Photochemical addition of amino acids and peptides to DNA

Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing

Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.

The protease SPRTN and SUMOylation coordinate DNA-protein crosslink repair to prevent genome instability

DNA-protein crosslinks (DPCs) are a specific type of DNA lesion in which proteins are covalently attached to DNA. Unrepaired DPCs lead to genomic instability, cancer, neurodegeneration, and accelerated aging. DPC proteolysis was recently identified as a specialized pathway for DPC repair. The DNA-dependent protease SPRTN and the 26S proteasome emerged as two independent proteolytic systems. DPCs are also repaired by homologous recombination (HR), a canonical DNA repair pathway. While studying the cellular response to DPC formation, we identify ubiquitylation and SUMOylation as two major signaling events in DNA replication-coupled DPC repair. DPC ubiquitylation recruits SPRTN to repair sites, promoting DPC removal. DPC SUMOylation prevents DNA double-strand break formation, HR activation, and potentially deleterious genomic rearrangements. In this way, SUMOylation channels DPC repair toward SPRTN proteolysis, which is a safer pathway choice for DPC repair and prevention of genomic instability.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

DNA-protein crosslink proteases in genome stability

Proteins covalently attached to DNA, also known as DNA-protein crosslinks (DPCs), are common and bulky DNA lesions that interfere with DNA replication, repair, transcription and recombination. Research in the past several years indicates that cells possess dedicated enzymes, known as DPC proteases, which digest the protein component of a DPC. Interestingly, DPC proteases also play a role in proteolysis beside DPC repair, such as in degrading excess histones during DNA replication or controlling DNA replication checkpoints. Here, we discuss the importance of DPC proteases in DNA replication, genome stability and their direct link to human diseases and cancer therapy.

Site-Specific Cross-Linking of a p19 Viral Suppressor of RNA Silencing Protein and Its RNA Targets Using an Expanded Genetic Code

The p19 viral suppressor of RNA silencing protein has useful applications in biotechnology due to its high affinity for binding to small RNAs such as small interfering RNAs (siRNAs). Also, its applications for the study and modulation of microRNAs are actively expanding. Here we demonstrate the successful site-specific incorporation of a photoactivatable unnatural amino acid, p-azido-l-phenylalanine (AzF), for cross-linking to RNA substrates into the p19 sequence. Incorporation of AzF was performed at three positions in the protein near the RNA binding site: K67, R115, and T111. Incorporation of AzF at position T111 of p19 did not affect the binding affinity of p19 for siRNAs and also showed nanomolar affinity for human microRNA miR-122. The affinity was less favorable with AzF incorporation at two other positions, suggesting the sensitivity of placement of the unnatural amino acid. Exposure of the T111AzF in complex with either siRNA or miRNA to ultraviolet light resulted in cross-linking of the protein with the RNA, but no cross-linking could be detected with the wild-type protein. Our results demonstrate that p19-T111AzF can be used for detection of small RNAs, including human miR-122, with high sensitivity and to irreversibly sequester these RNAs through covalent photo-cross-linking.

Regulation of two GTPases Toc159 and Toc34 in the translocon of the outer envelope of chloroplasts

The GTPases Toc159 and Toc34 of the translocon of the outer envelope of chloroplasts (TOC) are involved in recognition and transfer of precursor proteins at the cytosolic face of the organelle. Both proteins engage multiple interactions within the translocon during the translocation process, including dimeric states of their G-domains. The units of the Toc34 homodimer are involved in the recognition of the transit peptide representing the translocation signal of precursor proteins. This substrate recognition is part of the regulation of the GTPase cycle of Toc34. The Toc159 monomer and the Toc34 homodimer recognize the transit peptide of the small subunit of Rubisco at the N- and at the C-terminal region, respectively. Analysis of the transit peptide interaction by crosslinking shows that the heterodimer between both G-domains binds pSSU most efficiently. While substrate recognition by Toc34 homodimer was shown to regulate nucleotide exchange, we provide evidence that the high activation energy of the GTPase Toc159 is lowered by substrate recognition. The nucleotide affinity of Toc34G homodimer and Toc159G monomer are distinct, Toc34G homodimer recognizes GDP and Toc159G GTP with highest affinity. Moreover, the analysis of the nucleotide association rates of the monomeric and dimeric receptor units suggests that the heterodimer has an arrangement distinct from the homodimer of Toc34. Based on the biochemical parameters determined we propose a model for the order of events at the cytosolic side of TOC. The molecular processes described by this hypothesis range from transit peptide recognition to perception of the substrate by the translocation channel.

