Base-stacking

The UV spectra of polymer 17U in H2O and DMF, as a typical example, are given in Fig. 4, which showed a hyperchromicity of 30.1% in H2O (e=12,360, max=261 nm) and a hypochromicity of 29.7% in DMF (e=6690, imax=268 nm), compared with those of 2 -deoxyuridine in the relevant solvents (e=9500, Xmax=263nm in H2O and e=9350, imav-267 nm in DMF), respectively [11]. It is notable that hyperchromicity has rarely been found in aqueous solutions of nucleic acids though it was predicted theoretically. 

Polymer 17U was composed of uracil-1-yl furanoid as hydrophobic and di-carboxydimethylene as hydrophilic groups. The carboxyl groups of the polymer in an aqueous solution protruded outward interacting with the aqueous environment. Consequently, the polymer had a conformation such that the chromophores aggregated into head-to-tail order in H2O to cause the hyper-chromicity. On the other hand, the uracil groups in the polymer were stacked one upon another in DMF to cause hypochromicity, which was also consistent with the fact that the UV extinction of the polymer in DMF was about half of that in H2O. 

The UV extinction and maximal wavelength of the polymer were measured in solvent mixtures of DMF-H2O after equilibration for 24 h at 25 °C. When the water content was increased in the solvent mixture, the extinction was increased while the wavelength of absorption maxima was blue-shifted. At a solvent composition of water 50 vol %, the extinction was equal to that of free uracil as well as the mean value of the two forms. 

In order to confirm whether an equilibrium state can be attained at the same solvent composition, starting from either one of the two forms, the polymer was dissolved in H2O or in DMF and the time-dependent extinction changes were measured after diluting with DMF or H2O, respectively (Fig. 5) [11]. The equilibrium value of extinction was attained quickly from the hypo- 

Some of polymers 17 and 19 formed excimers in aqueous solution. Exci-mers are observed in bichromophoric molecules, where the aromatic chromo-phores are separated by a three-atom linkage. Excimer formation in these systems requires rotational motion around the bond of the linkage to allow two chromophores to have, within the lifetime of the excited state, a conformation suitable for complex formation in which two aromatic rings overlap in a sandwich-like arrangement [35, 36]. When these geometrical requirements are satisfied for the pendent chromophores on the polymer chains, the polymer shows an excimer fluorescence as observed in polyfvinyl aromatic)s [37] and polymers containing chromophoric pendant groups [38]. 

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Kaye and Chou39 also studied the effect of base stacking on the conformation of PA using osmometry, intrinsic viscosity, and light-scattering. The ideal behavior (under the 0 conditions) of PA existed at neutral pH (= 7.4) and at 26 and 40 °C from the osmotic measurements. 

H-HOESY and PGSE NMR studies of neutral trinuclear complexes of Aul and Hgll evidence for acid-base stacking in solution. Journal of the American Chemical Society, 124, 4570. 

Several papers describe extension of the Haure work to the scrubbing of industrial stack gases as one step of a carbon based stack-gas cleanup process referred to as the RTI-Waterloo Process (Gangwal et al., 1992 ... 

Bases stacked rather than hydrogen bonded have also been studied with quantum chemical methods [182, 244-247]. The nature of excited states in these systems has been debated and theoretical calculations are called to decide on the degree of excited state localization or delocalization, as well as the presence and energy of charge transfer states. The experimentally observed hypochromism of DNA compared to its individual bases has been known for decades [248], Accurate quantum chemical calculations are limited in these systems because of their increased size. Many of the reported studies have used TDDFT to calculate excited states of bases stacked with other bases [182, 244, 246, 247], However, one has to be cautious when us-... 

Crespo-Hernandez CE, Cohen B, Kohler B (2005) Base stacking controls excited-state dynamics in A-T DNA. Nature 436 1141-1144... 

Wu P, Norland TM, Gildea B, McLaughlin LW (1990) Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base. Biochem 29 6508-6514... 

Hardman SJO, Thompson KC (2006) Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochem 45 9145-9155... 

Jean JM, Hall KB (2001) 2-aminopurine fluorescence quenching and lifetimes role of base stacking. Proc Natl Acad Sci USA 98 37-41... 

Santoro F, Barone V, Improta R (2007) Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. Proc Natl Acad Sci... 

Fig. 1 The w-stack of double helical DNA. In this idealized model of B-DNA the stack of heterocyclic aromatic base pairs is distinctly visible within the sugar-phosphate backbone (schematized by ribbons) a view perpendicular to the helical axis b view down the helical axis. It is the stacking of aromatic DNA bases, approximately 3.4 A apart, that imparts the DNA with its unique ability to mediate charge transport. Base stacking interactions, and DNA charge transport, are exquisitely sensitive to the sequence-depen-dent structure and flexibility of DNA...

Fig. 5 Charge transfer occurs through the DNA /r-stack and is strongly dependent on minor base stack perturbations. Photoinduced electron transfer is observed from tethered intercalated ethidium to a rhodium intercalator bound to DNA up to 30 A away. The efficiency of electron transfer is drastically reduced in the presence of a stacking disruption, here a single base-pair mismatch... 

In order to directly probe the dynamics of CT between Et and ZG, and to understand how the intervening DNA base stack regulates CT rate constants and efficiencies, we examined this reaction on the femtosecond time scale [96]. These investigations revealed not only the unique ability of the DNA n-stack to mediate CT, but also the remarkable capacity of dynamical motions to modulate CT efficiency. Ultrafast CT between tethered, intercalated Et and ZG was observed with two time constants, 5 and 75 ps, both of which were essentially independent of distance over the 10-17 A examined. Significantly, both time constants correspond to CT reactions, as these fast decay components were not detected in analogous duplexes where the ZG was re-... 

In many investigations of CT, pendant redox probes interact with both bases of abase pair. However, studies of base-base charge transfer can differentiate between discrete intra- and interstrand reactions (Fig. 7). These investigations further attest to the critical role of base stacking in DNA-mediated CT. In B-DNA duplexes, stacking interactions are largely restricted to... 

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