Cytosine blues

Figure 7.7 Color codes for the recognition patterns at the edges of the base pairs in the major (a) and minor (b) grooves of B-DNA. Hydrogen-bond acceptors are red hydrogen-bond donors are blue. The methyl group of thymine is yellow, while the corresponding H atom of cytosine is white.

The following molecular models are representations of (a) adenine and (b) cytosine, constituents of DNA. Indicate the positions of multiple bonds and lone pairs for both, and draw skeletal structures (gray = C. red = O, blue = N, ivory = IT). 

Ap4A, diadenosine tetraphosphate BBG, Brilliant blue green BzATP, 2 - 3 -0-(4-benzoyl-benzoyl)-ATP cAMP, cyclic AMP CCPA, chlorocyclopentyl adenosine CPA, cyclopentyl adenosine CTP, cytosine triphosphate DPCPX, 8-cyclopentyl-1,3-dipnopylxanthine IP3, inosine triphosphate lpsl, diinosine penta phosphate a,p-meATP, a,p-methylene ATP p.y-meATP, p.y-meihylene ATP 2-MeSADP, 2-methylthio ADP 2-MeSAMP, 2-methylthio AMP 2-MeSATP, 2-methylthio ATP NECA, 5 -W-ethylcarboxamido adenosine PPADS, pyridoxal-phosphate-6-azophenyl-2, 4 -disulfonic acid PLC, phospholipase C RB2, reactive blue 2 TNP-ATP, 2, 3 -0-(2,4,6-trinitrophenyl) ATP. 

Figure 11-12. Sj pathways for cytosine and 5M2P from vertical excitations to the sofa and twist conical intersections. Cytosine paths are shown in blue, and 5M2P are shown in green. MRCI energies are given in eV. (From Ref. [144])...

Solvatochromic shifts for cytosine have also been calculated with a variety of methods (see Table 11-7). Shukla and Lesczynski [215] studied clusters of cytosine and three water molecules with CIS and TDDFT methods to obtain solvatochromic shifts. More sophisticated calculations have appeared recently. Valiev and Kowalski used a coupled cluster and classical molecular dynamics approach to calculate the solvatochromic shifts of the excited states of cytosine in the native DNA environment. Blancafort and coworkers [216] used a CASPT2 approach combined with the conductor version of the polarizable continuous (CPCM) model. All of these methods predict that the first three excited states are blue-shifted. S i, which is a nn state, is blue-shifted by 0.1-0.2 eV in water and 0.25 eV in native DNA. S2 and S3 are both rnt states and, as expected, the shift is bigger, 0.4-0.6eV for S2 and 0.3-0.8 eV for S3. S2 is predicted to be blue-shifted by 0.54 eV in native DNA. 

M The DNA bases guanine and cytosine can form three hydrogen bonds, whereas adenine and thymine only form two (gray carbon, white hydrogen, red oxygen, blue nitrogen). 

Color Plate 29 DNA Sequencing by Capillary Gel Electrophoresis with Fluorescent Labels (Section 26-6) Tall red peaks correspond to chains terminating in cytosine and short red peaks correspond to thymine. Tall blue peaks arise from adenine and short blue peaks indicate guanine. Two different fluorescent labels and two fluorescence wavelengths were required to generate this information. [From M. C. Ruiz-Martinez, J. Berka, A. Belenkii,... 

Fig. 1. Two ribbon representations of the crystal structure of the DNA decamer d(CCTCG -CTCTC/GAGAG CGAGG) containing a unique cisplatin interstrand cross-link at d(GpC)-d(GpC) site (asterisks indicate the chelated bases in the adduct). A front view (A) allows to see the structure with the lesion in the minor groove. A side view (B) shows the chicane of the backbone with the helix-sense reversal. Ptn atom, yellow ammine groups, navy blue sugars, pink guanines, navy blue adenines, red thymines, yellow cytosines, hght blue phosphodiester backbone, green.

A comparison of aliphatic amides, cyclic amides, cyclic imides and 2,4-dioxopyrimidines (uracils) in their deprotonated and diplatinated form (Scheme 4) reveals an increasing steric shielding of the V-bonded Pt ion (Ptx). With respect to formation of stacked and partially oxidized dinuclear species, it is evident that application of the binding principles seen in the blues of cyclic amides to the uracils and imides allows for tetranuclear species only. On the other hand, the presence of an additional O-donor in the imides and uracils (and likewise the cytosines, vide infra) provides an... 

