Theoretical Characterization of Sulfur-to-Selenium Substitution in an Emissive RNA Alphabet: Impact on H-bonding Potential and Photophysical Properties
KAUST DepartmentPhysical Sciences and Engineering (PSE) Division
Chemical Science Program
KAUST Catalysis Center (KCC)
Permanent link to this recordhttp://hdl.handle.net/10754/627208
MetadataShow full item record
AbstractWe 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.
CitationChawla M, Poater A, Besalu-Sala P, Kalra K, Oliva R, et al. (2018) Theoretical Characterization of Sulfur-to-Selenium Substitution in an Emissive RNA Alphabet: Impact on H-bonding Potential and Photophysical Properties. Physical Chemistry Chemical Physics. Available: http://dx.doi.org/10.1039/c7cp07656h.
SponsorsThe research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST). For computer time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia. A.P. thanks the Spanish MINECO for a project CTQ2014-59832-JIN. We thank Professor Yitzhak Tor for helpful comments.
PublisherRoyal Society of Chemistry (RSC)
- Structural and energetic characterization of the emissive RNA alphabet based on the isothiazolo[4,3-d]pyrimidine heterocycle core.
- Authors: Chawla M, Poater A, Oliva R, Cavallo L
- Issue date: 2016 Jul 21
- A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA.
- Authors: Zhang L, Kong X, Zheng M, Wang M
- Issue date: 2017 Oct
- Thieno analogues of RNA nucleosides: a detailed theoretical study.
- Authors: Samanta PK, Manna AK, Pati SK
- Issue date: 2012 Jul 5
- Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair.
- Authors: Chawla M, Autiero I, Oliva R, Cavallo L
- Issue date: 2018 Jan 31
- A TDDFT study of the excited states of DNA bases and their assemblies.
- Authors: Varsano D, Di Felice R, Marques MA, Rubio A
- Issue date: 2006 Apr 13