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Abstract
Synthesis of oligonucleotide ending with an aldehyde functional group at their 5'-end (5'-AON) is possible for both DNA (5'-AODN) and RNA (5'-AORN) series irrespectively of the nature of the last nucleobase. The 5'-alcohol of on-support ODN is mildly oxidized under Moffat conditions. Transient protection of the resulting aldehyde by N,N'-diphenylethylenediamine derivatives allows cleavage, deprotection, and RP-HPLC purification of the protected 5'-AON. Finally, 5'-AON is deprotected by usual acetic acid treatment. In the aggregates, 5'-AON can be now synthesized and purified as routinely as non-modified ODNs, following procedures similar to the well-known "DMT-On" strategy.
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Affiliation(s)
- Rémy Lartia
- Département de Chimie Moléculaire, Université Grenoble Alpes, Grenoble, France
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2
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Wickramaratne S, Seiler CL, Tretyakova NY. Synthesis of DNA Oligodeoxynucleotides Containing Site-Specific 1,3-Butadiene-Deoxyadenosine Lesions. ACTA ACUST UNITED AC 2015; 61:4.61.1-4.61.22. [PMID: 26344227 DOI: 10.1002/0471142700.nc0461s61] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Post-oligomerization synthesis is a useful technique for preparing site-specifically modified DNA oligomers. This approach involves site-specific incorporation of inherently reactive halogenated nucleobases into DNA strands using standard solid-phase synthesis, followed by post-oligomerization nucleophilic aromatic substitution (SNAr) reactions with carcinogen-derived synthons. In these reactions, the inherent reactivities of DNA and carcinogen-derived species are reversed: the modified DNA nucleobase acts as an electrophile, while the carcinogen-derived species acts as a nucleophile. In the present protocol, we describe the use of the post-oligomerization approach to prepare DNA strands containing site- and stereospecific N6-adenine and N1,N6-adenine adducts induced by epoxide metabolites of the known human and animal carcinogen 1,3-butadiene (BD). The resulting oligomers containing site-specific, structurally defined DNA adducts can be used in structural and biological studies to reveal the roles of specific BD adducts in carcinogenesis and mutagenesis.
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Affiliation(s)
- Susith Wickramaratne
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Christopher L Seiler
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
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Killelea T, Saint-Pierre C, Ralec C, Gasparutto D, Henneke G. Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5'-terminal Cy5 dyes. Electrophoresis 2014; 35:1938-46. [PMID: 24659099 DOI: 10.1002/elps.201400018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 11/10/2022]
Abstract
By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5'-indocarbo-cyanine 5 (5'-Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5'-Cy5-labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5'-Cy5-labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5'-carboxyfluorescein (5'-FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5'-labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5'-Cy5-labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5'-Cy5-labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3' to 5' exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.
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Affiliation(s)
- Tom Killelea
- IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Plouzané, France; Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, UMR 6197, Plouzané, France; CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197, Plouzané, France
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Kiyonari S, Egashira Y, Ishino S, Ishino Y. Biochemical characterization of endonuclease V from the hyperthermophilic archaeon, Pyrococcus furiosus. J Biochem 2014; 155:325-33. [PMID: 24535600 DOI: 10.1093/jb/mvu010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Endonuclease V (Endo V) is a DNA repair enzyme that recognizes deoxyinosine and cleaves the second phosphodiester bond on the 3' side of the deaminated base lesion. A database search revealed the presence of homologous genes for Endo V in most archaeal species, but the absence in some methanogenic species. We cloned a gene encoding the sequence homologous to Escherichia coli Endo V from the genome of the hyperthermophilic euryarchaeon, Pyrococcus furiosus and purified gene product (PfuEndoV) to homogeneity. In vitro characterization showed that PfuEndoV possesses specific endonuclease activity for the deoxyinosine-containing DNA strand. The activity of the enzyme was maximal at 90°C. Stable complex formation between PfuEndoV and nicked DNA produced by the cleavage reaction was detected by gel mobility shift assays. The molecular mechanisms of the inosine repair pathway including Endo V in the archaeal cells are discussed. Interestingly, PfuEndoV cleaved inosine-containing RNA strands as well as DNA substrates. PfuEndoV may also be involved in RNA metabolism.
