Probing the Binding Region of the Single-Stranded DNA-Binding Domain of Rat DNA Polymerase β Using Nanosecond-Pulse Laser-Induced Cross-Linking and Mass Spectrometry

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross-links in nucleic acid-protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross-linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross-linking study of the complex of the single-stranded DNA-binding domain of rat DNA polymerase β (pol β-ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross-linking reagent and matrix-assisted laser desorp-tion/ionization-time of flight mass spectrometry as an analytical tool to identify cross-linked peptides purified from proteolytic digests of the cross-linked complex. Six cross-linked peptides have been identified in tryptic digests of the protein-oligonucleotide conjugates that result from irradiation of the pol β-ss-d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross-linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.     

PHOTOCHEMICAL AND FREE RADICAL INITIATED REACTIONS OF 1,3-DIMETHYLTHYMINE WITH ETHANOL

The photochemically induced reaction of 1,3-dimethylthymine (DMT) with ethanol gives four major alcohol adducts. These have been identified as l,3-dimethyl-6-(1-hydroxy-1-ethyl)thymine ( 1 ), 1,3-dimethyl-5-(2-hydroxy-l-pyl)uracil ( 2 ), and the cis and trans isomers of 5,6-dihydro-l,3-di-methyl-6-(l-hydroxy-l-ethyl) thymine ( 3 and 4 ). The compounds 3 and 4 have been shown to be identical to the adducts produced in y-ray irradiated ethanolic aqueous solutions of DMT. Cyclobutane dimers of DMT are also found in the photochemical reaction mixture. Reaction of 1-hydroxyethyl radicals with DMT, initiated by decomposition of di-t-butyl peroxide, leads to formation of the same alcohol adducts, as well as to DMT adducts containing two molecules of ethanol. The acetone sensitized reaction of DMT with ethanol gives 1,3, and 4, along with a variety of adducts incorporating the acetone sensitizer.     

PHOTOCHEMICAL AND FREE RADICAL INITIATED REACTIONS OF1,3-DIMETHYLTHYMINE WITH ISOPROPANOL

Abstract— A photochemically induced reaction of 1 ,3-dimethylthymine (DMT) with isopropanol leads to the formation of four alcohol adducts. The products have been identified as the cis and trans isomers of 5 ,6-dihydro-1,3-dimethyll-6-(2-hydroxy-2-propyl) thymine (I and II), 2.4-diaza-8-hydroxy-2.4,6.8-tetramethylbicyclo[4.2.0]octan-1,3-dione (III), and 5 ,6-dihydro-1,3-dimethyl-6-(2-oxo-l-propyl)-thymine (IV). An acetone photosensitized reaction of DMT with isopropanol gives the same products in a similar relative yield distribution. In both of these reactions, cyclobutane dimers of DMT are produced as well. Free radical reactions of 2-hydroxyisopropyl radicals with DMT, initiated by decomposition of di- t -butyl peroxide, leads to formation of only one of the cis and trans isomers described above. along with 1 ,3-dimethyl-5-(2-hydroxy-2-methyl-1-propyl)uracil (V).     

The (5-4) and (6-4) adducts of 1-methylthymine and their Dewar valence isomers

Previous studies of the photochemical reaction of 1-methylthymine (MeT) in frozen aqueous solution have indicated that four cyclobutane type dimers are formed. We have restudied this system and have found that, in addition to cyclobutane dimers, both a (5-4) adduct and a (6-4) adduct of MeT are formed in significant amounts. Upon standing in aqueous solution, the (5-4) adduct is susceptible to reaction to form an isomeric form of the parent adduct, possibly via ring-opening and closure reactions at C-6 of the saturated pyrimidine ring component of the adduct. Irradiation of each of these three adducts with UVB light produces a pair of Dewar-type adducts. The nine products were individually characterized by mass spectrometry, proton NMR spectroscopy and UV spectroscopy. A less comprehensive study showed that irradiation of thymidine in frozen aqueous solution produces a diastereomeric pair of (5-4) adducts, along with the previously known diastereomeric pair of (6-4) adducts.     

The cyclobutane dimers of 2'-deoxyuridine, 2'-deoxycytidine, 5-methyl-2'-deoxycytidine and 5-bromo-2'-deoxyuridine

Irradiation of DNA and RNA pyrimidine nucleosides with UV light in frozen aqueous solution or in solution with acetone often results in the formation of cyclobutane dimers (CBDs). Many of these photodimers have not been characterized. We present here the results of work designed to achieve the isolation, spectroscopic characterization and determination of the stereochemical nature of a number of little studied or previously unstudied CBDs of four 2'-deoxyribonuclesides. These nucleosides are 2'-deoxyuridine (dUrd), 2'-deoxycytidine (dCyd), 5-methyl-2'-deoxycytidine (5-MedCyd) and 5-bromo-2'-deoxyuridine (5-BrdUrd). In particular, we have isolated and characterized six dUrd CBDs, five dCyd CBDs, five 5-MedCyd CBDs and four 5-BrdUrd CBDs. Photoproducts were studied by UV spectroscopy, mass spectrometry, proton NMR spectroscopy and via chemical approaches. Also presented are results from less definitive studies of a number of (6-4) (or 5-4) photoadducts of these nucleosides. In addition, results from exploratory photochemical studies of other 2'-deoxyribonucleosides in frozen solution, as well as some mixtures of two nucleosides, are given. The latter results indicate that 5-iodo-2'-deoxyuridine (5-IdUrd), 5-bromo-2'-deoxycytidine and 5-iodo-2'-deoxycytidine each form putative CBDs and that 5-BrdUrd is capable of forming putative mixed CBDs and (6-4) and/or (5-4) adducts with thymidine (Thd); 5-IdUrd similarly forms a (6-4) (or (5-4)) adduct with Thd.     

