Photochemical generation of oligodeoxynucleotide containing a C4'-oxidized abasic site and its efficient amine modification: dependence on structure and microenvironment

Bleomycin-induced oxidative DNA damage under limited oxygen conditions results in the formation of the C4'-oxidized abasic site (1). We synthesized the oligodeoxynucleotides (ODN) 5, which contains 4'-o-nitrobenzyloxythymidine (3), and 6, which contains 2-nitrobenzyloxy-4'-methoxy-2'-deoxy-d-ribofuranoside (4), as the caged precursors of 7, an ODN containing 1, to study its reactivity with amines. Photoirradiation of the single- and double-stranded 5 led to the formation of 7. Uncaging of the duplex was faster and the yield of 7 was higher with the double-stranded than with the single-stranded ODN. It was suggested that a low dielectric environment of the o-nitrobenzyloxy group in the minor groove of the duplex might accelerate the uncaging rate. Similarly, 6 and its duplex yielded 7 by photoirradiation. However, the yields of 7 were lower than those of 5, and duplex formation slowed the uncaging rate. Reaction of the obtained 7 with an amine resulted in the formation of the lactam 2b in good yield in both single- and double-stranded forms, showing that amine modification of biomolecules by an ODN containing 1 is possible under physiologic conditions.     

Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides

Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.     

Preparation and analysis of oligonucleotides containing the c4'-oxidized abasic site and related mechanistic probes

The C4'-oxidized abasic site (C4-AP) is produced by a variety of DNA damaging agents. This alkali labile lesion can exist in up to four diastereomeric cyclic forms, in addition to the acyclic keto-aldehyde. Synthetic oligonucleotides containing the lesion were prepared from a stable photochemical precursor. Chemical integrity of the lesion containing oligonucleotides was probed using phosphodiesterase lability. Analysis of the 3',5'-phosphate diester of the monomeric lesion released from single diastereomers of photolabile precursors by 1H NMR indicates that isomerization of the hemiacetal and/or hemiketal is rapid. The syntheses and characterization of oligonucleotides containing configurationally stable analogues of C4-AP, which serve as mechanistic probes for deciphering the structural basis of the biochemical and biological effects of the C4'-oxidized abasic lesion, are also described.     

Photochemical generation of ribose abasic sites in RNA oligonucleotides

[reaction: see text] A general method for the photochemical generation of ribose abasic sites within RNA oligonucleotides is reported. Photochemically caged nucleoside phosphoramidite analogues were prepared and incorporated into RNA oligonucleotides by automated RNA synthesis. Irradiation of the modified RNA at 350 nm efficiently produced ribose abasic sites at specific sites within RNA sequences. The current approach offers a chemical route to RNA abasic lesions for RNA biochemical studies.     

Synthesis and analysis of oligonucleotides containing abasic site analogues

DNA damage results in the formation of abasic sites from the formal hydrolysis of the glycosidic bond (AP) and several oxidized abasic lesions. Previous studies on AP sites revealed that DNA polymerases preferentially incorporated dA opposite them in approximately 80% of the replication events in Escherichia coli. These results were consistent with the hypothesis that the AP sites are noninstructive lesions due to the absence of a Watson-Crick base whose bypass adheres to the "A-rule." Recent replication studies of the oxidized abasic lesion, 2-deoxyribonolactone (L), revealed that DNA polymerase(s) does not apply the A-rule when bypassing it and incorporates large amounts of dG opposite L. These studies suggested that abasic sites such as L do direct polymerases to selectively incorporate nucleotides opposite them. However, it was not possible to determine the structural basis for this molecular recognition from these experiments. A group of oligonucleotides containing analogues of the AP and L lesions were synthesized and characterized as probes to gain insight into the structural basis for the distinct effect of 2-deoxyribonolactone on replication. These molecules will be useful tools for studying replication in cells and in vitro.     

Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms, such as cancer, due to their reduced probability to be repaired by the enzymatic repair machinery of the cell. Although experimental results have revealed that clustered DNA damage sites effectively retard the efficient function of repair enzymes, it remains unclear as to what particular factors influence this retardation. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of two lesioned sites, namely 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic (AP) site, located within a few base pairs of each other. After 1 ns of MD simulation, one of the six DNA molecules containing a clustered damage site develops specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8-oxoG and bases located on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity.     

