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The chemical structure of DNA base-pairs . A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA.
Base pair geometries. The geometry of a base, or base pair step can be characterized by 6 coordinates: shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix.
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 ...
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. In some cases, called reversed Hoogsteen base pairs, one base is rotated 180° with respect to the other.
In accordance with the VSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds are arccos(− 1 / 3 ) = 109.47°. For example, methane (CH 4) is a tetrahedral molecule. Octahedral: Octa-signifies eight, and -hedral relates to a face of a solid, so "octahedral" means "having eight faces". The bond ...
Although the two strands are aligned by hydrogen bonds in base pairs, the stronger forces holding the two strands together are stacking interactions between the bases. These stacking interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a large amount of local structural variability. [ 7 ]
Each bond consists of a pair of electrons, so if t is the total number of electrons to be placed and n is the number of single bonds just drawn, t−2n electrons remain to be placed. These are temporarily drawn as dots, one per electron, to a maximum of eight per atom (two in the case of hydrogen), minus two for each bond.
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.