Communication: UV photoionization of cytosine catalyzed by Ag+

Selective Tautomer Production and Cryogenic Ion Spectroscopy of Radical Cations: The Uracil and Thymine Cases

The vibrational and electronic spectroscopy of the radical cations of two nucleobases (NB) (uracil and thymine) was studied by cryogenic ion photodissociation spectroscopy. The radical cations have been generated from the photodissociation of NB-Ag+ complexes. A charge transfer process from the NB to Ag+ governs the deactivation mechanism, leading to the formation of the radical cation without further tautomerization. Single- and double-resonance spectroscopy allows for structural assignments of both the silver complexes and the radical cations by comparison with DFT-based calculations. Interestingly, a tautomer-dependent fragmentation is observed in the thymine enol form that involves the loss of NCO, a fragment which was never reported before for this NB. This selective photodissociation of silver complexes containing aromatic chromophore greatly expands the current technique to produce isomer-selected radical cations in the gas phase providing benchmark experimental data to assess calculations of open-shell species.

Reductant-dependent DNA-templated silver nanoparticle formation kinetics

DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.

Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation

The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.

Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA

To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC₂₀, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC₂₀ and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC₂₀ silver ion complex that is not seen in dC₂₀ in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag⁺-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO₃ solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag⁺ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag⁺-DNA complex decreased with an increase in Ag⁺ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO₃]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag⁺-DNA complex formation to a large extent.

Optical properties and charge distribution in rod-shape DNA–silver cluster emitters

Our results show that the experimental optical properties of DNA–Ag_n are theoretically reproduced by considering the zigzag rod-shape structure of the metal cluster.

Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H+ Pair

 Gas phase protonated guanine-cytosine (CGH⁺) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH⁺ pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm^-1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.

Non-radiative processes in protonated diazines, pyrimidine bases and an aromatic azine

The excited state lifetimes of DNA bases are often very short due to very efficient non-radiative processes assigned to the ππ*-nπ* coupling. A set of protonated aromatic diazine molecules (pyridazine, pyrimidine and pyrazine C4H5N2(+)) and protonated pyrimidine DNA bases (cytosine, uracil and thymine), as well as the protonated pyridine (C5H6N(+)), have been investigated. For all these molecules except one tautomer of protonated uracil (enol-keto), electronic spectroscopy exhibits vibrational line broadening. Excited state geometry optimization at the CC2 level has been conducted to find out whether the excited state lifetimes measured from line broadening can be correlated to the calculated ordering of the ππ* and nπ* states and the ππ*-nπ* energy gap. The short lifetimes, observed when one nitrogen atom of the ring is not protonated, can be rationalized by relaxation of the ππ* state to the nπ* state or directly to the electronic ground state through ring puckering.