Direct Chemical Evidence for Charge Transfer between Photoexcited 2-Aminopurine and Guanine in Duplex DNA

Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (^(CP)G), initiates hole transfer from Ap* followed by rapid ring opening of the ^(CP)G radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products

Effects of the Photooxidant on DNA-Mediated Charge Transport

A direct comparison of DNA charge transport (CT) with different photooxidants has been made. Photooxidants tested include the two metallointercalators, Rh(phi)_2(bpy‘)^(3+) and Ru(phen)(bpy‘)(dppz)^(2+), and three organic intercalators, ethidium (Et), thionine (Th), and anthraquinone (AQ). CT has been examined through a DNA duplex containing an A_6-tract intervening between two 5‘-CGGC-3‘ sites with each of the photooxidants covalently tethered to one end of the DNA duplex. CT is assayed both through determination of the yield of oxidative guanine damage and, in derivative DNA assemblies, by analysis of the yield of a faster oxidative trapping reaction, ring opening of N^2-cyclopropylguanine (d^(CP)G) within the DNA duplex. We find clear differences in oxidative damage ratios at the distal versus proximal 5‘-CGGC-3‘ sites depending upon the photooxidant employed. Importantly, nondenaturing gel electrophoresis data demonstrate the absence of any DNA aggregation by the DNA-bound intercalators. Hence, differences seen with assemblies containing various photooxidants cannot be attributed to differential aggregation. Comparisons in assemblies using different photooxidants thus reveal characteristics of the photooxidant as well as characteristics of the DNA assembly. In the series examined, the lowest distal/proximal DNA damage ratios are obtained with Ru and AQ, while, for both Rh and Et, high distal/proximal damage ratios are found. The oxidative damage yields vary in the order Ru > AQ > Rh > Et, and photooxidants that produce higher distal/proximal damage ratios have lower yields. While no oxidative DNA damage is detected using thionine as a photooxidant, oxidation is evident using the faster cyclopropylguanosine trap; here, a complex distance dependence is found. Differences observed among photooxidants as well as the complex distance dependence are attributed to differences in rates of back electron transfer (BET). Such differences are important to consider in developing mechanistic models for DNA CT

Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA–ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs

DNA オ バイタイ ト スル チョウキョリ デンカ イドウ ノ キコウ ニ カンスル ケンキュウ

京都大学0048新制・課程博士博士(工学)甲第9583号工博第2169号新制||工||1238(附属図書館)UT51-2002-G341京都大学大学院工学研究科合成・生物化学専攻(主査)教授 齋藤 烈, 教授 青山 安宏, 教授 森島 績学位規則第4条第1項該当Doctor of EngineeringKyoto UniversityDA

DNA オ バイタイ ト スル チョウキョリ デンカ イドウ ノ キコウ ニ カンスル ケンキュウ

京都大学0048新制・課程博士博士(工学)甲第9583号工博第2169号新制||工||1238(附属図書館)UT51-2002-G341京都大学大学院工学研究科合成・生物化学専攻(主査)教授 齋藤 烈, 教授 青山 安宏, 教授 森島 績学位規則第4条第1項該当Doctor of EngineeringKyoto UniversityDA