Mapping RNA interactions to proteins in virions using CLIP-Seq

RNA nanotechnology often involves protein-RNA complexes that require significant understanding of how the proteins and RNAs contact each other. The CLIP-Seq (cross-linking immunoprecipitation, and DNA sequencing) protocol can be used to probe the RNA molecules that interact with proteins. We have optimized the procedures for RNA fragmentation, immunoprecipitation, and library construction in CLIP-Seq to map the interactions between the RNA and the capsid of a simple positive-strand RNA virus. The results show that distinct portions of the viral RNA contact the capsid. The protocol should be applicable to other RNA virions and also RNA-protein nanoparticles.

Ring-opening photoreactions of 5-methylcytosine with 3-mercaptopropionic acid and other thiols

The photoproducts from reaction of thymine with cysteine, an amino acid containing a sulfhydryl group, have been studied in detail, whereas results of less extensive studies have been reported for the uracil-cysteine system. However, products arising from corresponding reactions of cytosine and related compounds with compounds containing a sulfhydryl group have not been similarly studied. We report here the results of our study of the photoreaction of 5-methylcytosine (5MeCyt), a minor base occurring in mammalian DNA, with 3-mercaptopropionic acid (3MP), a model compound for cysteine. We found that this reaction proceeds at pH 7 to yield N-(N'-(2'-carboxyethyl)thiocarbamoyl)-3-amino-2-methylacrylamidine (Ia) as a primary photoproduct. A secondary thermal product, identified as 3-(2'-carboxyethylthio)-2-methylacrylamidine (IIa), appears if photoreacted solution is allowed to stand for appreciable times prior to workup; this latter compound is formed via an intermediate product. Heating of purified Ia at 100°C or standing at lower temperatures produces 3-amino-2-methylacrylamidine (IId); similarly, irradiation of Ia with UVB light in aqueous solution converts it into IId. Results from exploratory studies suggest that 5MeCyt similarly reacts with other thiols (2-mercaptoethanol, 2-mercaptoacetic acid) to form analogs of Ia and IIa. Other preliminary results suggest that 5-methyl-2'-deoxycytidine and 1,5-dimethylcytosine photoreact with 3MP to form compounds similar to Ia.

Comprehensive in vivo RNA-binding site analyses reveal a role of Prp8 in spliceosomal assembly

Prp8 stands out among hundreds of splicing factors as a protein that is intimately involved in spliceosomal activation and the catalytic reaction. Here, we present the first comprehensive in vivo RNA footprints for Prp8 in budding yeast obtained using CLIP (cross-linking and immunoprecipitation)/CRAC (cross-linking and analyses of cDNAs) and next-generation DNA sequencing. These footprints encompass known direct Prp8-binding sites on U5, U6 snRNA and intron-containing pre-mRNAs identified using site-directed cross-linking with in vitro assembled small nuclear ribonucleoproteins (snRNPs) or spliceosome. Furthermore, our results revealed novel Prp8-binding sites on U1 and U2 snRNAs. We demonstrate that Prp8 directly cross-links with U2, U5 and U6 snRNAs and pre-mRNA in purified activated spliceosomes, placing Prp8 in position to bring the components of the active site together. In addition, disruption of the Prp8 and U1 snRNA interaction reduces tri-snRNP level in the spliceosome, suggesting a previously unknown role of Prp8 in spliceosomal assembly through its interaction with U1 snRNA.

Predicting thymine dimerization yields from molecular dynamics simulations

It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in <1 ps after ultraviolet excitation. The speed and low quantum yield of this reaction suggest that only a small fraction of the conformers of this structurally disordered oligonucleotide are in a position to react at the instant of photon absorption. In this work, we explore the hypothesis that conventional molecular dynamics simulations can be used to predict the yield of cyclobutane pyrimidine dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22 degrees.

