Highly sequence-selective photoreaction of 5-bromouracil-containing deoxyhexanucleotides

Sugiyama, Hiroshi; Tsutsumi, Yoshitaka; Saito, Isao

doi:10.1021/ja00174a046

Cited by 147 publications

(145 citation statements)

References 0 publications

Supporting

Mentioning

134

Contrasting

Unclassified

Order By: Relevance

“…These species include the hydroxyl radical, the product formed from water by γ-radiolysis, and the sigma radicals formed upon irradiation of 5-halopyrimdines in DNA (11)(12)(13)(14)(15). Until recently, when a method for synthesizing oligonucleotides containing C2-AP was reported, little was known about the lesion's biochemical effects (16).…”

mentioning

confidence: 99%

Replication of an Oxidized Abasic Site in Escherichia coli by a dNTP-Stabilized Misalignment Mechanism that Reads Upstream and Downstream Nucleotides

et al. 2006

View full text Add to dashboard Cite

Abasic sites (AP) and oxidized abasic lesions are often referred to as noninstructive lesions because they cannot participate in Watson-Crick base pairing. The aptness of the term noninstructive for describing AP site replication has been called into question by recent investigations in E. coli using single-stranded shuttle vectors. These studies revealed that the replication of templates containing AP sites or the oxidized abasic lesions resulting from C1′-(L) and C4′-oxidation (C4-AP) are distinct from one another, suggesting that structural features other than Watson-Crick hydrogen bonds contribute to controlling replication. The first description of the replication of the abasic site resulting from formal C2′-oxidation (C2-AP) is presented here. Full-length and single-nucleotide deletion products are observed when templates containing C2-AP are replicated in E. coli. Single nucleotide deletion formation is largely dependent upon the concerted effort of pol II and pol IV, whereas pol V suppresses frameshift product formation. Pol V utilizes the A-rule when bypassing C2-AP. In contrast, pol II and pol IV utilize a dNTP-stabilized misalignment mechanism to read the upstream and downstream nucleotides when bypassing C2-AP. This is the first example in which the identity of the 3′-adjacent nucleotide is read during the replication of a DNA lesion. The results raise further questions as to whether abasic lesions are noninstructive lesions. We suggest that abasic site bypass is affected by the local biopolymer structure in addition to the structure of the lesion.Abasic sites (AP 1 ), the most common DNA lesions formed, are produced in a variety of ways in DNA, including as intermediates during base excision repair (1-3). In addition, a variety of oxidized abasic lesions are produced when DNA is exposed to oxidative stress. DNA damaging agents selectively produce oxidized abasic lesions, including 2-deoxyribonolactone (L), and the C4′-oxidized abasic site (C4-AP) (Figure 1) (4-7). These agents take advantage of the accessibility and/or relatively low bond strength of the respective carbon-hydrogen bonds (8-10). The C2′-carbon-hydrogen bond is the strongest of the deoxyribose bonds in DNA. Consequently, the C2-AP lesion is only produced by highly reactive species, presumably via † Supported by NIGMS grants GM-063028 to M.M.G. and ES-012259 and GM-021422 to M.F.G. * To whom correspondence should addressed. . E-mail: mgreenberg@jhu.edu.. ‡ Johns Hopkins University. § University of Southern California.SUPPORTING INFORMATION AVAILABLE ESI-MS of the oligonucleotides (3) containing C2-AP used to prepare the single-stranded plasmids and a figure describing the REAP experiment. This material is available free of charge via the Internet at http://pubs.acs.org. 1 Abbreviations: C2′-oxidized abasic site, C2-AP; C4′-oxidized abasic site, C4-AP; abasic site, AP; 2-deoxyribonolactone, L; tetrahydrofuran abasic site model, F; polyacrylamide gel electrophoresis, PAGE; DNA polymerase II, pol II; DNA polymerase IV, pol IV; DNA...

