RNA-protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog

Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins

Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.

Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications

Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.

Photosensitized UVA-Induced Cross-Linking between Human DNA Repair and Replication Proteins and DNA Revealed by Proteomic Analysis

Long wavelength ultraviolet radiation (UVA, 320-400 nm) interacts with chromophores present in human cells to induce reactive oxygen species (ROS) that damage both DNA and proteins. ROS levels are amplified, and the damaging effects of UVA are exacerbated if the cells are irradiated in the presence of UVA photosensitizers such as 6-thioguanine (6-TG), a strong UVA chromophore that is extensively incorporated into the DNA of dividing cells, or the fluoroquinolone antibiotic ciprofloxacin. Both DNA-embedded 6-TG and ciprofloxacin combine synergistically with UVA to generate high levels of ROS. Importantly, the extensive protein damage induced by these photosensitizer+UVA combinations inhibits DNA repair. DNA is maintained in intimate contact with the proteins that effect its replication, transcription, and repair, and DNA-protein cross-links (DPCs) are a recognized reaction product of ROS. Cross-linking of DNA metabolizing proteins would compromise these processes by introducing physical blocks and by depleting active proteins. We describe a sensitive and statistically rigorous method to analyze DPCs in cultured human cells. Application of this proteomics-based analysis to cells treated with 6-TG+UVA and ciprofloxacin+UVA identified proteins involved in DNA repair, replication, and gene expression among those most vulnerable to cross-linking under oxidative conditions.

Identification of RNA binding proteins by UV cross-linking

One of the major focuses of modern biology is to understand the dynamics of RNA-protein interactions, including factors that interact with mRNA, rRNA, tRNA, snRNA, hnRNA, siRNA, and viral RNA. Identification the direct interactions between proteins and RNA has greatly advanced our knowledge about the function of RNA-protein machines. UV crosslinking is a straightforward and powerful tool in this endeavor.

Template-dependent incorporation of 8-N3AMP into RNA with bacteriophage T7 RNA polymerase

UV-induced photochemical crosslinking is a powerful approach that can be used for the identification of specific interactions involving nucleic acid-protein and nucleic acid-nucleic acid complexes. 8-AzidoATP (8-N(3)ATP) is a photoaffinity-labeling agent which has been widely used to elucidate the ATP binding site of a variety of proteins. However, its true potential as a photoactivatable nucleotide analog could not be exploited due to the lack of 8-azidoadenosine phosphoramidite, a monomer used in the synthesis of RNA, and the inability of 8-N(3)ATP to serve as an efficient substrate for bacteriophage RNA polymerase. In this study, we explored the ability of SP6, T3, and T7 RNA polymerases and metal ion cofactors to catalyze the incorporation of 8-N(3)AMP into RNA. Whereas transcription buffer containing 2.0-2.5 mM Mn(2+) supports T7 RNA polymerase-mediated insertion of 8-N(3)AMP into RNA, a mixture of 2.5 mM Mn(2+) and 2.5 mM Mg(2+) further improves the yield of 8-N(3)AMP-containing transcript. In addition, both RNA transcription and reverse transcription proceed with high fidelity for the incorporation of 8-N(3)AMP and complementary residue, respectively. Finally, we show that a high-affinity MS2 coat protein binding sequence, in which adenosine residues were replaced by 8-azidoadenosine, crosslinks to the coat protein of the Escherichia coli phage MS2.

Two novel dATP analogs for DNA photoaffinity labeling

Two new photoreactive dATP analogs, N(6)-[4-azidobenzoyl-(2-aminoethyl)]-2'-deoxyadenosine-5'-triphospha+ ++ te (AB-dATP) and N(6)-[4-[3-(trifluoromethyl)-diazirin-3-yl]benzoyl-(2-aminoethyl) ]-2 '-deoxyadenosine-5'-triphosphate (DB-dATP), were synthesized from 2'-deoxyadenosine-5'-monophosphate in a six step procedure. Synthesis starts with aminoethylation of dAMP and continues with rearrangement of N(1)-(2-aminoethyl)-2'-deoxyadenosine-5'-monophosphate to N(6)-(2-aminoethyl)-2'-deoxyadenosine-5'-monophosphate (N(6)-dAMP). Next, N(6)-dAMP is converted into the triphosphate form by first protecting the N-6 primary amino group before coupling the pyrophosphate. After pyrophosphorylation, the material is deprotected to yield N(6)-(2-aminoethyl)-2'-deoxyadenosine-5'-triphosphate (N(6)-dATP). The N-6 amino group is subsequently used to attach either a phenylazide or phenyldiazirine and the photoreactive nucleotide is then enzymatically incorporated into DNA. N(6)-dATP and its photoreactive analogs AB-dATP and DB-dATP were successfully incorporated into DNA using the exonuclease-free Klenow fragment of DNA polymerase I in a primer extension reaction. UV irradiation of the primer extension reaction with AB-dATP or DB-dATP showed specific photocrosslinking of DNA polymerase I to DNA.