Generation of an abasic site in an oligonucleotide by using acid-labile 1-deaza-2'-deoxyguanosine and its application to postsynthetic modification

We developed a new convenient method for generation of an abasic site at the 3'-terminus of an oligonucleotide. This method uses a 1-deaza-2'-deoxyguanosine residue, which easily undergoes depurination under acidic conditions. The abasic site of the oligonucleotide can be further modified with external functional groups. We report herein the chemical stability of 1-deaza-2'-deoxyguanosine in the oligodeoxynucleotide and the application to the postsynthetic modification of an oligonucleotide by utilizing the chemical property of 1-deaza-2'-deoxyguanosine. [Structure: see text]     

Photochemical generation of tetramethyldisilene and photoinduced 1,2-silyl-migration

Described herein is the first clear evidence of the photochemical generation of tetramethyldisilene which can be efficiently trapped by dienes. An intriguing 1,2-photo-induced silyl migration is also reported.     

Photochemical generation and matrix-isolation detection of dimethylvinylidene.

We report the spectroscopic characterization of dimethylvinylidene, (CH3)2C=C:, generated within an argon matrix at 14 K from a bisperoxyester precursor. The carbene was identified by comparison of the experimental IR spectrum with vibrational frequencies computed at the B3LYP/6-31G(d) level. Chemical trapping of the carbene within a 9% CO/Ar matrix to form dimethylpropadienone supports this analysis. Additional products produced during photolysis were identified by comparison to the appropriate computed vibrational frequencies. The potential energy surface of dimethylvinylidene and its intramolecular rearrangement products, 2-butyne and methylcyclopropene, were also investigated computationally at the B3LYP/6-31G(d) level. A spin-state analysis of this carbene using a variety of computational methods (CCSD(T), B3LYP, MP2) indicates the singlet state is more stable than the triplet by approximately 45 kcal mol-1. We anticipate the bisperoxyester precursor used here will be a convenient and general way for initiating future studies of alkylvinylidenes under matrix-isolation conditions.     

Photochemical modification of polymer surface by the pendant photobase generator containing oxime‐urethane groups and its application to an image‐recording material

Copolymers containing oxime‐urethane groups were prepared by the copolymerization of methyl methacrylate and benzophenoneoximinocarbonylaminoethyl methacrylate (BCM), and their photochemical properties were examined from the UV and IR absorption spectral changes. The decomposed fraction of oxime‐urethane groups in the copolymer increased with irradiation time, but it decreased with the content of BCM units in the copolymer. Changes of the surface properties of the copolymer film on irradiation were studied by measurements of the contact angle and dyeing with an acid dye. The surface of the copolymer film changed to become more hydrophilic upon irradiation with 254 nm of UV light. After the irradiated copolymer films were treated with HCl or methanol, changes of the contact angle of water on irradiation were compared. The copolymer film was dyed by acid dyes after treatment of the irradiated film with HCl. The degree of dyeing increased with irradiation time and BCM units in the copolymer, but it was unaffected by the film thickness. Various colors were developed on the irradiated area depending on the acid dye as the developer. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1200–1207, 2002     

Photochemical generation of dihydrogen complexes of chromium and tungsten

Photolysis of solutions of M(CO)(6) (M = Cr, W) at low temperature in the presence of hydrogen gas affords Cr(CO)(5)(H(2)) (1) and W(CO)(5)(H(2)) (2). Complexes 1 and 2 are characterized as dihydrogen complexes based on short T(1) values for the hydride resonances and the observation of a large HD coupling in the HD derivatives. Irradiation of a phosphine-substituted derivative (PMe(3))Cr(CO)(5) in the presence of hydrogen gas gave similar results. Thus cis-(PMe(3))Cr(CO)(4)(H(2)) (3) and trans-(PMe(3))Cr(CO)(4)(H(2)) (4) were prepared and characterized by (1)H and (31)P NMR spectroscopy. When the photolysis reactions were carried out in methylene chloride, solvent binding competitive with hydrogen binding was observed. This was not observed in less coordinating solvents such as alkanes. Subsequent displacement of solvent by H(2) leads to the dihydrogen complexes. Complexes 1 and 2 are moderately acidic, with deprotonation effected by mild bases.     