Detecting DNA-binding of proteins in vivo by UV-crosslinking and immunoprecipitation

The temporal and spatial binding of proteins on DNA is important to the regulation of genome expression and maintenance. However, examining how the protein-DNA complexes assemble in living cells is challenging. The development of UV-crosslinking/immunoprecipitation (UV-X-ChIP) technique and the progress of its applications show the powerful potential of this method in detecting such binding behavior in vivo. UV light is a zero length crosslinker and is believed to produce less perturbation of the complex than chemical crosslinker. The use of UV laser as UV light source allows the number of photons required for crosslinking to be delivered in nano- or pico- or femtosecond intervals, extremely shortening the irradiation time and achieving higher crosslinking efficiency than conventional UV lamp, thus being well suitable for kinetic studies. UV-X-ChIP technique has been successfully applied on the study of DNA replication, transcription, chromatin structure, and genome-wide location of DNA-binding proteins.

Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA

Protein-nucleic acid complexes are commonly studied by photochemical cross-linking. UV-induced cross-linking of protein to nucleic acid may be followed by structural analysis of the conjugated protein to localize the cross-linked amino acids and thereby identify the nucleic acid binding site. Mass spectrometry is becoming increasingly popular for characterization of purified peptide-nucleic acid heteroconjugates derived from UV cross-linked protein-nucleic acid complexes. The efficiency of mass spectrometry-based methods is, however, hampered by the contrasting physico-chemical properties of nucleic acid and peptide entities present in such heteroconjugates. Sample preparation of the peptide-nucleic acid heteroconjugates is, therefore, a crucial step in any mass spectrometry-based analytical procedure. This study demonstrates the performance of four different MS-based strategies to characterize E. coli single-stranded DNA binding protein (SSB) that was UV-cross-linked to a 5-iodouracil containing DNA oligomer. Two methods were optimized to circumvent the need for standard liquid chromatography and gel electrophoresis, thereby dramatically increasing the overall sensitivity of the analysis. Enzymatic degradation of protein and oligonucleotide was combined with miniaturized sample preparation methods for enrichment and desalting of cross-linked peptide-nucleic acid heteroconjugates from complex mixtures prior to mass spectrometric analysis. Detailed characterization of the peptidic component of two different peptide-DNA heteroconjugates was accomplished by matrix-assisted laser desorption/ionization mass spectrometry and allowed assignment of tryptophan-54 and tryptophan-88 as candidate cross-linked residues. Sequencing of those peptide-DNA heteroconjugates by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry identified tryptophan-54 and tryptophan-88 as the sites of cross-linking. Although the UV-cross-linking yield of the protein-DNA complex did not exceed 15%, less than 100 pmole of SSB protein was required for detailed structural analysis by mass spectrometry.

Photochemical and photophysical studies of guanine derivatives: intermediates contributing to its photodestruction mechanism in aqueous solution and the participation of the electron adduct

The low-intensity steady-state (254 nm), microsecond flash and nanosecond (266 nm) laser photolysis of some guanine (Gua) derivatives in aqueous solution were studied. A photodestruction yield between 10(-3) and 10(-2) at a base concentration of 75 microM was determined for 254 nm irradiation at room temperature using high-performance liquid chromatography. This yield decreases with increasing purine concentration. For a similar concentration of the purine bases (2 +/- 1) x 10(-5) M, the yield increases as follows: Gua approximately 9-ethylguanine < deoxyguanosine approximately guanosine (Guo) < guanosine 5'-monophosphate. At concentrations higher than 2 x 10(-4) M the Gua derivatives' photodestruction yield seems to converge to a limiting value of the order of 10(-4). This behavior is explained in terms of self-quenching and aggregation effects which deactivate the excited states of the bases. The yields of electron photoejection have been determined in the nanosecond laser photolysis (0.083) and in the low-intensity steady-state (5.8 x 10(-3)) for Guo. Competition experiments using electron scavengers suggest that the electron adducts of the bases are one of the principal species participating in the photodestruction mechanism of these monomeric Gua. Close to 75% of the total destruction yield has contributions from initial reactions of the photojected electron at neutral pH. The quantum yield of photodestruction of Guo increases when the pH is increased as follows: 4.7 x 10(-3) (pH 1.1), 6.5 x 10(-3) (pH 2.9), 7.7 x 10(-3) (pH 7.5) and 8.1 x 10(-3) (pH 11.9). This dependence on pH and the electron scavenger experiments provide further evidence for the radical anion or its protonated form as one of the principal species involved in the photodestruction of the bases at the different pH. Under oxygen saturated conditions a 22% increase in the destruction yield is observed for Guo. However, for the dinucleotides adenylyl (3'-->5')-guanosine and thymidylyl (3'-->5')2'-deoxyguanosine, the participation of the electron is 41 and 36%, respectively, suggesting that going into a more DNA or RNA-like structure, the participation of the electron adducts species in the photodamage of DNA and RNA decreases. A mechanism of photodestruction for the Gua derivatives is proposed which takes into account these findings.

