Investigation of the Origin of the Sequence Selectivity for the 5-Halo-2‘-deoxyuridine Sensitization of DNA to Damage by UV-Irradiation

Abstract

A contrathermodynamic sequence selectivity (5′-deoxyadenosine > 5′-deoxyguanosine) for UVirradiation-induced strand damage in duplex DNA containing 5-bromo-2′-deoxyuridine was reported several years ago (Saito, I.; Sugiyama, H. J. Am. Chem. Soc. 1990, 112, 6720.). In contrast, much smaller sequence selectivity was observed for similar duplexes containing 5-iodo-2′-deoxyuridine. We investigated the mechanism of UV-irradiation-induced cleavage of duplex DNA containing 5-bromo-2′-deoxyuridine (1, BrdU) and 5-iodo-2′-deoxyuridine (2, IdU) under anaerobic conditions using a variety of structural probes. The preference for UV-induced cleavage in 5′-dABrdU sequences is a confluence of at least three factors, photoinduced forward electron transfer, charge recombination, and electron migration within the DNA duplex. Our results also indicate that UV-irradiation of duplexes (32 nucleotides long) containing 5-iodo-2′-deoxyuridine results in strand scission involving initial photoinduced single electron transfer. The selectivity for 5′-dAIdU sequences is smaller than that in the analogous 5-bromo-2′-deoxyuridine duplexes and may be the result of faster dehalogenation of the initially formed 5-halopyrimidine radical anion and/or competitive direct carbon-iodine bond homolysis.5-Bromo-2′-deoxyuridine (1, BrdU) and 5-iodo-2′-deoxyuridine (2, IdU) exhibit a number of interesting and potentially useful chemical properties. 1 For instance, incorporation of these molecules in nucleic acids sensitizes the biopolymers to γ-radiolysis. 2 In addition, the 5-halopyrimidine nucleosides' sensitivity to UV-irradiation has been exploited in the application of these molecules as structural probes of protein-nucleic acid interactions and nucleic acid structure. 3,4 The enhancement of DNA damage caused by UV-irradiation of duplexes containing 1 and 2 has received considerable attention. 5-8 Approximately 10 years ago Saito and Sugiyama reported that UV-induced strand damage in duplex DNA containing 1 was highly dependent on the identity of the nucleotide bonded to the 5′-phosphate of 5-bromo-2′-deoxyuridine. 5 In contrast to previous studies, it was observed that UV-irradiated duplexes containing the sequence 5′-dABrdU exhibited significantly greater amounts of alkali-labile lesion formation than analogous molecules containing either a 2′-deoxyguanosine (dG) or 2′-deoxycytidine (dC) in place of the adjacent 2′-deoxyadenosine (dA). 9 These researchers postulated a novel mechanism involving initial photoinduced single electron transfer (PSET) from a 2′-deoxyadenosine bonded to the 5′-phosphate of 1 (Scheme 1). Preferential damage observed in 5′-dABrdU (3) sequences via PSET compared to those containing a 2′-deoxyguanosine nucleotide bonded to the 5′-phosphate of the halopyrimidine was surprising, given that electron transfer from deoxyguanosine is more favorable thermodynamically. 10 We now wish to report on studies that support this proposal, and demonstrate that the origin of this unexpected sequence selectivity for DNA damage in biopolymers ...

Komplexe Sequenzabhängigkeit beim Transport von Überschusselektronen durch DNA mit verschieden starken Acceptoren

“…In der Vergangenheit wurde die Auswertung des Überschusselektronentransfers durch DNA mit 5-BrdU als Acceptor durchgeführt, indem man das Ausmaß der Spaltung der DNA-Stränge bestimmte, die vom neutralen dU-Radikal nach Erhitzen mit Piperidin verursacht worden war. [35] Kapillarelektrophorese (CE) ermöglichte uns nun, direkt den Verlust des Br-Anions aus der 19-mer-Haarnadel nach Elektronenaufnahme zu detektieren. Als Beispiel für eine CE-Analyse ist in Abbildung 2 ein typisches Belichtungsexperiment mit der DNA-Haarnadel 1 a dargestellt.…”

DNA Radiosensitization: The Search for Repair Refractive Lesions Including Double Strand Breaks and Interstrand Crosslinks

“…The strand break positions migrate along the DNA strand, however, there is a clear preference for the dA 5'-flanking BrdU. Similarly, 5'-dABrdU-sequence preference has been observed in UV-induced BrdU DNA cleavage (Chen et al, 2000). This is to be expected since in B-DNA the 5' proximal 2'-deoxyribose would be the ultimate H-atom donor to the uracil-5-yl radical, whereas in A-DNA conformational (spatial) restrictions render the same 5'dA 2'-deoxyribose a lessaccessible H-donor.…”

“…The radiation dose-response for strand break formation was linear for both the brominated and the opposite, non-brominated strand within the single-stranded regions of a standard model scDNA containing a bulge formed by up to five mismatched bases (Dextraze et al, 2007). Interestingly, UVB-irradiation of BrdU-substituted DNA also demonstrated DNA-structure specificity, but in this situation BrdU greatly enhances breakage of only the brominated strand in dsDNA, or either the brominated or the non-brominated strand in the case of scDNA (Cecchini et al, 2005b;Chen et al, 2000). The different effects initiated by radiolysis and photolysis, especially with BrdU-dsDNA, underline the role of DNA structure-conformation properties in solution as a prerequisite for the initial electron-capture by BrdU and/or the propagation of an excess-electron along the polymer after gamma-irradiation.…”

Chemical Biology that Controls DNA Structure and Function: Lessons in Organic Chemistry from Nature

“…The Greenberg group has also confirmed this type of selectivity. 74 Since G is a better electron-donating base, the reactivity has been labeled a ''contrathermodynamic reaction.'' Recently, Br U was used as a probe of excess electron transfer.…”