Photochemical vapor generation of selenium: Mechanisms and applications

Selenium was the first reported element that could be converted into its volatile compounds via photochemical vapor generation (photo-CVG) process before its atomic spectrometric detection. Photo-CVG is a newly emerging vapor generation technique, offering its inherent advantages of matrix interferences eliminated and high vapor efficiency etc., photo-CVG has been combined with various methods for selenium determination and mechanism exploration. Herein, we summarize the development of selenium in photo-CVG from the first report in 2003, the mechanisms of selenium with or without TiO₂ were discussed and its applications for selenium determination, speciation analysis and prereduction were summarized.     

Photochemical generation and trapping of radicals from bisphenyl carbodiazone

UV irradiation at 350 nm of bisphenyl carbodiazone creates nitrogen, phenyl and (phenyldiazenyl)carbonyl radicals under mild conditions. The radicals formed were trapped by olefins and tetramethylpiperidinoxyl radicals.     

Photochemical generation of six- and five-membered cyclic vinyl cations

The photochemical solvolyses of 4-tert-butylcyclohex-1-enyl(phenyl)iodonium tetrafluoroborate (1) and cyclopent-1-enyl(phenyl)iodonium tetrafluoroborate (2) in methanol yield vinylic ethers and vinylic cycloalkenyliodobenzenes and cycloalkenylbenzene, which are the trapping products of the geometrically destabilized C6-ring and C5-ring vinyl cation with the solvent and with the leaving group iodobenzene. Iodonium salt 2 also yields an allylic ether and allylic cyclopentenyliodobenzenes and cyclopentenylbenzene, which are the trapping products of the C5-ring allylic cation produced from the C5-ring vinyl cation by a hydride shift in a typical carbocationic rearrangement.     

Photochemical modification and patterning of SU-8 using anthraquinone photolinkers

Bioactive protein patterns and microarrays achieved by selective localization of biomolecules find various applications in biosensors, bio-microelectromechanical systems (bio-MEMS), and in basic protein studies. In this paper we describe simple photochemical methods to fabricate two-dimensional patterns on a Novolac A derivative polymer (SU-8) and, subsequently, their functionalization with biomolecules. Anthraquinone (AQ) derivatives are used to chemically modify and pattern SU-8 surfaces. Features as small as 20 mum are obtained when using uncollimated light. The X-Y spatial resolution of micropatterned AQ molecules is improved to 1.5 mum when a collimated light source is used. This micropatterning process will be important for the functionalization of MEMS-based biosensors. The method saves several processing steps and can be integrated in cleanroom fabrication thus avoiding contamination of the sensor surfaces.     

