Qixia Song

Theoretical study on absorption and emission spectra of size-expanded Janus-type AT nucleobases and effect of base pairing.

Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we design benzo- and naphtha-expanded Janus AT base analogues, using DFT, TDDFT, and CIS methods to investigate the structural and optical properties of the Janus AT base analogues (termed as J-AT, xJ-AT, yyJ-AT, BF, xBF and yyBF), and also consider the effect of base pairing. The results show that the Janus AT base analogues can pair with T and A simultaneously to form stable H-bonded WC base pairs. The ground state structure of J-AT is similar to BF, the size expansion is 2.42Å for the x-Janus AT bases and 4.86Å for the yy-Janus AT bases. The excited state geometries of J-AT and BF change dramatically, while the other bases are similar to the ground state geometries. The lowest excited singlet transitions of the Janus AT base analogues are predicted to be of ππ(*) character and mainly dominated by the configuration HOMO-LUMO. The maximum absorption wavelengths of size expansion Janus AT base analogues are greatly red shifted compared with J-AT (or BF). BF, xBF and yyJ-AT have larger oscillator strengths than J-AT, xJ-AT and yyBF. The emission wavelengths of the Janus AT base analogues also exhibit red shifts from x-Janus AT bases to yy-Janus AT bases. However, the emission wavelengths of J-AT and BF change greatly, which are coincident with the structures observed in the excited state geometries. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of some base pairs are charge transfer excitation, while the other base pairs are local excitation. The CAM-B3LYP functional predicts that all the lowest transitions are localized on the Janus AT bases, and show good agreement with the results of the M062X functional.

Theoretical study on absorption and emission spectra of adenine analogues

AbstractFluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we use theoretical calculations to investigate the structural and optical properties of four adenine analogues (termed as A1, A2, A3, and A4), and also consider the effects of aqueous solution and base pairing. The results show that the fluorescent adenine analogues can pair with thymine to form stable H-bonded WC base pairs. The excited geometries of both adenine analogues and WC base pairs are similar to the ground geometries. The absorption and emission maxima of adenine analogues are greatly red shifted compared with nature adenine, the oscillator strengths of A1 and A2 are stronger than A3 and A4 in both absorption and emission spectra. The calculated low-energy peaks in the absorption spectra are in good agreement with the experimental data. In general, the aqueous solution and base pairing can slightly red-shift both the absorption and emission maxima, and can increase the oscillator strengths of absorption spectra, but significantly decrease the oscillator strengths of A3 in emission spectra. FigureAdenine analogues

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases

AbstractN6-methyladenine (m6A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH3. Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m6A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH3 changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m6A:G and trans-m6A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m6A to cis-m6A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m6A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory. FigureFigure The most stable configurations of the base pairs

Optical absorption and emission properties of benzene-expanded Janus AT nucleobase analogues: A DFT study

We design benzene-expanded Janus AT bases (J-AT1, J-AT2, BF1 and BF2) and investigate the structural and optical properties of these bases using DFT and TDDFT methods and also consider the effect of water solution and base pairing. The results show that J-AT1 has a nonplanar structure and its amino group is more asymmetric than the other three bases. J-AT1 and BF1 exist intramolecular H-bonds. The Janus AT base pairs exist three intermolecular H-bonds: NH···N has the largest energy, followed by NH···O and CH···O. The Janus AT base pairs retain the strength of H-bonds and maintain the stability of the base pair. The lowest absorption and emission wavelengths of the benzene-expanded Janus AT bases are all assigned to ππ* character arising from HOMO to LUMO transition, and they exhibit redshift due to the increase in effective conjugation length with the introduction of benzene. The excited state assignments in water solution are one-to-one correspondence to those in gas phase. The lowest absorption and emission wavelength of J-AT1 is blueshift, while J-AT2, BF1 and BF2 bases are redshift as compared to those in gas. The TD-B3LYP method predicts that the first excitation wavelengths of Janus AT base pairs are local excitation on the Janus AT base moieties, which is coincident with the result of CAM-B3LYP and M062X functional. Base pair can influence the excitation properties of base monomer. The results obtained from this theoretical investigation confirm that the position of benzene ring significantly influences the structure and optical properties of the Janus AT bases.