Abstract
Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2′-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1′-β-D-2′- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.
Highlights
In the field of biochemistry, the four natural nucleotide letters [guanine (G), cytosine (C), adenine (A), and thymine (T)] can encode virtually all genetic information
It is found that the double proton transfer in the gas phase is a concerted mechanism both in ground (S0) and the first excited (S1) states, while the process in solution turns to be stepwise along the S0-potential energy surfaces (PESs) and only single proton transfer is available in the S1 state
We investigated the intermolecular proton-transfer mechanism and photoisomerization of artificial base pair-ZP
Summary
In the field of biochemistry, the four natural nucleotide letters [guanine (G), cytosine (C), adenine (A), and thymine (T)] can encode virtually all genetic information. In the past few years, Romesberg et al reported a class of unnatural base pairs formed between nucleotides containing hydrophobic nucleobases, successfully replicating artificial base pairs in vivo (McMinn et al, 1999; Tae et al, 2001; Malyshev et al, 2014). They have optimized different components of semisynthetic organisms by using genetic and chemical approaches, eventually making them grow robustly and be capable of storing the increased. It has been revealed that DNA strands containing artificial ZP base pairs could better combine with breast cancer cells by exponential enrichment experiment and can be transformed into “cancer cell hunters” (Sefah et al, 2014)
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