不同模板剂含量MCM-49分子筛的CTAB修饰及在苯甲醚酰基化反应中的应用

芳香族化合物的Friedel-Crafts酰基化反应是制备芳香酮的一类重要反应,传统的Lewis酸(如AlCl3)和质子酸(如H2SO4)催化剂易制备,价格便宜,但存在对环境污染严重、与产物难分离等问题.因此,近年来研究者一直致力于环境友好催化剂的研发,其中分子筛因选择性好、与产物易分离、可再生和无污染等优点而日益受到人们的重视,尤其是MWW分子筛,由于具有较多的外表面酸性位,而在酰基化反应中表现出良好的抗积碳性能.本课题组曾讨论了对一系列不同模板剂(六亚甲基亚胺, HMI)含量的MCM-49分子筛进行NaOH与十六烷基三甲基溴化铵(CTAB)共处理的情况,而本文重点考察的是只用CTAB处理不同HMI含量的MCM-49分子筛时,其结构与酸性会如何变化,改性前后样品的结构与酸性借助XRD, N2吸脱附等温线测试,29Si与27Al MAS NMR, NH3-TPD, Py-IR与漫反射傅里叶变换红外光谱(DRIFTS)等技术进行表征.另外,将一系列样品用于催化苯甲醚(AN)与乙酸酐(AA)的酰基化反应,考察CTAB处理对MCM-49分子筛催化性能的影响.将含模板剂HMI的MCM-49分子筛原粉在不同温度(250,350,450或550°C)下焙烧,得到一系列不同孔道系统内保留HMI的样品,随后采用CTAB溶液(0.27 mol/L)对其在70°C下进行后处理1 h.结构表征的结果表明,在脱除模板剂HMI及CTAB处理的过程中,分子筛骨架结构基本未被破坏,同时, CTAB处理不能向分子筛中引入任何形式的介孔,无论是晶内介孔还是晶间介孔.在CTAB处理时,可以清除分子筛中部分无定形物种,尤其是无定形Al物种,同时也可能发生部分非骨架Al原子重新进入分子筛骨架的情况,造成骨架铝的比例相对提高.根据29Si与27Al MAS NMR结果可以推断,进入分子筛骨架的Al原子可能会取代T3位置上的Si原子,亦或直接进入T2或T3位置缺陷位.酸性表征的结果表明, CTAB修饰后样品Br?nsted酸量比HMCM-49明显提高,并随HMI含量的逐渐降低呈现先增加后降低的趋势,而Lewis酸量则相对于HMCM-49有所降低.将一系列CTAB修饰前后的MCM-49样品用于催化AN与AA的酰基化反应,反应条件为：压力1.0 MPa、温度110°C、总质量空速WHSV(AN+AA)为10.2 h?1及原料中AN与AA的摩尔比为5：1.反应数据表明,相对于HMCM-49样品, CTAB修饰后样品对应的AA转化率显著提高(初始转化率由51.4%最高增加至85.0%),并随CTAB处理过程中HMI含量的逐渐降低呈现先增加后降低的趋势,而产物选择性则基本没有变化.各样品的AA初始转化率与其Br?nsted酸量基本呈现正向关联.通过间二甲苯歧化反应预积碳堵塞超笼及碱性探针分子2,4-二甲基喹啉吸附覆盖表面半超笼的方法,研究CTAB修饰前后各样品的不同孔道系统对酰基化反应的催化贡献.结果表明,酰基化反应主要发生在MCM-49分子筛的表面半超笼,其次为超笼,正弦孔道的贡献很小.另外, CTAB修饰后样品催化活性的提高主要来自于不含HMI的孔道系统的贡献,进一步验证在CTAB处理过程中,改性作用主要发生在MCM-49分子筛中不含HMI的区域.结合表征和反应评价结果,提高酰基化反应活性需尽可能提高催化剂的Br?nsted酸量,这是分子筛催化剂今后改进的一个主要方向.     

Photochemical Reactions in Gaseous Mixtures of C2F4 and CF3I

Products of photochemical reactions occurring in gaseous mixtures of C₂F₄ and CF₃I under vacuum-UV irradiation were studied. The major photolysis products are linear perfluoroparaffins C _n F_2n+2 and linear perfluoroalkyl iodides C _n F_2n+2I. The product ratio is consistent with the suggested kinetic scheme of chain reactions of telomers.     

Photochemical generation of carbonate radicals and their reactivity with phenol

The reaction of carbonate radical with phenol in aqueous solution has been investigated in systems in which carbonate radicals were generated by UV irradiation of an aqueous solution of [Co(NH₃)₅CO₃]⁺ (pH 8.0 phosphate buffer). Both steady state and time resolved photolysis experiments were performed. Upon continuous irradiation of complex phenol mixtures, phenol was converted into benzoquinone and dihydroxybenzenes. Benzoquinone was the major by-product in the early stages of the reaction. Laser flash excitation (266 and 355 nm) of the cobalt complex clearly showed the formation of the carbonate radical. When phenol was added to the solution of the complex, a second species was observed which was assigned to the phenoxyl radical. The second-order rate constant of reaction between phenol and carbonate radical was found to be equal to 1.6 × 10⁷ M⁻¹ s⁻¹, in agreement with literature data of 2.2 × 10⁷ M⁻¹ s⁻¹.     

Synthesis and incorporation into DNA of a chemically stable, functional abasic site analogue

[reaction: see text] The abasic site building block 7 for DNA synthesis, containing a methylenephosphinic acid group at C3', was prepared in six steps and was incorporated into DNA via a combination of H-phosphonate and phosphoramidite chemistry. Corresponding oligodeoxynucleotides were shown to be chemically stable under basic conditions and fully functional at the respective hemiacetal center.