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A common example is the C-loop motif, [78] [79] where the bulging loop residues make non-canonical base pairing with the bases of double helical regions forming non-canonical base pairing (Figure 9). The extra base pairs in these cases give rise to additional stabilization to the composite double helix containing motif.
Bifurcated H-bond systems are common in alpha-helical transmembrane proteins between the backbone amide C=O of residue i as the H-bond acceptor and two H-bond donors from residue i + 4: the backbone amide N−H and a side-chain hydroxyl or thiol H +. The energy preference of the bifurcated H-bond hydroxyl or thiol system is -3.4 kcal/mol or -2. ...
Chemical structures for Watson–Crick and Hoogsteen A•T and G•C+ base pairs. The Hoogsteen geometry can be achieved by purine rotation around the glycosidic bond (χ) and base-flipping (θ), affecting simultaneously C8 and C1 ′ (yellow). [1] A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A
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.
Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. Hydrogen bonding is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form ...
In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site.
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.
[17]: 39 Most importantly, the N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier; this repeated i + 3 → i hydrogen bonding defines a 3 10-helix. Similar structures include the α-helix (i + 4 → i hydrogen bonding) and the π-helix i + 5 → i hydrogen bonding.