Base pair bond distances

The two strands, in which opposing bases are held together by hydrogen bonds, wind around a central axis in the form of a double helix. Double-stranded DNA exists in at least six forms (A-E and Z). The B form is usually found under physiologic conditions (low salt, high degree of hydration). A single turn of B-DNA about the axis of the molecule contains ten base pairs. The distance spanned by one turn of B-DNA is 3.4 nm. The width (helical diameter) of the double helix in B-DNA is 2 nm. 

Of the three principal classes of crystals, ionic crystals, crystals containing electron-pair bonds (covalent crystals), and metallic crystals, we feel that a good understanding of the first class has resulted from the work done in the last few years. Interionic distances can be reliably predicted with the aid of the tables of ionic radii obtained by Goldschmidt1) by the analysis of the empirical data and by Pauling2) by a treatment based on modem theories of atomic structure. The stability,... 

We now analyze the chemical species prevalent in water at these extreme conditions by defining instantaneous species based on the O-H bond distance. If that distance is less than a cut-off value rc, we count the atom pair as being bonded. Determining all bonds in the system gives the chemical species at each point in time. Species with lifetimes less than an O-H bond vibrational period (10 fs) are transient and do not represent bound molecules. The optimal cut-off rc between bonded and nonbonded species is given by the location of the maximum in the free energy surface.83... 

FIGURE 10.8 Hydrogen bonding between preferred base pairs in DNA. Top structures illustrate the number of hydrogen bonds and the bottom the bond distances between preferred base pairs. 

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