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Affiliation(s)
- Shinichi Kiyonari
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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Meulenbroek EM, Peron Cane C, Jala I, Iwai S, Moolenaar GF, Goosen N, Pannu NS. UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions. Nucleic Acids Res 2012; 41:1363-71. [PMID: 23221644 PMCID: PMC3553973 DOI: 10.1093/nar/gks1127] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Repairing damaged DNA is essential for an organism’s survival. UV damage endonuclease (UVDE) is a DNA-repair enzyme that can recognize and incise different types of damaged DNA. We present the structure of Sulfolobus acidocaldarius UVDE on its own and in a pre-catalytic complex with UV-damaged DNA containing a 6-4 photoproduct showing a novel ‘dual dinucleotide flip’ mechanism for recognition of damaged dipyrimidines: the two purines opposite to the damaged pyrimidine bases are flipped into a dipurine-specific pocket, while the damaged bases are also flipped into another cleft.
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Affiliation(s)
- Elisabeth M Meulenbroek
- Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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6
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Abstract
Research in nucleic acids has made major advances in the past decade in multiple fields of science and technology. Here we discuss some of the most important findings in DNA and RNA research in the fields of biology, chemistry, biotechnology, synthetic biology, nanostructures and optical materials, with emphasis on how chemistry has impacted, and is impacted by, these developments. Major challenges ahead include the development of new chemical strategies that allow synthetically modified nucleic acids to enter into, and function in, living systems.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA. Fax: +1 650 725 0259; Tel: +1 650 724 4741
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Kiyonari S, Tahara S, Shirai T, Iwai S, Ishino S, Ishino Y. Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. Nucleic Acids Res 2009; 37:6439-53. [PMID: 19734344 PMCID: PMC2770678 DOI: 10.1093/nar/gkp720] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites are the most frequently found mutagenic lesions in DNA, and they arise mainly from spontaneous base loss or modified base removal by damage-specific DNA glycosylases. AP sites are cleaved by AP endonucleases, and the resultant gaps in the DNA are repaired by DNA polymerase/DNA ligase reactions. We identified the gene product that is responsible for the AP endonuclease activity in the hyperthermophilic euryarchaeon, Pyrococcus furiosus. Furthermore, we detected the physical interaction between P. furiosus AP endonuclease (PfuAPE) and proliferating cell nuclear antigen (PCNA; PfuPCNA) by a pull-down assay and a surface plasmon resonance analysis. Interestingly, the associated 3′–5′ exonuclease activity, but not the AP endonuclease activity, of PfuAPE was stimulated by PfuPCNA. Immunoprecipitation experiments using the P. furiosus cell extracts supported the interaction between PfuAPE and PfuPCNA in the cells. This is the first report describing the physical and functional interactions between an archaeal AP endonuclease and PCNA. We also detected the ternary complex of PfuPCNA, PfuAPE and Pfu uracil-DNA glycosylase. This complex probably functions to enhance the repair of uracil-containing DNA in P. furiosus cells.
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Affiliation(s)
- Shinichi Kiyonari
- Department of Genetic Resources Technology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, BIRD-Japan Science and Technology Agency, Fukuoka-shi, Fukuoka, Japan
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Meulenbroek EM, Paspaleva K, Thomassen EAJ, Abrahams JP, Goosen N, Pannu NS. Involvement of a carboxylated lysine in UV damage endonuclease. Protein Sci 2009; 18:549-58. [PMID: 19241382 DOI: 10.1002/pro.54] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
UV damage endonuclease is a DNA repair enzyme that can both recognize damage such as UV lesions and introduce a nick directly 5' to them. Recently, the crystal structure of the enzyme from Thermus thermophilus was solved. In the electron density map of this structure, unexplained density near the active site was observed at the tip of Lys229. Based on this finding, it was proposed that Lys229 is post-translationally modified. In this article, we give evidence that this modification is a carboxyl group. By combining activity assays and X-ray crystallography on several point mutants, we show that the carboxyl group assists in metal binding required for catalysis by donating negative charge to the metal-coordinating residue His231. Moreover, functional and structural analysis of the K229R mutant reveals that if His231 shifts away, an increased activity results on both damaged and undamaged DNA. Taken together, the results show that T. thermophilus ultraviolet damage endonuclease is carboxylated and the modified lysine is required for proper catalysis and preventing increased incision of undamaged DNA.