Creatinine, which has a close structural similarity with cytosine as far as potential metal-binding sites are concerned, has likewise shown to form blues , with both K2PtCl4 and ds-(NH3)2Ptn as reactants [81]. These blues can be positively charged, neutral or negatively charged, but structural data are not available. 

Figure 1 Electrostatic potentials on the molecular surfaces of (a) cytosine, 1, and (b) guanine, 2, computed at the Hartree-Fock 6-31G level. Color ranges, in kcal/mol red, more positive than 17 blue, more negative than —20 (see legend). The relative positions of the molecules are such that the portions that hydrogen bond are facing each other, showing how the extended positive and negative regions will interact. (See color plate at end of chapter.)...

MeT as one base, and neutral cytosine, guanine or adenine as second nucleobase proceeds without formation of undesired side products only if the anionic ligand is attached to Pt first. On the other hand, reaction of cis-Pt(II) with uracil or thymine in 1 1 ratio results in formation of the complicated platinum blues... 

FIGURE 50-3 Intracellular activation of nucleoside analog reverse transcriptase inhibitors. Drugs and phosphory-lated anabolites are abbreviated the enzymes responsible for each conversion are spelled out. The active antiretroviral anabolite for each drug is shown in the blue box. Key ZDV, zidovudine d4T, stavudine ddC, dideoxycytidine FTC, emtricitabine 3TC, lamivudine ABC, abacavir ddl, didanosine DF, disoproxil fumarate MP, monophosphate DP, diphosphate TP, triphosphate AMP, adenosine monophosphate CMP, cytosine monophosphate dCMP, deoxycytosine monophosphate IMP, inosine 5 -monophosphate PRPP, phosphoribosyl pyrophosphate NDR, nucleoside diphosphate. 

A comparison of the lowest singlet mi transition of cytosine tautomers presented in Tables 19 and 20 suggests that, widi respect to the keto-NlH tautomer, the transition in the keto-N3H tautomer is appreciably red-shifted for both the isolated and hydrated forms. While in the case of the enol and imino tautomers, the isolated forms show a blue-shift with respect to the isolated form of the keto-NlH tautomer for hydrated species, the imino form shows a slight blue-shift, and the enol form does not show any shift (Tables 19 and 20). The observed red-shift in the first mt transition of the keto-N3H tautomer is in accordance with the experimental fact that the absorption spectrum of 3-methylcytosine in aqueous media shows a significant red-shift with a peak near 289 nm (4.29 eV) compared to the corresponding transition of cytosine observed near 266 nm (4.66 eV). The observ transitions of 3-methylcytosine near 4.29 and 5.47 eV can be explained in terms of the computed transitions of hydrated forms of the keto-N3H tautomer near 4.25 and 5.68 eV, respectively (Table 20). The computed transitions of the imino form can be compared with the observed transitions of 3-methylcytidine in a water solution. Table 20 shows that the observed transition near 4.64 and 5.59 eV of 3-methylcj4idine can be explained in terms of the computed transitions of the imino form of cytosine within an error of about 0.3 eV. Therefore, it appears that the absorption spectra of aqueous solutions of cytosine would be mainly dominated by the keto-NlH tautomer and contributions fix>m other tautomers will not be significant. 

Both, purine and pyrimidine bases incorporated into nucleic acids, or in synthetic nucleic acid analogs, are able to bind specifically different metal ions [138]. For example, thymine yields a thymine-Hg -thymine complex, while cytosine forms specifically a cytosine-Ag -cytosine complex. Such properties of the nucleic acids were utilized to develop QDs-based Hg -ion and Ag + -ion sensors, with differentsized QDs being implemented for the multiplexed analysis of Hg and Ag + [139]. Two different-sized CdSe/ZnS QDs were modified with nucleic acids of specific ionbinding properties blue-emitting QDs ()iem = 560 nm) were functionalized with the thymine-rich nucleic acid (16) that binds Hg + -ions, while the red-emitting QDs (Xem = 620nm) were functionalized with the cytosine-rich nucleic acid (17) that associated with Ag + -ions (Figure 6.9a). The formation of Hg -modified complexes... 

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]...

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