Cytosine dimer

Nir E, Kleinermanns IHK, de Vries MS (2003) The nucleobase cytosine and the cytosine dimer investigated by double resonance laser spectroscopy and ab initio calculations. Phys Chem Chem... 

Sponer, J., J. Leszczynski, and P. Hobza. 1996. Base Staking in Cytosine Dimer. A Comparison of Correlated Ab Initio Calculations with Three Empirical Models and Density Functional Theory Calculations. J. Comp. Chem. 17, 841. 

The increase in absorbance at 240 nm upon saturation of the 5,6 double bond is considerably more pronounced for cytosine than for thymine and uracil. Thus the cross section of the cytosine dimer for monomerization at 240 nm is high, and the equilibrium concentration of dimer at various wavelengths is smaller for cytosine than for the other two pyrimidines.57... 

The existence of photoreversible, but not of heat-reversible, absorbance change in irradiated poly dI dC was taken to prove that the photoproducts are entirely dimers (in contrast to those in poly C irradiations where the product is almost entirely the hydrate82a). It was possible to detect dimers of uracil as well as those of cytosine, by means of the much slower photoreversal of uracil dimers. In the acid hydrolysates of irradiated dl-dC, both uracil dimers and uracil could be identified. Enzymatic hydrolysis (snake venom phosphodiesterase) does not split pyrimidine dimers, and the products of such hydrolysis of irradiated tritium-labeled poly dl dC contained trinucleotides shown by radioactivity to contain cytosine dimers. Thymine dimers were formed in the photolysis of the poly dA dT, and were detected and assayed by the same methods. The yield of thymine dimers in irradiated poly... 

Spoiler J, Leszczynski J, Hobza P (1998) Base staking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical models and density functional theory calculations, J Comp Chem, 17 841-850... 

Figure 12-7 shows clusters involving 9-methylguanine, demonstrating how tautomeric blocking can be used to confirm structural assignments [47], Figure 12-8 shows REMPI spectra of cytosine dimers and their methyl derivatives [48], We used... 

Figure 12-8. REMPI spectra of various cytosine dimers. Asterisks indicate origins of different structures as determined by UV-UV double resonance spectroscopy. The corresponding structures, as determined by IR-UV double resonance spectroscopy are shown below...

Figure 16-14. Computed energy levels for the ground state (S0) and the lowest triplet excited state (T) of the cytosine dimer in its triplet locally excited state 3(LE), step-wise intermediate 3(SWI), and ground-state cyclobutane cytosine (CBC) dimer. The main intermolecular geometric parameters (in A) for 3(SWI) are included. At the 3(SWI) optimized structure a singlet-triplet crossing, (T1/S0)x, takes place...

The hydrogen-bonded cytosine-cytosine dimers illustrated in Fig. 16.2 are observed in the following compounds ... 

Hobza, R, Sponer, J., and Polasek, M., H-honded and stacked DMA base pairs cytosine dimer. An ab initio second-order M0ller-Plesset study, J. Am. Chem. Soc. 117, 792-798 (1995). 

Hobza, R, Sponer, J., and Polasek, M., H-honded and stacked DNA base pairs cytosine dimer. An ab initio second-order M0ller-Plesset study, J. Am. Chem. Soc. 117, 792-798 (1995). McDowell, S. A. C. and Buckingham, A. D., Isotope effects on the stability of the carbon monoxide-acetylene van der Waals molecule and the hydrogen fluoride dimer, Chem. Phys. Lett. 182, 551-555 (1991). 

Potential energy surface of the cytosine dimer MP2 complete basis set limit interaction energies, CCSD(T) correction term, and comparison with the AMBER force field109... 

The enzyme-DNA complex absorbs light and uses the photon energy to cleave specific C-C bonds of the cy-clobutylthymidine dimer. Photolyase is also active against cytosine dimers and cytosinethymine dimers, which are also formed by UV irradiation but much less frequently. 

V. Subramanian, D. Sivanesan, and T. Ramasami, The role of solvent on the base stacking properties of the stacked cytosine dimer, Chem. Phys. Lett. 290, 189-192 (1998). 

R. Parthasarathi and V. Subramanian, Stacking interactions in benzene and cytosine dimers from molecular electron density perspective. Struct. Chem. 16, 243-255 (2005). 

According to IR spectra, the diamino form 207 predominates for N-unsubstituted cytosine dimers, whereas N4-disubstituted analogs favor the bis(imino-oxo) form. Both... 

Figure 19 shows the A/l/i o — curves of cytosine, thymine, and their derivatives. In the case of cytosine, A // o begins to increase at about —0.5 V. The curve shows a quasi-bell shape having a maximum at the pzc at lower concentrations but aquires a somewhat more complex shape at higher concentration, with some increase in A // ol at potentials more positive than 0.1 V (curve b in Fig. 19A). This seems to indicate that the adsorption process is accompanied by reorientation or formation of the cytosine dimer on the positively charged surface. Since such complicated shapes are observed only in the curves of cytosine and guanine, having the same substituent groups, the interaction of —NH2 and =0 may be partly responsible for their complicated behavior on the electrode surface.

Fig. 4.1 Spin densities of a guanine-cytosine dimer radical cation, (GC)j. a KS-DFT supramole-cular calculation using PW91 functional, b FDE calculation considering two subsystems where the left side subsystems blue contour) is positively charged and c FDE calculation for four subsystems with one subsystems blue contour) is positively charged. The nucleobases structures and spin densities were taken from Ref. [48]...

Replacement of pyrimidine dimers. UV irradiation of DNA causes dimerization of adjacent thymine residues on the same strand intrastrand cytosine dimers and thymine-cytosine dimers are also formed, but at much lower rates. The resulting dimer cannot fit into a double helix, and therefore prevents normal transcription and replication. 

Figure 6 demonstrates this principle for cytosine dimers. Figure 6c-g, with both a free and a bound (shifted) NH2 vibration clearly point to structure 1. Figure 6h with only free NH2 is consistent with structure 2, while structure 3 can be excluded for all of these spectra, since it would contain no free NH2 modes. Furthermore, the 3,600 cm OH frequency, characteristic for the enol form, appears only in Fig. 6f. 

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