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Paspaleva K, Moolenaar GF, Goosen N. Damage recognition by UV damage endonuclease from Schizosaccharomyces pombe. DNA Repair (Amst) 2009; 8:600-11. [PMID: 19152795 DOI: 10.1016/j.dnarep.2008.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 12/02/2008] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
Abstract
UV damage endonuclease (UVDE) from Schizosaccharomyces pombe initiates repair of UV lesions and abasic sites by nicking the DNA 5' to the damaged site. In this paper we show that in addition UVDE incises DNA containing a single-strand nick or gap, but that the enzymatic activity on these substrates as well as on abasic sites strongly depends on the presence of a neighbouring pyrimidine residue. This indicates that, although UVDE may have been derived from an ancestral AP endonuclease its major substrate is a UV lesion and not an AP site. We propose that UVDE rotates two nucleotides into a pocket of the protein in order to bring the scissile bond close to the active site and that purine bases are excluded from this pocket. We also show that in the DNA complex residue Tyr-358 of UVDE penetrates the DNA helix causing unstacking of two residues opposite the lesion, thereby stabilizing the protein-DNA interaction, most likely by promoting bending of the DNA. In the absence of Tyr-358 the enzyme exhibits an increased catalytic activity on UV-induced lesions, but only at a lower pH of 6.5. At physiological conditions (pH 7.5) the mutant protein completely looses its catalytic activity although it can still bind to the DNA. We propose that in addition to stabilizing the bend in the DNA the hydrophobic side chain of Tyr-358 shields the active site from exposure to the solvent.
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Affiliation(s)
- Keti Paspaleva
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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Angelico R, Ceglie A, Cuomo F, Cardellicchio C, Mascolo G, Colafemmina G. Catanionic systems from conversion of nucleotides into nucleo-lipids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:2348-2355. [PMID: 18237203 DOI: 10.1021/la702580j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This article focuses on reactions performed in nanostructured environments where the pair of complementary nucleotides, 5'-AMP and 5'-UMP, are converted into their amphiphilic derivatives. The synthesis is carried out by using the hydrophobic reactant dodecyl epoxide (DE) dispersed in a micellar solution based on the cationic surfactant cetyltrimethylammoniumbromide (CTAB). Novel nucleo-lipids monomers and CTAB molecules give rise to the spontaneous self-assembly of catanionic supramolecular structures in water, showing typical Maltese crosses in optical microscopy. In the final colloidal suspensions, mono- and dichained derivatives have been identified in the system incubated with 5'-UMP through LC-QqTOF-MS analysis, whereas only mono-alkylated adducts are found in the analogue reaction with 5'-AMP. A new di-alkylated 5'-UMP adduct is obtained from the 1:1 mixture of both complementary nucleotides, in addition to the nucleo-lipids found in separate systems. Time-resolved DLS measurements reveal very different kinetic processes for aggregates' formation when 5'-UMP, 5'-AMP, or their equimolar combination are used in the reaction mixture. This system as a whole represents a potential experimental model where the effect of both intermolecular interactions and self-association processes can be investigated by tuning the type of nucleobases in the reaction mixtures.
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Affiliation(s)
- Ruggero Angelico
- Consorzio per lo sviluppo dei Sistemi a Grande Interfase (CSGI) c/o Università del Molise (DISTAAM), v. De Sanctis, I-86100 Campobasso, Italy.
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Koissi N, Lönnberg H. Synthesis of modified nucleosides for incorporation of formyletheno and carboxyetheno adducts of adenine nucleosides into oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1203-6. [PMID: 18058566 DOI: 10.1080/15257770701527836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Three protected derivatives of 1,N(6)-ethenoadenine nucleosides, viz. 3-[5-O-(4,4'-dimethoxytrityl) of 7-formyl-(1) and 7-(1,2-diacetyloxypropyl)-2'-deoxyadenosine (2), and 3-[5-O-(4,4'-dimethoxytrityl)-2-O-(tert-butyldimethylsilyl)-7-(ethoxycarbonyl)adenosine (3), expected to allow introduction of formyletheno and carboxyethenoadenine adducts into oligonucleotides by the conventional phosphoramidite chemistry, have been synthesized.
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Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease. Structure 2007; 15:1316-24. [PMID: 17937920 DOI: 10.1016/j.str.2007.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 05/31/2007] [Accepted: 05/31/2007] [Indexed: 11/24/2022]
Abstract
The ultraviolet damage endonuclease (UVDE) performs the initial step in an alternative excision repair pathway of UV-induced DNA damage, nicking immediately adjacent to the 5' phosphate of the damaged nucleotides. Unique for a single-protein DNA repair endonuclease, it can detect different types of damage. Here we show that Thermus thermophilus UVDE shares some essential structural features with Endo IV, an enzyme from the base excision repair pathway that exclusively nicks at abasic sites. A comparison between the structures indicates how DNA is bound by UVDE, how UVDE may recognize damage, and which of its residues are involved in catalysis. Furthermore, the comparison suggests an elegant explanation of UVDE's potential to recognize different types of damage. Incision assays including point mutants of UVDE confirmed the relevance of these conclusions.
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