Natural double-helical complementary

While the complementary double helical structure explained how particular sequences of bases could be used to store a genetic instruction it was not immediately clear how replication occurred or, indeed, how these instructions were used. Later work by Gamow linked DNA base pair sequences to protein synthesis [15] but it was not until 1961, when Nirenberg and Matthaei demonstrated that cell-free protein synthesis relied upon synthetic or natural polynucleotides [16], that the final link was made. The information held within the linear DNA sequence is replicated every time a cell divides. Replication is possible because of the unique double helical structure of DNA as shown in Fig. 2.7. 

One well-established observation is that, under conditions where single-stranded polynucleotides give rise to a d.c. polarographic reduction wave, both native DNA and other double-helical natural and synthetic polynucleotides are inactive 22 23,46-47, 58,59,61) Tjjjs js rea(ji]y interpretable in that, in such helical structures, the adenine and cytosine residues are located in the interior of the helix, and hydrogen bonded in complementary base pairs (see below). Z-DNA, in which cytosine residues are at the surface of the helix, is of obvious interest in this regard, and the B - Z transition in the synthetic poly(dG dC) has been investigated with the aid of differential pulse polarography and UV spectroscopy 60). 

During the past half a century, fundamental scientific discoveries have been aided by the symmetry concept. They have played a role in the continuing quest for establishing the system of fundamental particles [7], It is an area where symmetry breaking has played as important a role as symmetry. The most important biological discovery since Darwin s theory of evolution was the double helical structure of the matter of heredity, DNA, by Francis Crick and James D. Watson (Figure 1-2) [8], In addition to the translational symmetry of helices (see, Chapter 8), the molecular structure of deoxyribonucleic acid as a whole has C2 rotational symmetry in accordance with the complementary nature of its two antiparallel strands [9], The discovery of the double helix was as much a chemical discovery as it was important for biology, and lately, for the biomedical sciences. 

The discovery that DNA from natural sources exists in a double-helical form with Watson-Crick base pairs suggested, but did not prove, that such double helices would form spontaneously outside biological systems. Suppose that two short strands of DNA were chemically synthesized to have complementary sequences so that they could, in principle, form a double helix with Watson—Crick base pairs. Two such sequences are CGAT-TAAT and ATTAATCG. The structures of these molecules in solution can be examined by a variety of techniques. In isolation, each sequence exists almost exclusively as a single-stranded molecule. However, when the two sequences are mixed, a double helix with Watson-Crick base pairs does form (Figure 1.8). T his reaction proceeds nearly to completion. If each of the strands are initially present at equal concentrations of 1 mM, then more than 99.99% of the strands are in the double helix at 25°C and in the presence of 1 M NaCl. 

It is interesting to note that 15a alone in 10% ethanolic aqueous solution formed a double helical rope of 1-2 xm in width and several himdred pm in length. Approximately equal amounts of the right-handed and left-handed double helical ropes were observed. Detailed NMR and model studies indicated that the presence of small amounts of a natural light-induced [2 + 2] photodimer between adjacent thymine units was responsible for formation of the ropes. The presence of complementary base. A, suppressed formation of the photodimer, leading to the formation of the nanofibers described above. 

Watson-Crick base pairing in complementary oligonucleotide strands keeps two rules of complementarity in both size and hydrogen-bonding patterns. Hydrophobicity and planarity in the bases also appear to be important for the stability of the double-helical structure. Designing new base pairs that vary in shape, size, and functionality has been usefiil in rmderstanding what is essential in the natural base pairing. 

Unlike the double-stranded nature of DNA, RNA molecules usually occur as single strands. This does not mean they are unable to base-pair as DNA can. Complementary regions within an RNA molecule often base-pair and form complex tertiary structures, even approaching the three-dimensional nature of proteins. Some RNA molecules, such as transfer RNA (tRNA) possess several helical areas and loops as the strand interacts with itself in complementary sections. Other hybrid molecules such as the enzyme RNase P contain protein and RNA portions. The RNA part is highly complex with many circles, loops, and helical regions creating a convoluted structure. 

This helicate formation mechanism can be extended to interactions with other materials. In the example shown in Fig. 4.2, hgands carrying nucleobases are used. The helicate forms a helical structure similar to the double helix of DNA, where the nucleobases in the helicate are on the outside of the helix. This helixate can form complexes with actual nucleic acid through complementary base pairing. The artificial supramolecular complex can read the programs of naturally-occurring molecules. 

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