Ring opening photoreactions of cytosine and uracil with ethylamine

The photochemical reactions of cytosine (Cyt) and uracil (Ura) with ethylamine, an analog of the side chain of the amino acid lysine, have been studied. After irradiation of Cyt in aqueous ethylamine at lambda = 254 nm, N-(N'-ethylcarbamoyl)-3-aminoacrylamidine (Ia) and N-(N'-ethylcarbamoyl)-3-ethylaminoacrylamidine (Ib) were isolated as products, while irradiation of Ura gave N-(N'-ethylcarbamoyl)-3-aminoacrylamide (IIa) and N-(N'-ethylcarbamoyl)-3-ethylaminoacrylamide (IIb) as products. Studies in which Ia and IIa were incubated with ethylamine at various pH values indicate that Ib and IIb are secondary products produced via thermal reactions of Ia and IIa with ethylamine. Heating of Ia and Ib leads to ring closure with the resultant formation of 1-ethylcytosine; small amounts of 1-ethyluracil are also produced. Heating of IIa and IIb produces 1-ethyluracil as the sole product. Spectroscopic properties were determined for each of these opened ring products, as well as for N-(N'-ethylcarbamoyl)-3-amino-2-methylacrylamidine (III) and N-(N'-ethylcarbamoyl)-3-amino-2-methylacrylamide (IV). Quantum yield measurements showed that Ia was formed with a phi of 1.6 x 10(-4) at pH 9.8, while phi for formation of IIa was 7.2 x 10(-4) at pH 11.5. A profile of the relative quantum yield for formation of Ia, determined as a function of pH, showed that the maximum quantum yield occurs at around pH 9.5; the analogous profile for IIa shows a maximum quantum yield at pH 11.3 and above. Acetone sensitization does not produce Ia in the Cyt-ethylamine system, which indicates that the known triplet state of Cyt is not involved in reactions leading to this opened ring product.

Mechanisms for the processing of a frozen topoisomerase-DNA conjugate by human cell-free extracts

The metabolic fate of covalently linked DNA-protein complexes (cross-links) is not clearly understood. Our aim was to investigate the processing of protein-DNA cross-links by cellular enzymes. As an example of a DNA-protein cross-link, we have constructed frozen topoisomerase-DNA conjugates and investigated their processing by human cell-free extracts. A suicide DNA substrate was constructed that upon reaction with vaccinia type I topoisomerase yielded a highly stable covalent DNA-protein cross-link. When this conjugate was treated with human nuclear or whole cell extracts, two sites of DNA breakpoints were detected: one set of double-stranded breaks occurred close to the 3' side of the topoisomerase (topo) conjugation site, and there was another set of nicks about 30 nucleotides 3' to the topo site. The double-stranded breaks were not made by extracts from xeroderma pigmentosum group A mutant cells, suggesting that the xeroderma pigmentosum group A damage recognition protein may be required for the occurrence of DNA breakage. In addition to these DNA breakage reactions, there was an activity that resulted in the delinking of the frozen topoisomerase (or proteolytic fragments thereof) from the DNA substrate, which was followed by a ligation step that restored the continuity of the broken DNA strand at the erstwhile topo attachment site. We suggest that frozen topoisomerase-DNA conjugates (and perhaps other types of covalent DNA-protein complexes) are processed by multiple pathways that may involve the cleavage of the DNA in the covalent protein-DNA complex and/or enzymatic delinking followed by ligation of the broken DNA ends. These processes may represent the "repair" of DNA-protein cross-links.

Photocross-linking of nucleic acids to associated proteins

Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.

