A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA

Quasi-intrinsic fluorescent probes for detecting the DNA adduct (ABPdG) based on an excited-state intermolecular charge transfer mechanism

N'-(2'-Deoxyguanosin-8-yl)-4-aminobiphenyl (^ABPdG) is one of the most representative carcinogenic DNA adducts formed by human exposure to 4-aminobiphenyl (4-ABP) during dye production, rubber-manufacturing processes and cigarette smoke. Accordingly, the ultrasensitive detection of ABP-derived adducts in DNA with minimal interference to the native structures becomes key for elucidating carcinogenesis mechanisms and mitigating the risk of cancer. In view of the lack of efficient optical emission in ^ABPG, we report a theoretical study on the photophysical properties of a set of quasi-intrinsic fluorescent C-analogues, which can form stable W-C base pairs with ^ABPG. It is found that fluorophore replacement and ring-expansion can bring a red-shifted absorption and bright photoluminescence due to additional π-conjugation. In particular, because the tricyclic cytosine analogue 1,3-diaza-2-oxophenoxazine (tC^O) possesses distinct optical properties, it is proposed as a biosensor to identify ^ABPG. The TDDFT-calculated absorption maximum of tC^O is red-shifted by 97 nm in comparison with that of the native C base, which contributes to selective excitation after incorporating into the nucleic acids. Although the fluorescence is insensitive to base pairing with natural guanine, the excited state intermolecular charge transfer (ESICT)-governed "OFF-ON" signal can be observed in the presence and absence of ^ABPG. Moreover, to evaluate the direct availability of the bright C-analogues with high selectivity for the deoxyguanosine adduct ^ABPG in DNA, we further investigated thoroughly the effects of its linking to deoxyribose on its absorption and emission, which shows little difference from that of experiment.

Fluorescent adenine analogues with ESPT characteristic utilized for real-time detecting DNA adduct

The 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG) is the representative damaged nucleoside that may increase the risk of developing diseases. Accordingly, the selective detection of 8-oxoG in DNA with minimal disturbance to the native structure is important to have an in-depth understanding of the formation mechanism and becomes an attractive tool for genomic research. To identify the DNA adduct in real-time efficiently, a series of quasi-intrinsic optical probes are performed based on the natural adenine, which has preference to form a stable base pair with 8-oxoG in the syn conformation. The calculations revealed that the A-analogues in solution could bring red-shifted absorption spectra and bright photoluminescence arisen from the additional π-conjugation by means of fluorophore modification and the ring expansion. Especially, A1 possesses large Stokes shifts and the highest fluorescence intensity in emission, which is proposed as the biosensor to monitor the optical changes in the presence and absence of the considered 8-oxoG. It is found that the fluorescence is insensitive to base pairing with thymine, while the excited state intermolecular proton transfer (ESPT) induced efficient fluorescence quenching is observed upon pairing with the 8-oxoG. To evaluate the direct usefulness of the bright adenine analogues in biological environment, we further examined the influences of linking deoxyribose on the absorption and emission, which are consistent with the experimental data.

Theoretical characterization of sulfur-to-selenium substitution in an emissive RNA alphabet: impact on H-bonding potential and photophysical properties

We employ density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to investigate the structural, energetic and optical properties of a new computationally designed RNA alphabet, where the nucleobases, ^tsA, ^tsG, ^tsC, and ^tsU (ts-bases), have been derived by replacing sulfur with selenium in the previously reported tz-bases, based on the isothiazolo[4,3-d]pyrimidine heterocycle core. We find out that the modeled non-natural bases have minimal impact on the geometry and energetics of the classical Watson-Crick base pairs, thus potentially mimicking the natural bases in a RNA duplex in terms of H-bonding. In contrast, our calculations indicate that H-bonded base pairs involving the Hoogsteen edge of purines are destabilized as compared to their natural counterparts. We also focus on the photophysical properties of the non-natural bases and correlate their absorption/emission peaks to the strong impact of the modification on the energy of the lowest unoccupied molecular orbital. It is indeed stabilized by roughly 1.1-1.6 eV as compared to the natural analogues, resulting in a reduction of the gap between the highest occupied and the lowest unoccupied molecular orbital from 5.3-5.5 eV in the natural bases to 3.9-4.2 eV in the modified ones, with a consequent bathochromic shift in the absorption and emission spectra. Overall, our analysis clearly indicates that the newly modelled ts-bases are expected to exhibit better fluorescent properties as compared to the previously reported tz-bases, while retaining similar H-bonding properties. In addition, we show that a new RNA alphabet based on size-extended benzo-homologated ts-bases can also form stable Watson-Crick base pairs with the natural complementary nucleobases.