Biological macromolecules double helix

The year 2003 is the tenth anniversary of the first Femtochemistry Conference and the fiftieth anniversary of Watson and Crick s celebrated discovery of the DNA double helix [1], Remarkable progress has been made in both fields femtosecond spectroscopy has made decisive contributions to Chemistry and Biology, and advances in the elucidation of static nucleic acid structures have profoundly transformed the biosciences. However, much less is known about the dynamical properties of these complex macromolecules. This is especially true of the dynamics of the excited electronic states, including their evolution toward the photoproducts that are the end result of DNA photodamage [2],... 

When the oxidizing species, an electron acceptor, and the electron donor are both embedded within a biological macromolecule (e.g., in a protein or DNA molecules), the reaction kinetics are entirely different from those in solution in which both species can diffuse freely and encounter one another in order to undergo chemical reaction. An example of such intramolecular processes is the one-electron oxidation of guanine (G) by a 2AP neutral radical, both site-specifi-cally positioned within a DNA duplex [28]. Here, both reaction partners are fixed within a DNA helix and the bimolecular reaction model is not suitable for describing the reaction kinetics (4.16). Instead, the kinetics of oxidation of G by 2AP(-H) radicals in double-stranded DNA follow first-order kinetics with the magnitudes... 

Olby Robert. The Path to the Double Helix, chapters 1-3. Seattle University of Washington Press, 1974. This book provides a superb discussion of the understandings and confusions associated with biological macromolecules in the early 20th century. 

Discrimination between stereoisomers in biological environments should in fact not be unexpected, as at a molecular level such environments are composed of handed macromolecules, i.e., proteins, glycolipids and nucleic acids, from the chiral precursors of L-amino acids and D-carbo-hydrates. In addition, the macromolecular structures of these biopolymers also give rise to chirality as a result of helicity, e.g., the protein a-helix and DNA double helix. Such helical structures may have either a left or right handed turn in the same way that a spiral staircase may be left or right handed. In the case of the DNA double helix and the protein ot-helix, the biopolymers have a right-handed turn. 

The rewinding of DNA in the presence of zinc can therefore be considered a template effect. In spite of the similarity to the template effect in a mini-molecular system, the phenomenon is not quite the same in the biological macromolecule. With minimolecules the metal ions cause the formation of covalent bonds that would not otherwise be produced. In DNA covalent (7-bond formation involving the ligand is not necessarily required. The regeneration of the double helix depends upon the recognition of complementary bases which reform hydrogen bonds, and the stabilization of the double helix by Tc-interaction. 

Even though we stated at the beginning of this section that it is not our purpose to discuss the biological function of the macromolecules described, it is hard to resist saying a few words about some of their most important interactions. First, it is easy to visualize how the structure of DNA leads to its replication and hence the transfer of genetic information which is coded in the sequence of bases along the chain. Specifically, when the DNA double helix opens up it exposes the sequence of bases in each strand of the molecule. In a solution where bases, sugars and phosphates are available or can be synthesized, it is possible to form the complementary strand of each of the two strands of the parent molecule. This results in... 

While many biological macromolecules can undergo conformational transitions, these are typically between well defined structures. In many cases these structures persist in a wide variety of molecular environments, e.g. the B form of the deoxyribonucleic acid (DNA) double-helix determined from X-ray fibre diffraction is observed with relatively little conformational variation in solution, in association with a number of different proteins and in fibres in a range of crystalline and semicrystalline arrays. Such observations comprise just one aspect of the large body of data which bears testimony to the biological relevance of structural information obtained from diffraction studies of macromolecules in fibres, films and single crystals. 

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