Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0.

Oxidative damage to DNA nucleotides has many cellular outcomes that could be aided by the development of sequencing methods. Herein, the previously reported click-code-seq method for sequencing a single damage type is redeveloped to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0).

Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes.

The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor and helicase brake, which is also a sensor, was applied to the rRNAs. Nanopore current levels, base calling profile, and helicase dwell times for the modifications relative to unmodified synthetic rRNA controls found signatures for nearly all modifications. Signatures for clustered modifications were determined by selective sequencing of writer knockout E. coli and sequencing of synthetic RNAs utilizing some custom-synthesized nucleotide triphosphates for their preparation. The knowledge of each modification's signature, apart from 5-methylcytidine, was used to determine how metabolic and cold-shock stress impact rRNA modifications. Metabolic stress resulted in either no change or a decrease, and one site increased in modification occupancy, while cold-shock stress led to either no change or a decrease. The double modification m4Cm1402 resides in 16S rRNA, and it decreased with both stressors. Using the helicase dwell time, it was determined that the N4 methyl group is lost during both stressors, and the 2'-OMe group remained. In the ribosome, this modification stabilizes binding to the mRNA codon at the P-site resulting in increased translational fidelity that is lost during stress. The E. coli genome has seven rRNA operons (rrn), and the earlier studies aligned the nanopore reads to a single operon (rrnA). Here, the reads were aligned to all seven operons to identify operon-specific changes in the 11 pseudouridines. This study demonstrates that direct sequencing for >16 different RNA modifications in a strand is achievable.

Fluorophore-mediated Photooxidation of the Guanine Heterocycle.

Fluorescent dyes are routinely used to visualize DNA or RNA in various experiments, and some dyes also act as photosensitizers capable of catalyzing oxidation reactions. The present studies explored whether the common labeling dyes fluorescein, rhodamine, BODIPY, or cyanine3 (Cy3) can function as photosensitizers to oxidize nucleic acid polymers. Photoirradiation of each dye in the presence of the guanine (G) heterocycle, which is the most sensitive toward oxidation, identified slow rates of nucleobase oxidation in the nucleoside and DNA contexts. For all four fluorophores studied, the only product detected was spiroiminodihydantoin (Sp) suggesting the dyes functioned as Type II photosensitizers and generate singlet oxygen (1O2). The nucleoside reactions were then conducted in D2O solutions, known to increase the lifetime of 1O2, which resulted in a ~6-fold increase in the Sp yield, further supporting the classification of these dyes as Type II photosensitizers. Lastly, we inspected the pattern of G reactivity with the dyes upon photoirradiation in the context of a parallel-stranded G-quadruplex. The G nucleotides in the two exterior G-tetrads were found to be oxidation prone, providing the third line of evidence that the dyes are Type II photooxidants. The present work found that the common dyes fluorescein, rhodamine, BODIPY, or Cy3 can drive G oxidation but with a slow rate and low overall yield. This will likely not impact many experiments using dyes to study nucleic acids except for those that have long exposures with high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.

Pseudouridine and N1-Methylpseudouridine Display pH-Independent Reaction Rates with Bisulfite Yielding Ribose Adducts.

In RNA, pseudouridine (Ψ) and 5-methylcytidine (m5C) are located by their differential reactions with NaHSO3 at pH 5. The pyrimidines were allowed to react with NaHSO3, NaN3, NaCN, or NaSCN at pH 5 to find that NaHSO3 was unique in achieving quantitative yields. Pseudouridine reaction selectivity with NaHSO3 was found at pH 7 supported by the reaction rate constants. The Ψ derivative N1-methylpseudouridine found in mRNA vaccines reacts similarly with bisulfite to yield ribose adducts.

Oxidation of 8-thioguanosine gives redox-responsive hydrogels and reveals intermediates in a desulfurization pathway.

A disulfide made by oxidation of 8-thioguanosine is a supergelator. The hydrogels are redox-responsive, as they disassemble upon either reduction or oxidation of the S-S bond. We also identified this disulfide, and 2 other compounds, as intermediates in oxidative desulfurization of 8-thioG to guanosine.

Drawing with Iron on a Gel Containing a Supramolecular Siderophore.

Guanosine-5'-hydroxamic acid (3) forms hydrogels when mixed with guanosine (1) and KCl. The 5'-hydroxamic acid (HA) unit is pH-responsive and also chelates Fe3+ . When gels are prepared under basic conditions, the 5'-HA groups are deprotonated and the anionic hydrogel binds cationic thiazole orange (TO), signaled by enhanced fluorescence. The HA nucleoside 3, when immobilized in the G-quartet gel, acts as a supramolecular siderophore to form red complexes with Fe3+ . We patterned the hydrogel's surface with FeCl3 , by hand and by using a 3D printer. Patterns form instantly, are visible by eye, and can be erased using vitamin C. This hydrogel, combining self-assembled G-quartet and siderophore-Fe3+ motifs, is strong, can be molded into different shapes, and is stable on the bench or under salt water.

A G4·K+ hydrogel made from 5'-hydrazinoguanosine for remediation of α,ß-unsaturated carbonyls.

A G4·K+ hydrogel made from 5'-hydrazinoguanosine and KCl reacts with α,ß-unsaturated carbonyls of different electrophilicities (acrolein, methyl vinyl ketone and methyl acrylate) in water and the gas phase to form cyclic adducts. This aza-Michael addition/cyclization domino reaction by the 5'-hydrazino G4·K+ hydrogel has promise for environmental remediation of toxic α,ß-unsaturated carbonyls from water and the atmosphere.

G4-quartet hydrogels from 5'-hydrazino-guanosine for the non-covalent and covalent remediation of contaminants from water.

The creation of supramolecular hydrogels from relatively simple building blocks demonstrates the power of molecular self-assembly to make functional materials. G4-quartet hydrogels are appealing for a number of applications, including the environmental remediation of pollutants in water. We find that the guanosine analog, 5'-deoxy-5'-hydrazinoguanosine (HG 2) self-assembles into a self-standing hydrogel in the presence of stoichiometric amounts (0.25 equiv.) of KCl. The higher water solubility of HG 2 (14.5 mM), compared to that of the parent compound G 1 (2.1 mM), likely contributes to its enhanced gelation. The structural basis for this HG 2·KCl hydrogel, confirmed by PXRD, IR and CD, is the G4·K+ quartet, which forms extended 1D ion-channel assemblies that entangle to give a stable and long-lived hydrogel. We also find that adding KCl to a saturated solution of HG 2 triggers the generation of colloidal G4·K+ assemblies in situ that selectively and efficiently binds the anionic dye naphthol blue black (NBB) over a cationic dye. In addition to this non-covalent electrostatic binding of anions, the nucleophilic 5'-hydrazino group in the HG 2·KCl hydrogel HG 2 enables the efficient absorption of propionaldehyde from both the gas phase and from water solution via the formation of covalent hydrazone linkages with the gel matrix.