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Ligation is the joining of two nucleotides, or two nucleic acid fragments, into a single polymeric chain through the action of an enzyme known as a ligase. The reaction involves the formation of a phosphodiester bond between the 3'-hydroxyl terminus of one nucleotide and the 5'-phosphoryl terminus of another nucleotide, which results in the two ...
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 ...
Purines form hydrogen bonds to pyrimidines, with adenine bonding only to thymine in two hydrogen bonds, and cytosine bonding only to guanine in three hydrogen bonds. This arrangement of two nucleotides binding together across the double helix (from six-carbon ring to six-carbon ring) is called a Watson-Crick base pair.
The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair). Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content.
This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.
DNA ligase is able to form a phosphodiester bond between the nucleotides on each side of the gap. [2] Phosphodiesters are negatively charged at pH 7. [5] The negative charge attracts histones, metal cations such as magnesium, and polyamines [needs citation]. Repulsion between these negative charges influences the conformation of the polynucleic ...
In nucleic acid, nucleobases are held together by hydrogen bonding, which only works efficiently between adenine and thymine and between guanine and cytosine. The base complement A = T shares two hydrogen bonds, while the base pair G ≡ C has three hydrogen bonds. All other configurations between nucleobases would hinder double helix formation.
Base pairing: Two base pairs are produced by four nucleotide monomers, nucleobases are in blue. Guanine (G) is paired with cytosine (C) via three hydrogen bonds, in red. Adenine (A) is paired with uracil (U) via two hydrogen bonds, in red. Purine nucleobases are fused-ring molecules. Pyrimidine nucleobases are simple ring molecules.