Mechanisms of the T-A to C-G transition studied by SMD simulations: Deamination vs tautomerisation

Tolosa, S.; Sansón, J.A.; Hidalgo, Antonio

doi:10.1016/j.molliq.2020.113036

Cited by 6 publications

(3 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The combined studies of the hydrogen-bonded and dissociated forms of the DNA bases indicate that the tautomeric state is more likely to be formed via proton tunnelling in the hydrogen-bonded conformation over the single-stranded configuration. However, any quantum tunnelling is expected to compete with other environmental mechanisms; such as the deamination pathway, 57 or the polarisation interactions of aqueous solution. 58 The inclusion of more direct environmental interactions, such as the phosphate groups of the DNA backbone and p-p stacking interactions with the adjacent nucleotides, could alter the energy landscape.…”

Section: Discussionmentioning

confidence: 99%

Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs

Slocombe

Al-Khalili

Sacchi

2021

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs

Slocombe

Al-Khalili

Sacchi

2021

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

show abstract

“…If the single-stranded tautomeric base is exposed to the solvent, then it could exchange hydrogen atoms with the solvent to revert to the canonical form. In addition, this transition could even occur via an intramolecular proton transfer, from one hydrogen bonding site to the other, within the same nucleotide base [307,308].…”

Section: Spontaneous Mutagenesismentioning

confidence: 99%

Quantum Biology: An Update and Perspective

et al. 2021

View full text Add to dashboard Cite

Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.

show abstract

“…In addition, another work reports the DNA damage due to hydrogen-bonded proton transfer in the protonated GC base pairs (Lin et al, 2011). Recently, one steered molecular dynamic simulation presents that the tautomerization of the T * -A * mispair via double proton transfer is an effective pathway of the T-A to C-G transition (Tolosa et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP

Cui

Zhao

et al. 2020

Front. Chem.

View full text Add to dashboard Cite

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.

show abstract

Mechanisms of the T-A to C-G transition studied by SMD simulations: Deamination vs tautomerisation

Cited by 6 publications

References 48 publications

Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs

Quantum and classical effects in DNA point mutations: Watson–Crick tautomerism in AT and GC base pairs

Quantum Biology: An Update and Perspective

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP

Contact Info

Product

Resources

About