The DNA binding site(s) of the Escherichia coli RecA protein

Photochemical cross-linking has been used to identify residues in the Escherichia coli RecA protein that are proximal to and may directly mediate binding of DNA. Ultraviolet irradiation promotes specific and efficient cross-linking of the RecA protein to poly(deoxythymidylic) acid. Cross-linked peptides remaining covalently attached to the polynucleotide following proteolytic digestion with trypsin correspond to amino acids 61-72, 178-183, and 233-243 of the RecA protein primary sequence. Their location and surface accessibility in the crystal structure, along with the behavior of various recA mutants, support the assignment of the cross-linked regions to the DNA binding site(s) of the RecA protein. Functional overlap of amino acids 61-72 with an element of the ATP binding site suggests a structural mechanism by which nucleotide cofactors allosterically affect the RecA nucleoprotein filament.

Formation of thymine-lysine and cytosine-lysine adducts in DNA-lysine photoconjugate

Lysine was covalently conjugated to calf thymus DNA by irradiation with UV light (wavelength, 253.7 nm). The results showed monofunctional covalent photobinding of lysine molecules with bases in DNA. Only the epsilon-amino group of lysine participated in the photoconjugation reaction. Thymine and cytosine were modified by 60% and 25% respectively. The kinetics of the DNA-lysine photoreaction showed that one lysine molecule was in the photobound state per 10, 6, 5 and 4 nucleotide base pairs of DNA on irradiation for 20, 30 40 and 60 min respectively.

The photochemistry of adenosine: intermediates contributing to its photodegradation mechanism in aqueous solution at 298 K and characterization of the major product

The steady-state (254 nm) photolysis of 9-(beta-D-erythropentofuranosyl)adenine (adenosine) in aqueous solution was studied. Photodestruction yields on the order of 1.3 x 10(-3) were determined at room temperature by measuring the initial decrease in the absorption maximum as a function of irradiation time. The use of high performance liquid chromatography (HPLC) permitted a more exact determination of the yield (2.5 x 10(-3). The formation of photoproducts was also studied using HPLC. In the photolysis of 50 microM aqueous solutions of adenosine under anaerobic conditions at least 11 stable photoproducts are formed that absorb at 260 nm, the wavelength of maximum absorption of adenosine. The major photoproduct was also isolated and characterized as adenine; its formation yield was determined to be 4.5 x 10(-4). This yield is affected by the presence of oxygen and by the initial concentration of adenosine employed. Fluorescence emission and excitation spectra were used to monitor the formation of highly fluorescent photoproducts that emit with maxima at 365, 398, and 430 nm and absorb in the wavelength region of 240-380 nm. The reactive species in the photodestruction mechanism were established using substrates that react selectively with the respective short-lived species. Photoionization is a primary photoprocess implied by these studies. The triplet state of adenosine also contributes to the photodestruction mechanism.

Laser cross-linking of proteins to nucleic acids: photodegradation and alternative photoproducts of the bacteriophage T4 gene 32 protein

Pulsed laser cross-linking provides a means of introducing a covalent bond between proteins and the nucleic acids to which they are bound. This rapid cross-linking effectively traps the equilibrium that exists at the moment of irradiation and thus allows examination of the protein-nucleic acid interactions that existed. Laser irradiation may also induce photodestruction of protein and we have used the bacteriophage T4 gene 32 protein to investigate this phenomenon. Our results show that both nonspecific and specific photoproducts can occur, specifically at wavelengths where the peptide backbone of proteins is known to absorb. These results demonstrate that nonspecific photodegradation can be correlated with the formation of a specific photodegradation product. The formation of this product was monitored to show that product yield is nonlinearly dependent on laser power and wavelength. We have also investigated an unexpected photoproduct whose formation is dependent on the length of the polynucleotide to which the gene 32 protein binds and that further demonstrates the complexities of analyzing protein-nucleic acid interactions through the use of UV laser cross-linking. These data provide essential information for the establishment of appropriate conditions for future studies that use UV cross-linking of protein-nucleic acid complexes.

Conformation of DNA packaged in bacteriophage T7. Analysis by use of ultraviolet light-induced DNA-capsid cross-linking