Photochemically induced reaction of 1, N4-dimethylcytosinewith isopropanol

Photoexcited 1, $\text{N}$⁴-dimethylcytosine (I) adds isopropanol to form 5,6-dihydro-1, $\text{N}$⁴-dimethyl-6-(2-hydroxy-2-propyl)cytosine (II) as the major product; a small amount of 5,6-dihydro-1-methyluracil (III) is formed as well.     

PHOTOCHEMICAL REACTIONS OF CYTOSINE AND 5-METHYLCYTOSINE WITH METHYLAMINE AND n-BUTYLAMINE

Abstract The photoinduced exchange reactions of cytosine ( la ) and 5-methylcytosine (IIa) with two primary amines have been studied. The reactions of Ia and IIa with methylamine lead, respectively, to 1-methylcytosine ( Ib ) and 1,5-dimethylcytosine (IIb) as final products; the reactions of the same two starting materials with n -butylamine gives the corresponding n -butyl compounds. The reactions of IIa with the two amines also gave small amounts of 1-methylthymine and 1- n -butylthymine. An opened ring intermediate, N-(N'-methylcarbamoyl)-3-arnino-2-methylacrylamidine ( IVa ), was isolated from the IIa -methylamine system irradiated at pH 7 and shown to be a precursor of both IIb and 1-methylthymine. The pH profiles for rate of production of IIb , 1-methylthymine and IVa in the reaction of IIa with methylamine were determined and found to be similar in shape. All three profiles show a maximum in reactivity at about pH 8.7 with some reactivity being detectable at pH values as low as 5.     

Opened-ring adducts of 5-methylcytosine and 1,5-dimethylcytosine with amines and water and evidence for an opened-ring hydrate of 2'-deoxycytidine

A variety of nucleic acid components and related compounds undergo photoreaction with water to form so-called "photohydrates" (e.g. uracil forms 6-hydroxy-5,6-dihydrouracil). However, the corresponding hydrates of 5-methylcytosine (a minor nucleobase in eukaryotic DNA) and related compounds have not been characterized. We report the preparation of opened-ring forms of such products for 5-methylcytosine (m5C) and 1,5-dimethylcytosine (DMC). This was accomplished via thermal reaction of ring-opened amine adducts (e.g. N-carbamoyl-3-amino-2-methylacrylamidine (IVa) or N-(N'-methylcarbamoyl)-3-amino-2-methylacrylamidine (IVb)) produced by photo-induced reactions of m5C with ammonia or methylamine. When these adducts were treated with dilute trifluoroacetic acid, the amino group at the 3-position was replaced with a hydroxyl group; with IVa, N-carbamoyl-3-hydroxy-2-methylacrylamidine (Va) was formed, while reaction of IVb led to N-(N'-methylcarbamoyl)-3-hydroxy-2-methylacrylamidine (Vb). These compounds are ring-opened isomers of 5,6-dihydro-6-hydroxy-5-methylcytosine (Ia and IIa) and 5,6-dihydro-6-hydroxy-1,5-dimethylcytosine (Ib and IIb). Compounds Va and Vb each undergo thermal ring closure reactions to form two unstable compounds with chemical and UV spectral properties expected for Ia and IIa (or Ib and IIb). The latter compounds have been identified as minor products in UV-irradiated aqueous solutions of m5C and DMC. Evidence is also presented that the 2'-deoxycytidine photohydrates coexist with an opened-ring form, possibly similar in nature to Vb.     

PHOTOCHEMICAL EXCHANGE REACTIONS OF THYMINE, URACIL AND THEIR NUCLEOSIDES WITH SELECTED AMINO ACIDS

The photoinduced exchange reactions of thymine with lysine at basic pH, using 254 nm light, have been studied. Three products have been isolated, namely, 6-amino-2-(1-thyminyl)hexanoic acid ( Ia ), 2-amino-6-(1-thyminyl)hexanoic acid ( IIa ) and 1-amino-5-(1-thyminyl)pentane ( IIIa ). Compound IIIa was shown to be a secondary product, produced by photochemical decarboxylation of Ia . Photochemical reaction of thymine with glycine and alanine at basic pH led, respectively, to formation of 2-(1-thyminyl)acetic acid ( Ic ) and 2-(1-thyminyl)propionic acid ( Id ). Compounds Ic and Id underwent photolysis to produce the decarboxylated secondary products 1-methylthymine and 1-ethylthymine, respectively. Thymidine reacts photochemically with glycine and alanine to produce the same products.
Irradiation of DNA in the presence of lysine at basic pH led to the formation of the same products formed in the thymine-lysine system, namely Ia , IIa and IIIa .
Uracil was found to undergo analogous photochemical exchange reactions with lysine to form 6-amino-2-(1-uracilyl) hexanoic acid ( Ib ), and 2-amino-6-(1-uracilyl)hexanoic acid ( IIb ). Compound Ib was found to undergo photodecarboxylation to form 1-amino-5-(1-uracilyl)pentane ( IIIb ), analogous to the secondary photoreaction of Ia . Photoreaction of uracil with 1,5-diaminopentane (cadaverine) likewise led to formation of IIIb .