Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides.

With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation. Activated electron photodetachment dissociation (a-EPD) has also been used as an alternative to capitalize on the dominant charge-reduction pathway prevalent in UVPD, facilitate dissociation, and produce high abundances of fragment ions. Here, we compare higher-energy collisional activation (HCD), UVPD using 193 and 213 nm photons, and a-EPD for the top-down sequencing of modified nucleic acids, including methylated, phosphorothioate, and locked nucleic acid-modified DNA. The presence of these modifications alters the fragmentation pathways observed upon UVPD and a-EPD, and extensive backbone cleavage is observed that results in the production of fragment ions that retain the modifications and allow them to be pinpointed. LNA and 2'-O-methoxy phosphorothioate modifications caused a significant suppression of fragmentation for UVPD but not for a-EPD, whereas phosphorothioate bonds did not cause any significant suppression for either method. The incorporation of 2'-O-methyl modifications suppressed fragmentation of the antisense strand of patisiran, which resulted in some gaps in sequence coverage. However, UVPD provided the highest sequence coverage when compared to a-EPD.

Photochemically induced RNA and DNA abasic sites.

Two phosphoramidite building blocks were synthesized that can easily be deprotected by UV light to reveal natural abasic sites in oligoribonucleotides as well as in oligodeoxyribonucleotides. Another building block which releases a 2'-O-methylated abasic site upon UV radiation is also described.

Dynamics of the RNA hairpin GNRA tetraloop.

The dynamics of RNA hairpin tetraloops of the GNRA type [sequence G- any ribonucleotide (N)-purine (R)-A] was analyzed by fluorescence spectroscopy and by fluorescence-detected temperature-jump relaxation, using RNA oligomers with 2-aminopurine (2AP) substituted in two different positions of the loop sequence, Gp2APpApA (HP1) and GpAp2APpA (HP2), as indicator. The fluorescence of HP1 is much higher than that of HP2, indicating a lower degree of 2AP-stacking in HP1. Addition of Mg(2+) or Ca(2+) ions leads to an increase of fluorescence in HP1, whereas a decrease of fluorescence is observed in HP2. In both cases at least two ion-binding equilibria are required to fit titration data. T-jump experiments using fluorescence detection show a relaxation process with a time constant of 22 micros for HP1, whereas two relaxation processes with time constants 5 and 41 micros, are found for HP2. These results clearly demonstrate the existence of more than the single conformation state detected by NMR analysis. The T-jump amplitudes decrease with increasing bivalent ion concentration, indicating that one of the states is favored in the presence of bivalent ions. The loop relaxation processes are slower than standard stacking processes, probably because of activation barriers imposed by a restricted mobility of loop residues, and are assigned to a stacking rearrangement, probably between the 5' and the 3'-side. A similar process has been observed previously for the anticodon loop of tRNA(Phe). The rate constants of the transition are in the range of 10(4) s(-1) in the case of HP1. The data demonstrate the existence of structures that are not resolved by standard NMR because of fast exchange and are not found by X-ray analysis because of restrictions by crystal packing.

Photo-regulation of DNA/RNA duplex formation by azobenzene-tethered DNA towards antisense strategy.

Modified DNA carrying an azobenzene was successfully applied to the photo-regulation of DNA/RNA hybridization. When the azobenzene was isomerized from trans- to cis-form on UV-irradiation, the melting temperature of the duplex was significantly lowered. This process was totally reversible so that the Tm increased by cis-->trans isomerization induced by visible light irradiation.

Preparation of oligoribonucleotides containing 4-thiouridine using Fpmp chemistry. Photo-crosslinking to RNA binding proteins using 350 nm irradiation.

The preparation of a 4-thiouridine phosphoramidite suitable for RNA synthesis and its subsequent incorporation into oligoribonucleotides is described. The thiol group is protected with a 2-cyanoethyl group and the 2'-OH with a 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl function. Thiouridine-containing oligoribonucleotides were used as 350 nm UV crosslinking probes for the photoaffinity labelling of RNA binding proteins. Specific crosslinking was demonstrated between the Rev protein of HIV-1 (as a glutathione S-transferase fusion protein) and its RNA target, the Rev-responsive element. It was not possible to generate crosslinks between the RNA bacteriophage MS2 coat protein and the initiator stem-loop of the replicase gene, to which it binds. These results are consistent with the structural data available on both systems.

