Cytosine base pairing and

It is a potent antitumor antibiotic isolated from Streptomyces organism. It binds tightly to double stranded DNA through intercalation between adjacent guanine cytosine base pair and inhibit all forms of DNA dependent RNA synthesis. 

J. Gu et al., H-bonding patterns in the platinated guanine-cytosine base pair and guanine-cytosine-guanine-cytosine base tetrad An electron density deformation analysis and aim study. J. Am. Chem. Soc. 126, 12651-12660 (2004)... 

Zendlova, L. Hobza, R Kabelac, M. Potential energy surfaces of the microhydrated guanine - cytosine base pair and its methylated analogue, ChemPhysChem 2006, 7, 439-447. 

LNA has been used in a variety of other biological applications. LNA, and its 2 -amino analogue, has been incorporated into aptamers (see section 2) for enhanced binding affinity." LNA has been substituted into i-motif structures, where it can have a significant effect on the structural stability. The presence of LNA in the structure alters the stability of the hemiprotonated cytosine base pairs, and as there is a sequence effect it is possible to tune the stability of the i-motif." Substituting LNA into quadruplex structures also has a sequence-dependent effect on stability, where in only certain positions are well-defined structures obtained." More recently the use of LNA nucleotides as polymerase substrates has been examined." KOD DNA polymerase has been shown to be a useful polymerase for the incorporation of LNA triphosphates into DNA, including its use as the polymerase in PCR reactions with LNA modifications." ... 

Figure 13 (A) Gonzalez-Rodriguez s cyclic H-bonded tetramer based on guanine-cytosine base pairing and (B) the reference system (R and R are solubilizing groups). (C) An alternative base pairing system based on aminoadenine—thymine.

To account for the observed base ratios and uniform thickness of DNA, Watson and Crick postulated that purine and pyrimidine bases project inward toward the axis of the helix and always pair in a specific manner. According to scale models, the dimensions of an adenine-thymine base pair are almost identical to the dimensions of a guanine-cytosine base pair, and the length of each pair is consistent with the core thickness of a DNA strand (Figure 20.7). Thus, if the purine base in one strand is adenine, then its complement in... 

Examine AT pair and GC pair, adenine-thymine and guanine-cytosine base pairs, respectively. Identify the hydrogen bonds in each. Are they the same as those you sketched Are the base pairs flat as normally drawn in textbooks, or are they significantly puckered or twisted ... 

Sowers LC, Fazakerley GV, Eritja R, Kaplan BE (1986) Base pairing and mutagenesis observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc Natl Acad Sci USA 83 5434-5438... 

These definitions apply to any atomic system, molecule or crystal. Fig. 7.3 a illustrates their application to the charge distribution of the guanine-cytosine base-pair. Fig. 7.3 b shows the molecular structure defined by the bond paths and the associated CPs that clearly and uniquely define the three hydrogen bonds that link the two bases. Fig. 7.3 c shows the atomic boundaries and bond paths overlaid on the electron density in the plane of the nuclei. All properties of the atoms can be determined, enabling one, for example, to determine separately the energy of formation of each of the three hydrogen bonds. 

Fig. 14 Use of two different DNA duplexes with inserted cytosine loops working as synthetic scaffolds to generate fluorescent silver clusters for the identification of the sickle cell anemia gene mutation (black dots represent hydrogen bonds formed in base pairing and black dashed lines the sugar-phosphate backbone) [74]...

Density of states weighted Franck-Condon factor Deoxyribonucleic acid Barrier height for the adiabatic hole motion Difference in ionization potentials of adenine-thymine and guanine-cytosine base pairs... 

Dimensions and hydrogen bonding of (a) thymine to adenine and (b) cytosine to guanine. Note that two hydrogen bonds are formed in the A-T base pair and three in the G-C base pair. The overall dimensions of the base pairs are the same. Consequently they fit at any position in an otherwise regular polymeric structure. (Source Adapted from S. Arnott, M. H. F. Wilkins, L. D. Hamilton, and R. Langridge, Fourier synthesis studies of lithium DNA, part III Hoogsteen models, J. Mol. Biol. I l 39l, 1965.)... 

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