Cytosine-guanine dimer

Key words. Artificial dinucleotide, molecular recognition, cytosine-guanine dimer. 

The authors claim that these associations, which are destroyed in fixed compounds, play an important role in the calculation of Ty.The cases of 1,2,4-triazole-5-thiones 74 [97SA(A)699] and of pyridone dimers 15a-15a and 15a-15b were also studied [96MI(13)65]. (3) The recording of IR spectra in solution at different temperatures to determine the effect of the temperature on Kj-, for instance, in pyrazolinones [83JPR(325)238] and in cytosine-guanine base pairs [92MI(9)881]. (4) The determination of the equilibrium 2-aminopyridine/acetic acid 2-aminopyridinium acetate (see Section III.E) in the acid-base complex was carried out by IR (97NKK100). 

Figure 5.2. Adenine-thymine(uracil) (left) and guanine-cytosine (right) dimers.

Fig. 5-3. (a) The structure of acetic acid dimer which has an enthalpy of dissociation of 57.9 kJ mol-1 (A. D. H. Ciague and H. J. Bernstein, Spectrochim. Acta, 1959, 25A, 593). (b) Hydrogen bonding between base pairs such as adenine-thymine or cytosine-guanine. 

Figure 4. Porphyrin dimers 1 and 2 formed via H bonds between cytosine-guanine base pairs.

Fig.11 Representation of the cytosine-guanine hydrogen-bonded dimer and subsequent energy transfer from ZnP to H2P.

Attention should be given to the selection of primers. Typically, primers used are between 15 and 30 bases in length, with guanine-cytosine composition between 40 and 60%. The primer should not have within its sequence any unusual composition such as stretches of polypurines or polypyrimidines. The primer pair should not be complementary at the 3 ends, since otherwise the DNA synthesizing enzyme can extend one primer over the other primer, creating a double-stranded product whose length approximates the sum of the two primers. This artifact is called primer dimer, which could very well become the predominant and undesirable PCR product when primer pairs complementary at the 3 ends are used (B4, N3). 

LCA toward amino acids and nucleic bases has also been measured. Wesdemiotis and Cerda measured the alkali metal ion affinities of nucleobases in the gas phase from the dissociation of metal ion-bound heterodimers [nucleobase + B]M+, in which B represents a reference base of known affinity and M is an alkali metal. By assessing the dimer decomposition for two different internal energies, entropy is deconvoluted from enthalpy and LCA values are obtained. For guanine, cytosine, adenine, thymine and uracil, the corresponding Li+-nucleobase bond energies are as follows 57.2, 55.5, 54.1,... 

At 77 K, the DNA and RNA fluorescence increases. This fluorescence is due to the formation of adenine and thymine dimers, while the fluorescence of guanine and cytosine is inhibited. Ethidium bromide, acridine and Hoechst 33258 intercalate between DNA and RNA bases, thereby inducing a fluorescence increase. 

Since coiled chains of proteins are known to uncurl because of ionic repulsions when ionization occurs, Reid (1957) suggested that excited state dissociation acts as a trigger in rapid biological processes. The 7-azaindole dimer, which undergoes photo-induced double proton transfer (see Section 4), has similarities to the adenine-thymine and guanine-cytosine base pairs of DNA. Its excited state proton transfers have been proposed as possible mechanisms of mutagenesis (Ingram and El-Bayoumi, 1974). 

Figure 12.10. Potential-energy functions of the S0 state, the locally excited 1 hit states of guanine and cytosine, the lowest1 rnr state, and the tt-jt charge-transfer state of the WC conformer (a), the conformer B (b), and the conformer C (c) of the CG dimer. The PE functions have been calculated along the linear-synchronous-transit proton-transfer reaction path from the S0 minimum to the biradical minimum. Insets show the potential-energy function of the locally excited 1mr state of guanine calculated along the minimum-energy path for stretching of the NH bond...

Fig. 22. The complexation induced shifts of the energies of the lowest excitations of nucleic acid bases in the dimers. Shifts are calculated with respect to the free molecule (guanine or cytosine in the guanine-cytosine complex and adenine or thymine in the adenine-thymine complex). For each monomer four excitations are given singlet-singlet A , singlet-singlet A , singlet-triplet A , and singlet-triplet A . Data taken from [Wesolowski, J. Am. Chem. Soc., 126, (2004) 11444].

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.

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