Targeted photochemical modification of HIV-derived oligoribonucleotides by antisense oligodeoxynucleotides linked to porphyrins.

Antisense oligodeoxynucleotides directed against a 24-mer RNA derived from the long terminal repeat (LTR) region of HIV were linked to proto- and methylpyrroporphyrin and their zinc derivatives. The oligonucleotide-porphyrin conjugates were tested for their ability to induce photodamage on the target RNA. Upon hybridization followed by irradiation at 405 nm, the photochemical reaction led to photocross-linking of the antisense derivative to the RNA substrate. The protoporphyrin exhibited a much higher cross-linking yield than the methylpyrroporphyrin while the Zn-porphyrin derivatives were found to be less efficient than their corresponding nonmetallated congeners. The specificity of the photocross-linking reaction between the porphyrin-oligomer and its target RNA was demonstrated by the following evidence: (1) hybrid formation was required for photocross-linking to occur, (2) the sites of cross-linking on the target RNA were identified at G residues located in close proximity to the porphyrin photoactive center in the hybrid and (3) addition of bulk calf liver RNA did not affect the photocross-linking efficiency.

Further biochemical characterization of rabbit reticulocyte eIF-4B.

In this report, it is shown that eIF-4B exhibits ATP hydrolysis activity in a ribosome-dependent fashion. This activity is significantly enhanced by the addition of eIF-4A and eIF-4F, although neither of these factors, alone or together, display a significant ribosome-dependent ATPase activity. Sepharose-6B gel filtration experiments with combinations of nonlabeled and 14C reductively methylated initiation factors (eIF-4A, eIF-4B, eIF-4F, and eIF-3) provide evidence that both eIF-4B and eIF-4F, but not eIF-4A, interact with ribosomes in the presence of specific factors and ATP. It is not known with which ribosomal subunit(s) these factors interact. In ultraviolet radiation-induced crosslinking studies, an eIF-4A and/or eIF-4F and ATP-dependent crosslinking of eIF-4B to radiolabeled oligo(A)12-18 was observed. Past studies with oxidized-cap mRNA achieved cross-linking of all three of these factors, driven by the specific interaction of eIF-4F p24 with the m7GTP cap structure; this is the first reported instance of only eIF-4B cross-linking to RNA.

Photochemical crosslinking in oligonucleotide-protein complexes between a bromine-substituted 2-5A analog and 2-5A-dependent RNase by ultraviolet lamp or laser.

2',5'-oligoadenylates known as 2-5A [px(A2'p)nA; chi = 2 or 3, n greater than or equal to 2] are produced in interferon-treated cells in response to double-stranded RNA. 2-5A binds with high affinity to a 2-5A-dependent RNase resulting in the cleavage of single-stranded RNA. An efficient, rapid, and extremely sensitive photoaffinity labeling method was developed to facilitate detection of 2-5A-dependent RNase. A bromine-substituted and radioactive derivative of 2-5A, the 5'-monophosphate, p(A2'p)2(br8A2'p)2A3'-[32P]Cp, was synthesized as probe for 2-5A-dependent RNase. Even though this bromine-substituted analog of 2-5A bore no 5'-terminal triphosphate or diphosphate, it bound to 2-5A-dependent RNase with the same high affinity as did 2-5A per se but it was a less effective activator of the RNase under the present assay conditions. The presence of bromine atoms in the 2-5A analog enhanced by more than 200-fold crosslinking to 2-5A-dependent RNase under a uv lamp; many additional polypeptides were also labeled but at much lower levels. Furthermore, using high-intensity uv laser irradiation (308 nm) covalent attachment of the bromine-substituted 2-5A analog to 2-5A-dependent RNase was readily achieved within 10(-6) s.

Stacking-controlled phototransformations of the 5-fluorouracil residues in dinucleotide model compounds.

5-Fluorouracil residues can form cyclobutane-type photodimers in a direct excitation stacking-controlled process. The stacking also has an important effect on the photohydration of uracil and 5-fluorouracil in our model compounds 5RUra(CH2)35FUra, where R = H, CH3, C2H5, C3H7, F or Cl.

Abiogenic synthesis of oligonucleotides on kaolinite under the action of ultraviolet radiation.

