Double helix deformation

R. Bonaccorsi, E. Scrocco, and J. Tomasi, Int. ]. Quantum Chem., 29, 717 (1986). Structural Deformations of the DNA Double Helix in the First Stages of DNA Transcription Studied with a Simple Model. 

The main reaison for this remcirkable property of the DNA molecule is its general shape. The double helix sits on a helicoid, and therefore it shares the properties of that surface. The most important of these is the way the helicoid can be deformed, via the Bonnet transformation. 

Double helical DNA is of course just a polymer, but a very peculiar one -in many respects. One peculiarity is that double helix has twisting rigidity. Usual chemical polymer chains, such as the ones shown in Figure 2.1, or protein chains in Figure 5.4, if we twist one end with respect to the other, can relax the deformation by turning around the single covalent bonds of... 

Lindsay SM, Thundat T, Nagahara L (1988) Adsorbate deformation as a contrast mechanism in stm images of bio-polymers in an aqueous environment - images of the unstained, hydrated dna double helix. J Microsc-Oxford 152 213-220... 

The deformation of the DNA double helix plays an important role in structural biology, and the molecular nature of sequence-dependent axis bending, both intrinsic and induced. 

It is interesting to add that simple modifications of the glycosidic angle x. which fixes the base plane with respect to the phosphodiester backbone, are also a powerful way of provoking important conformational transitions. This was demonstrated in early modeling by Olson which lead to unusual ribbon-like structures of DNA. More recently, it has been shown that such deformations are related to certain protein induced DNA deformations, leading to the so-call TA-DNA conformation and to the conformations created by extreme stretching of the double helix (see Section 3.5 and Protein-Nucleic Acid Interactions). 

The DNA is bound to the histone by electrostatic forces, which are large at physiological ionic strength. Assuming that the DNA forms a supercoil with the dimensions of the nucleosome by continuous deformation of the DNA double helix, it can be calculated that 20-28 kcal/ mol of nucleosome are required for formation of the supercoil (Finch et al., 1977). Each octomer of core histones induces super-coiling in closed circular DNA (Fuller, 1971 Crick, 1976). There is conversion between relaxed and nucleosomal DNA. The arginine-rich histones H3 and H4 are necessary and sufficient for the formation of nucleosomes (Camer-ini-Otero et al., 1976 Sollner-Webb et al., 1976) and induce supercoil-ing in closed circular DNA (Camerini-Otero and Felsenfeld, 1977 Bina-Stein and Simpson, 1977). 

Two kinds of the vibrations, known as amide I and amide II vibrations, are directly correlated to the molecular structure of proteins and polypeptides. The stretching of the carbonyl C = O double bonds is linked to the amide I vibration, and the deformation of the N-H bonds causes the amide II vibration. FTIR determines the amount of light absorbed corresponding to each of the vibrations over a wide range of frequencies (Kumosinski and Farrell, 1993). Empirical correlations between the frequency of the amide I and amide II absorptions of the protein and the secondary structure composition in helix, extended P-sheets, loops and unordered structures have been determined (Jackson and Mantsch, 1995). 

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