The conformation of the linear, double-stranded, 39,936 kilobase-pair DNA packaged in the protein capsid of bacteriophage T7 is investigated here by use of short wavelength ultraviolet light-induced DNA-capsid cross-linking. To detect both DNA-capsid and DNA-DNA cross-links, DNA is expelled from the T7 capsid and the products of expulsion are analyzed by use of Nycodenz buoyant density centrifugation, followed by either pulsed field gel electrophoresis or invariant field gel electrophoresis. Short wavelength ultraviolet light is found to progressively induce both DNA-DNA and DNA-protein cross-links in intact bacteriophage T7, but not in T7 from which DNA had been expelled before exposure to ultraviolet light. Protein-protein cross-links are not induced. When DNA expelled from previously cross-linked T7 is cleaved with restriction endonuclease (1 to 3 sites cleaved), analysis of the resulting fragments reveals no regions on T7 DNA that are excluded from cross-linking to the capsid. However, the efficiency of cross-linking decreases as the distance from the left end (last end packaged) of the packaged DNA increases. Electron microscopy of negatively stained capsid-DNA complexes reveals no DNA-retaining structure other than the outer shell of the capsid. Together with previously reported data that indicate lack of protein-based specificity for ultraviolet light-induced cross-linking, these observations are interpreted by the assumptions that, within the limits of resolution of these experiments: (1) no region of packaged T7 DNA is excluded from contact with the outer shell of the T7 capsid; (2) the probability of contacting the outer shell decreases as the distance from the left end of packaged T7 DNA increases. Thus, T7 DNA packaging concentrates the last end packaged near the inner surface of the outer shell of the T7 capsid.

Ring-opening photoreactions of cytosine and 5-methylcytosine with aliphatic alcohols

Several reports in the late 1950s and early 1960s indicated that ultraviolet irradiation of dilute solutions of cytosine or 5-methylcytosine in aliphatic alcohols, such as methanol or ethanol, leads to reaction mixtures containing products with an absorption maximum around 300 nm. The present work reports the isolation and characterization of the products responsible for this absorption in the photochemical reactions of cytosine and 5-methylcytosine with methanol, ethanol and 2-propanol at concentrations in the neighborhood of 200 microM. Under these conditions the reactions have been shown, in each nucleobase/alcohol system, to give almost exclusively a single type of primary photoproduct; each product shows an absorption maximum in the region of 300 nm. Structural analysis showed the products to be alcohol adducts with an ester linkage at C2 of the ring-opened base and an enamine structure at C6. For example, in the case of the reaction of cytosine with methanol, the product is N-carbomethoxy-3-aminoacrylamidine (IIIa). The occurrence of this type of photoreaction suggests a mode by which alcoholic functional groups on amino acid side chains could contribute to photoinduced DNA-protein cross-linking.

Photoexchange products of cytosine and 5-methylcytosine with N alpha-acetyl-L-lysine and L-lysine

The photoinduced exchange reactions of cytosine (Ia) and 5-methylcytosine (IIa) with N alpha-acetyl-L-lysine, a derivative of the common amino acid L-lysine, were studied. These reactions of Ia and IIa at pH 7.5 produce, respectively, 2-N-acetylamino-6-(1-cytosinyl)hexanoic acid (Ib) and 2-N-acetylamino-6-(1-(5-methylcytosinyl]hexanoic acid (IIb) as major final products. In addition, small amounts of the corresponding deamination products were formed in the 5-methylcytosine-N alpha-acetyl-L-lysine and cytosine-N alpha-acetyl-L-lysine systems, namely 2-N-acetylamino-6-(1-thyminyl)-hexanoic acid and 2-N-acetylamino-6-(1-uracilyl)hexanoic acid. The compounds Ib and IIb were deacetylated by acid hydrolysis to yield the corresponding lysine products: 2-amino-6-(1-cytosinyl)hexanoic acid (Ic) and 2-amino-6-(1-(5-methylcytosinyl]hexanoic acid (IIc). The compound Ic was identified as a product in the photoreaction of cytosine with L-lysine at near neutral pH, while IIc is found as a product in the corresponding reaction of 5-methylcytosine. The occurrence of the above photoexchange reactions at pH values near those found in physiological systems could have biological implications; in particular, our observations suggest that cytosine and 5-methylcytosine residues, contained in DNA, might react with the epsilon-amino groups of lysine residues in proteins upon UV irradiation of nucleosomes and other DNA-protein complexes under physiological conditions.

Recent aspects of the photochemistry of nucleic acids and related model compounds

This survey focuses on recent developments in the far ultraviolet photochemistry of nucleic acids and related model compounds. The photoproducts discussed are the cyclobutidipyrimidines, the pyrimidine-pyrimidone adducts, the purine-pyrimidine adducts and the addition products of amino acids to pyrimidine bases. The specific aspects of the high-intensity laser photochemistry of nucleic acid components are also briefly reviewed.