DNA model

FIGURE 28 2 Molecular modeling—1953 style James Watson (left) and Francis Crick (right) with their DNA model A Barrington Brown/Science Source Photo Researchers Inc... 

Semiempirical calculations on the interaction between [Me2Sn(IV)] and a dinuclide triphosphate duplex (DD), mimicking a DNA model system, were performed with the PM3 method and published by Barbieri et al. The results indicate that the [Me2Sn(IV)] moiety binds to two adjacent phosphate groups. 

Maccubbin, A., Evans, M., Paul, C.R., Budzinski, E.L., Przybyszewski, J. and Box, H.C. (1991). Enzymatic excision of radiation-induced lesions from DNA model compounds. Radiat. Res. 126, 21-26. 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Implicit in the functioning of the Watson-Crick DNA model is the idea that the strands of a DNA molecule must separate and new daughter strands must be synthesized in response to the sequence of bases in the mother strand. This is called semiconservative replication. Still, conservative replication, in which both strands of a daughter molecule are newly synthesized, could not be ruled out by consideration of the structure of DNA alone. 

A, B, and Z DNA structure are found in Table 2.3 as adapted from Table 1.10 of reference 15 and the Jena image library at http //www.imb-jena.de/IMAGE DNA MODELS.html. 

Fig. 5. Three views of the NCP from Harp et al. [31]. (a) Ventral surface view, (b) Side view, (c) View down the molecular pseudo-dyad axis. The histones are represented by Ca ribbon models of the secondary structure elements, and the DNA model indicates the base pairing between complementary strands. The DNA is positioned asymmetrically by one-half base pair on the NCP. This results in a two sides arbitrarily referred to a dorsal and ventral (the surface shown here). The ventral surface of the NCP is best recognized by the extended N-terminal H3 tail protruding to the right. In these images, the pseudo-dyad axis is represented by vertical bars for both the ventral and side view. The pseudo-dyad axis passes through the center of the dyad view orthogonal to the plane of the page, (d) Color code for histone chains in the figures in this chapter. Note the change in hue denoting the two sides of the histone octamer.

It has been recently shown that the selective alkylation and strand scission of deoxytetranucleotide d(GTAG)-27 chosen as DNA model, results from the formation of covalent adducts 28 and 29 on the N-7 of guanine and N-3 of adenine with opening of the cyclopropane ring, respectively. Thermal treatment of 28 (90 °G, 5 min) afforded the d(deoxyribose-TAG) 30 with liberation of N-7 alkyl-guanine 31, while treatment of 29 provided the d(GT-deoxyribose-G) 32 and the N-3 alkyladenine 33 [27]. The stabilities of adducts 28 and 29 were tj/2 = 31 h and 3.2 h, respectively therefore, the cleavage reaction of adduct 29 proceeds much faster than that of 28, Eq. (11) [27]. 

Electron and Hole Transfer from the Hydration Layer to DNA. - Debije et al. investigated the transfer of X-radiation-induced electrons and holes (H20 +) from the hydration layer of crystalline oligonucleotides into the oligo itself.57 Results from these Q-band ESR experiments at 4 K suggest that ionization of hydration water results in both electron and hole transfer to the DNA model structures. The proton transfer reaction from H20 + to form the hydroxyl radical occurs on the timescale of a few molecular vibrations, thus it limits hole transfer distance from a water hole to DNA. 

Tie began working with Francis Crick in 1950 at the Cavendish laboratories. Ill 1953, Watson and Crick, using the photographs of Rosalind Franklin, which exposed crystallized molecules from the nucleus, identified the material that biologists were viewing in the nucleus as DNA. Watson and Crick created a three-dimensional structure DNA model, which provided scientists with a valuable tool in the study of heredity. In 1962 Watson-Crick were awarded the Nobel Prize for their work. 

In accordance with the above discussion, most of the damage encountered in DNA model systems (Mead et al. 1975 Kondo et al. 1988a,b, 1989, 1990) and in DNA (Fuciarelli et al. 1995) is due to OH reactions. Interestingly, ultrasound of... 

The -N02 radical (and also the C03 radical) are of some biological interest (Augusto et al. 2002) because they play some role in the reactions of peroxyni-trite (Chap. 2.4). For example, "N02 oxidizes tyrosine to nitrotyrosine (Prutz et al. 1985b), and the latter has been considered a promoter of free-radical damage in DNA model systems (Prutz 1986). In this context, it may be of interest that CCV reacts with a self-complementary ODN (k = 1.9 x 107 dm3 mol-1 s 1) exclusively at G (by ET) (Chap. 11.2). 

Prutz WA(1986) Nitro-tyrosineas promoter of free radical damage in a DNA model system. Free Rad Res Commun 2 77-83... 

Steenken S, Behrens G, Schulte-Frohlinde D (1974) Radiation chemistry of DNA model compounds, part IV. Phosphate ester cleavage in radicals derived from glycerol phosphates. Int J Radiat Biol 25 205-210... 

Steenken S, Jagannadham V (1985) Reaction of 6-yl radicals of uracil, thymine, and cytosine and their nucleosides with nitrobenzenes via addition to give nitroxide radicals. OH catalyzed ni-troxide heterolysis. J Am Chem Soc 107 6818-6826 Steenken S, Jovanovic SV (1997) How easily oxidizableis DNA One-electron reduction potentials of adenosine and guanosine radicals in aqueous solution. J Am Chem Soc 119 617-618 Steenken S, Behrens G, Schulte-Frohlinde D (1974) Radiation chemistry of DNA model compounds, part IV. Phosphate ester cleavage in radicals derived from glycerol phosphates. Int J Radiat Biol 25 205-210... 

Steenken S, Jovanovic SV, Candeias LP, Reynisson J (2001) Is frank" DNA-stand breakage via the guanine radical thermodynamically and sterically possible Chem Eur J 7 2829-2833 Steinmaus H, Rosenthal I, Elad D (1969) Photochemical and y-ray-induced reactions of purines and purine nucleosides with 2-propanol. J Am Chem Soc 91 4921-4923 Steinmaus H, Rosenthal I, Elad D (1971) Light- and y-ray-induced reactions of purines and purine nucleosides with alcohols. J Org Chem 36 3594-3598 Stelter L, von Sonntag C, Schulte-Frohlinde D (1974) Radiation chemistry of DNA-model compounds, V. Phosphate elimination from ribose-5-phosphate after OH radical attack at C-4. Int J Radiat Biol 25 515-519... 

Stelter L, von Sonntag C, Schulte-Frohlinde D (1975a) Radiation chemistry of DNA-model compounds VIII. Dephosphorylation products from reactions of OH radicals with ribose-5-phos-phate in aqueous solution. The effect of oxygen. Z Naturforsch 30b 609-615 Stelter L, von Sonntag C, Schulte-Frohlinde D (1975b) Radiation chemistry of DNA-model compounds, VII. On the formation of 5-deoxy-D-eryffrro-pentos-4-ulose and the identification of 12 further products from y-irradiated aqueous solutions of ribose-5-phosphate. Z Naturforsch 30b 656-657... 

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