show abstract

mentioning

confidence: 99%

Replication of an Oxidized Abasic Site in Escherichia coli by a dNTP-Stabilized Misalignment Mechanism that Reads Upstream and Downstream Nucleotides

et al. 2006

View full text Add to dashboard Cite

show abstract

“…The formed 5-uracyl radical abstracts a hydrogen form the 5' adjacent deoxyribose, which eventually affords alkali label products under aqueous conditions. [14] The EET efficiency can then be evaluated by fragment analysis using polyacrylamide gel electrophoresis (PAGE) and control sequences as markers for the specific fragments (see figure 2). With the phosphoramidites of C-AP, phen, CN phen,…”

mentioning

confidence: 99%

Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

Roethlisberger

Kaliginedi

Leumann

2017

Chemistry A European J

View full text Add to dashboard Cite

The modulation of excess electron transfer (EET) within DNA containing a dimethylaminopyrene (C-AP) as an electron donor and 5-bromouracil ( Br dU) as a electron acceptor through phenanthrenyl pairs (phen-R) could be achieved by modifying the phenanthrenyl base surrogates with electron withdrawing and donating groups. Arranging the phenanthrenyl units to form a descending LUMO gradient increased the EET efficiency compared to the electron transfer through uniform LUMOs or an ascending LUMO gradient.The well-defined double helical structure of DNA with the linear arranged base pairs represents a suitable scaffold for charge transfer and is therefore subject to intense studies in DNA damage, [1] sensors [2] and applications in molecular electronics.[3]The reductive electron transfer also called excess electron transfer (EET) in DNA is a process that is directed through the lowest unoccupied molecular orbital (LUMO) of the DNA bases. Investigations elucidated that the charge transfer over longer distances occurs via electron hopping mostly through thymine bases (k = 10 10 s -1). [4] In earlier studies it was shown that the replacement of the natural base pairs by non-hydrogen bonding base surrogates with extended aromatic surfaces such as phenanthrene could have beneficial conducting properties and could overcome the physico-chemical limitations of the natural nucleobases.[5] Regarding the reduction of such base surrogates the choice of the electron injector is crucial for the success of the experiments. Investigations by Grigorenko et. al. revealed that pyrene ( Py dU, Ered* = -2.2 V vs NHE) [6] only enables a superexchange mechanism, whereas phenothiazine (PTZ, Ered* = -2.7 V vs SCE) [7] allowed to trigger the system into an electron hopping mechanism with a transport that spreads over longer distances.[5] A photoexcitable dimethyl amino-pyrenyl donor attached to a deoxyuracil ( AP dU, Ered* = -2.2 V vs NHE) [8] that exhibits suitable redox properties for long range charge transfer experiments was successfully used by Bätzner et. al. to inject an electron in hydroquinoline base surrogates. [9] In this study, we investigated the EET through DNA containing phenanthrenyl base surrogates with different reduction potentials and LUMO energy levels. It is believed that the electron transfer within DNA can be modulated by the installation of a potential energy gradient.[10] The predicted advantage of such a redox/LUMO gradient was envisioned to be the unidirectionality of the electron transfer and therefore a gain in efficiency. The installation of the different reduction potentials was deemed to be possible by the introduction of electron withdrawing (CN) and donating (NH2) groups at the 7-position of the phenanthrene (phen). The synthesis of the NH2 phen and phen phosphoramidites applicable for automated DNA synthesis was performed according to published procedures.[11] The introduction of a cyano group required a palladium catalyzed substitution of the intermediate 9 with copper-(I)-cyanide. Tritiylation and phosphiti...

show abstract

“…Recently, Br U has been used as an electron trap in DNA-mediated excess electron transfer processes (12, 13), because the formation of the anion radical of Br U rapidly eliminates bromo anions, to generate the uracil-5-yl radical (14,15). Recently, we examined the photoreactions of 5-iodouracil ( I U)-containing 5Ј-d(GTAAT-I UAC)-3Ј and the Sso7d chromosomal protein from the hyperthermophilic archaeabacteria Sulfolobus solfataricus (8, 9) and demonstrated that the uracil-5-yl radical abstracts hydrogen from the methyl group of T 5 at the sharp kink (16).…”

