and Z-DNA, while RNA double helices have structures similar to the A form of DNA.
The stability of i-motif DNA can be influenced by increasing ionic concentration. [34] The addition of Na has shown to increase the destabilization of the i-motif structure from the c-jun proto-oncogene at pH 4.8. A decrease in stability of i-motif corresponded with an increase in ionic concentration in a study of i-motif DNA from n-MYC. [35]
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Cruciform DNA is a form of non-B DNA, or an alternative DNA structure. The formation of cruciform DNA requires the presence of palindromes called inverted repeat sequences. [1] These inverted repeats contain a sequence of DNA in one strand that is repeated in the opposite direction on the other strand.