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Top, a G.C base pair with three hydrogen bonds. Bottom, an A.T base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the bases are shown as dashed lines. The wiggly lines stand for the connection to the pentose sugar and point in the direction of the minor groove.
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.
Left: the nucleotide base pairs that can form in double-stranded DNA. Between A and T there are two hydrogen bonds, while there are three between C and G. Right: two complementary strands of DNA. Complementarity is achieved by distinct interactions between nucleobases: adenine, thymine (uracil in RNA), guanine and cytosine.
An ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of water molecules with one hydrogen bond between them, which is called the water dimer and is often used as a model system. When more molecules are present, as is ...
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.
Hoogsteen pairs have quite different properties from Watson–Crick base pairs.The angle between the two glycosidic bonds (ca. 80° in the A• T pair) is larger and the C1 ′ –C1 ′ distance (ca. 860 pm or 8.6 Å) is smaller than in the regular geometry.
One hydrogen bond from the Watson-Crick base pair is maintained (guanine O6 and cytosine N4) and the other occurs between guanine N7 and a protonated cytosine N3 (note that the Hoogsteen G-C base pair has two hydrogen bonds, while the Watson-Crick G-C base pair has three). [65] Figure 6: Four examples of wobble base pairs.
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 ...