Section: Resultsmentioning

confidence: 99%

Photoreactivation of DNA by an Archaeal nucleoprotein Sso7d

Tashiro

Wang

Sugiyama

2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Archaea ͉ DNA repair ͉ electron transfer ͉ thymine dimer U ltraviolet light from the sun causes various types of DNA damage that induce mutations, carcinogenesis, and cell death. Pyrimidine-pyrimidine photodimers are typical products of photoinduced damage (1). Photolyase repairs thymine dimers by using electron transfer from cofactor domains under light. Recently, Barton and colleagues (2-4) proposed an attractive hypothesis that some repair enzymes use electron transfer from redox cofactors for detection of oxidatively generated DNA damage. Evidence that photolyase can also repair thymine dimers without the involvement of a cofactor (1, 5) suggests that the amino acid itself has the potential to repair DNA by a photoinduced electron transfer mechanism. In the living cell, DNA is usually associated with various types of nucleoproteins, which implies the existence of DNA repair activities in nucleoproteins. In fact, Cullis et al. (6) demonstrated that the guanine radical formed in DNA is reduced by electron transfer from histone, even though the detailed mechanisms is not known. The Archaea, as representatives of one of the oldest lineages, offer special insight into the origin of cellular life and the ancestry of eukaryotes (7). Sso7d and Sac7d are nucleohistone-like proteins of archaea, and structures of their DNA complexes have been solved by x-ray crystallography and NMR (refs. 8-10 and Fig. 1). In this article, we demonstrate electron transfer from the archaeal nucleosomal protein Sso7d to DNA by using 5-bromouracil ( Br U) residue. We also demonstrate that the electron transfer from Sso7d effectively repairs a TϽϾT dimer. Results and DiscussionDetection of Electron Transfer from Sso7d to DNA by Using Br U.5-Halouracil, a photoreactive analogue of thymine, has been widely used for biological assays and studies of DNA chemistry (11-14).Recently, Br U has been used as an electron trap in DNA-mediated excess electron transfer processes (12, 13), because the formation of the anion radical of Br U rapidly eliminates bromo anions, to generate the uracil-5-yl radical (14,15). Recently, we examined the photoreactions of 5-iodouracil ( I U)-containing 5Ј-d(GTAAT-I UAC)-3Ј and the Sso7d chromosomal protein from the hyperthermophilic archaeabacteria Sulfolobus solfataricus (8, 9) and demonstrated that the uracil-5-yl radical abstracts hydrogen from the methyl group of T 5 at the sharp kink (16).Because we recently found that photoinduced electron transfer occurs from guanine (G) to Br U through an A͞T bridge in duplex DNA (17), evaluation of the contribution of the electron transfer process in this system might be important. Therefore, we examined the photoreactivity of 5Ј-d(GTAAT Br UAC)-3Ј (ODN1) in the presence and absence of Sso7d.HPLC product analysis indicated that photoirradiation of ODN1 alone mainly gave 2-deoxyribonolactone-containing octamers, 1 (Fig. 2A). This result is consistent with previous observations (16,17). Upon addition of Sso7d to the reaction mixture, the photoreactivity of ODN1 was enhanced, ...

show abstract

Highly sequence-selective photoreaction of 5-bromouracil-containing deoxyhexanucleotides

Cited by 147 publications

References 0 publications

Replication of an Oxidized Abasic Site in Escherichia coli by a dNTP-Stabilized Misalignment Mechanism that Reads Upstream and Downstream Nucleotides

Replication of an Oxidized Abasic Site in Escherichia coli by a dNTP-Stabilized Misalignment Mechanism that Reads Upstream and Downstream Nucleotides

Modulation of Excess Electron Transfer through LUMO Gradients in DNA Containing Phenanthrenyl Base Surrogates

Photoreactivation of DNA by an Archaeal nucleoprotein Sso7d

Contact Info

Product

Resources

About