B-DNA, double helix

DNA in cells exists mainly as double-stranded helices. The two strands in each helix wind about each other with the strands oriented in opposite directions (antiparallel strands). The bases of the nucleotides are directed toward the interior of the helix, with the negatively charged phosphodiester backbone of each strand on the outside of the helix. This is the famous B-DNA double helix discovered by Watson and Crick (Figure 3.3). 

An interesting feature of B-DNA diffractogram in Figure 8a is the presence of additional meridional reflections on every third layer line which makes the true B-DNA double helix to have a turn angle of 240° for each pentanucleotide as the real repeating unit. 

An X-ray crystallography structure of the duplex from d(ATA UAT) and d( ATAT AT) demonstrates that an alternative to the classical B-DNA double helix is possible. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. The structure is not related to those found in triplexes or to parallel DNA duplexes, though its conformational parameters are very similar to those of B-form DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. 

The A-DNA Double Helix Is Shorter and Wider Than the More Common B-DNA Double Helix... 

FiQ. OS.B. DNA double helix, made up of sugar-phosphate backbone, with pairing between A-T and C-G bases to create coiled shape. (D. Leja, National Human Genome Research Institute. Reproduced by permission.)... 

Each nucleotide has a direction and therefore the chemical direction is inherent in each of the DNA single strands. In the B-DNA double helix, the two strands have opposite directions. In B-DNA, base-pairs are planar and perpendicular to the axis of the double helix. 

The most obvious stimulus to ehiral induction is the use of stereogenie eenters, but external perturbation, such as physical fields ean also be used to induce chirality. The term is applied to traditional asymmetric synthesis through covalent bonds as well as to supramolecular synthesis, which is our interest here. Mention the word "chirality" to any chemist, and thoughts will be conjured of the right-handed B-DNA double helix, the right-handed a-helices formed by peptides of the natural L-amino acids, of thalidomide, and other emblematic and dramatic examples of the importanee of stereochemistry. It is clear that the chirality of the eomponents of biological systems play a key role in their function, in which induction of chirality through noncovalent bonds is inherent. But beyond natural systems and related phenomena, there is a wealth of unnatural chemical systems that display remarkable and important properties. 

Figure 20.9 shows more detail of an idealized B-DNA double helix. The major and minor grooves are clearly recognizable in this model. 

Fig. 24.1 Structure of the B-DNA double helix. Enlarged Lewis structures depict the single strand and the canonical base pairs (AT and GC) with their hydrogen bond donor/acceptor pattern inside the minor and major groove indicated by arrows...

Results are reported of ab initio Hartree-Fock CO calculations using a minimal atomic basis set for the single stranded periodic B-DNA models of cytosine (C), thymine (T), adenine (A) and guanine (G) stacks and two polynucleotides with adenylic acid (ASP) and th)miidine (TSP) as repeating unit, respectively. Further the energy band structures of two poly(base pairs), poly(adenine-thymine), (A-T),and poly(guanine-cytosine), (G-C), representing a simple model of B-DNA double helix are discussed. 

In the last years the problem of the proper theoretical treatment of solvation effects in DNA has been solved to a great extent (17). In a number of publications the interaction energy between water molecules and the nucleotide bases (28), base pairs (29), single (30), and double helices (31) of DNA has been calculated. Recently, also the complete solvent structure of a B-DNA double helix fragment with 12 base pairs and the corresponding sugar and phosphate units has been determined (32). In these Monte Carlo simulations, 447 water molecules have been included and their interaction energies and probability distributions (at a temperature of 300 K) have been calculated. In recent publications the Na+ ion structure of B-DNA at different humidities, ionic concentrations and temperature has been presented (33). 

---