The present work deals with the processes involved in the abiogenic polycondensation of nucleotides adsorbed on the clay mineral kaolinite under the action of ultraviolet (UV) radiation. The dependence of the yield of synthesis products on irradiation dose was studied. The maximum yield corresponds to a 6-h exposure. The newly synthesized substances were analyzed by ion-exchange chromatography. Some fractions were studied for the type of bonds they contained by venom phosphodiesterase and RNase T2 enzymatic hydrolysis. It was determined that some of the products synthesized by exposure of AMP adsorbed on the surface of clay particles to UV radiation may be looked upon as oligonucleotides in which some fragments have 2'-5'-bonded and others 3'-5'-bonded nucleotides.

Interferon action. Covalent linkage of (2'-5')pppApApA(32P)pCp to (2'-5')(A)n-dependent ribonucleases in cell extracts by ultraviolet irradiation.

One of the mediators of interferon action is an endonuclease system. This consists of (2'-5')(A)n synthetase, which, if activated by double-stranded RNA, converts ATP into (2'-5')(A)n and RNase L, a latent endoribonuclease, which binds (2'-5')(A)n and is thereby activated. We report here that a derivative of (2'-5')(A)n (i.e. (2'-5')pppApApA[32P]pCp) can be covalently cross-linked by UV irradiation to a protein in cytoplasmic extracts from mouse Ehrlich ascites tumor cells. This protein has an apparent molecular weight of 77,000 as determined by gel electrophoresis in sodium dodecyl sulfate. It appears to be identical with RNase L according to the following criteria: co-chromatography on DEAE-cellulose and Sephacryl S300. The gel filtration in Sephacryl S300 reveals that the apparent molecular weight of the protein is between 70,000 and 90,000, indicating that it is a monomer. The cross-linking is oligonucleotide specific. It is inhibited by 10 nM (2'-5')pppApApA or 1 microM (2'-5')ApApA, i.e, compounds known to block, even at low concentration, the binding of (2'-5')pppApApApCp to RNase L. (3'-5')ApApA inhibits only at a 0.1-1 mM concentration, and 1 mM ATP, 2'-AMP, or 5', 3'-pCp have no effect. (2'-5')pppApApApCp was also cross-linked to a protein with a molecular weight of about 78,000 (as determined by gel electrophoresis in sodium dodecyl sulfate) in cytoplasmic extracts from human (HeLa) cells and to protein(s) with molecular weight(s) of 75,000-77,000 (as determined by gel electrophoresis in sodium dodecyl sulfate) in nuclear extracts from Ehrlich ascites tumor cells.

Study of the interaction between yeast tRNAphe and yeast phenylalanyl-tRNA synthetase by monochromatic ultraviolet irradiation at various wavelengths. Advantages and limits of the method.

The interactions between yeast tRNAphe and phenylalanyl-tRNA synthetase were studied by analysis of the covalent adducts obtained upon monochromatic ultraviolet irradiation at different wavelengths (248, 282, 292, 302 and 313 nm). The high extent of inactivation of phenylalanyl-tRNA synthetase, together with the partial modification of tRNA, as well as the peculiar instability of most of the covalent bonds formed upon irradiation constitute severe limitations to the use of the technique and to the interpretation of the results. These disadvantages led us to select an irradiation wavelength of 248 nm and to use only mild isolation procedures allowing a good recovery of the covalent adducts formed. Seven major tryptic peptides of the enzyme were found to be cross-linked to tRNAPhe whereas six major T1-oligonucleotides were covalently linked to the protein, among these, the three cross-linked oligonucleotides previously described by Shoemaker and Schimmel (J. Biol. Chem. 250 (1975) 4440-4444) in the same system. The difference in the number of covalently linked oligonucleotides is discussed in the light of the instability of the covalent linkages. The localization of the six oligonucleotides at the inside of the two branches forming the L-shaped tRNA molecule is similar to that observed in the yeast valine system (Renaud et al., Eur. J. Biochem. 101 (1979) 475-483) and is consistent with the interaction model previously described (Rich and Schimmel, Nucl. Acids Res. 4 (1977) 1649-1665 and Ebel et al. in Transfer RNA: structure, properties and recognition, (1979) pp. 325-343 Cold Spring Harbor Laboratory, NY). The occurrence of covalent cross-linking upon irradiation in the tryptophan absorption band (302 nm) strongly suggests the participation of this residue in the stabilization of the tRNA enzyme complex.