Thymine orientation

In order to gain a more detailed insight into how the flavin and thymine dimer orientation may influence the excess electron transfer process, rigid... 

Single-stranded DNA or RNA may adopt hairpin structures in which the distance between two sequences is much shorter than in the absence of hairpin. Figure B9.4.1 shows two synthetic targets, both containing 45 nucleotides, but only the first one is able to form a hairpin via a loop of four thymines. The second one is used as a control. Both contain the complementary sequences for ethidium-13-mer and 11-mer-coumarin separated by the same number of bases. The efficiency of energy transfer from coumarin to ethidium is dose to zero for the control, whereas it is about 25% in the hairpin structure. This value is low but the spatial conformation of this particular three-way junction is only partially known, and the transfer efhdency depends on the relative orientation and/or distance between coumarin and ethidium. 

The EPR spectrum of irradiated DNA is not very well resolved. Attempts to improve the spectral resolution have used deuterated DNA and samples of oriented DNA. Using oriented DNA, Graslund et al. [35] suggested the thymine anion Thy and the cytosine cation Cyt were also considered possibilities. Later work reported that only Gua " and Thy were present [47]. 

The high rate of dimer formation in frozen solution reflects the necessity for a preferred orientation of the two thymine molecules concerned, but it is still considered that water plays an important part. Thymine in dried films,32,34 and on filter paper33 can be converted to dimer by ultraviolet light, but the maximum conversions are much lower, 1732-55%34 (depending upon the humidity34). 

Lamola and Eisinger169 have shown that the oriented adjacent pairs of 1,3-dimethyl-thymine monomers formed by photosplitting of the appropriate dimer in frozen solution will photodimerize again with a quantum yield of close to unity, and that the pair of monomers shows no fluorescence, but an exciton splitting in the absorption spectrum. 

Figure 12. Concentration dependence of the responses to 5 -GMP and 5 -AMP of the oriented membranes based on (a) cytosine derivative 10b, (b) thymine derivative 11b, and (c) cytosine derivative 22. The response factor, R(sample), is expressed by the decrease in the oxidation peak current (/e) upon analyte addition [/ (sample) = [/p(blank) - /p(sample)]//p(blank)l. Measured at 20 °C with a 0.1 M phosphate buffer solution (pH 6.0, 20 °C) containing 1.00 mM [FeICNIel .

Irradiation of frozen aqueous thymine solutions produces the cis head-to-head (chh) dimer, the high quantum yield (0.5-1.0) being attributed to the preferred orientation of adjacent molecules in the microcrystalline thymine hydrate. The gradual isolation of substrate molecules in the photodimer matrix is associated135 with the appearance and increase in intensity of molecular fluorescence as photodimerization proceeds identical behavior... 

The second experimental measure of the orientation of the dipole moment in the ground state of the bases was made by Seibold and Labhart405 for uracil and thymine. The direction of the ground state dipole moment with respect to the transition moment in the lowest excited singlet state has been determined from the influence of an... 

Figure 6.2. Molecular architecture of DNA. Each strand of DNA is composed of alternating pentose sugar (deoxyribose) and phosphate moieties linked to each other via phosphodiester linkage. The first carbon position of the sugar is attached to one of the four nitrogenous bases (A, T, G, or C). The two strands are in opposite orientation to each other with respect to a 5 or 3 phosphate group attached to the sugar moiety. Cytosine (C) pairs with guanine (G) via three hydrogen bonds, and adenine (A) pairs with thymine (T). (Reproduced from Textbook of Biochemistry with Clinical Correlations, T. M. Devlin, ed., Wiley, New York, 1982.)...

TRANSITION MUTATION A base-pair substitution mutation in which the purine pyrimidine base-pair orientation is preserved, as in adenine thymine -+ guanine cytosine. 

The orientation of the amino proton attached to the N2 donor on G differentiates the G C and C G base pairs from each other as well as from the A-T and T-A pairs. The latter base pairs can be discriminated by small synthetic molecules that take advantage of both the asymmetric steric structure of the adenine C2-H and the capability of the thymine 02 (with two sets of lone pair electrons) to form an additional hydrogen bond not possible with the pseudo-symmetrically related adenine N3 (37, 38). It is not yet clear whether naturally occurring, DNA-binding proteins use similar principles to distinguish between A T and T A base pairs in the minor groove. 

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