Effect of Loop Length and Sequence on the Stability of DNA Pyrimidine Triplexes with TAT Base Triplets

Short-Range Charge Transfer in DNA Base Triplets: Real-Time Tracking of Coherent Fluctuation Electron Transfer

The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear-electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between -0.040 and -0.056. The time-dependent Marcus-Levich-Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.

One-electron oxidation of TAT-motif triplex DNA and the ensuing Hoogsteen hydrogen-bonding dissociation

One-electron oxidation of adenine (A) leads initially to the formation of adenine radical cation (A^•+). Subsequent deprotonation of A^•+ can provoke deoxyribonucleic acid (DNA) damage, which further causes senescence, cancer formation, and even cell death. However, compared with considerable reports on A^•+ reactions in free deoxyadenosine (dA) and duplex DNA, studies in non-B-form DNA that play critical biological roles are rare at present. It is thus of vital importance to explore non-B-form DNA, among which the triplex is an emerging topic. Herein, we investigate the deprotonation behavior of A^•+ in the TAT triplex with continuous A bases by time-resolved laser flash photolysis. The rate constants for the one-oxidation of triplex 8.4 × 10⁸ M^-1 s^-1 and A^•+ deprotonation 1.3 × 10⁷ s^-1 are obtained. The kinetic isotope effect of A^•+ deprotonation in the TAT triplex is 1.8, which is characteristic of a direct release of the proton into the solvent similar to free base dA. It is thus elucidated that the A^•+ proton bound with the third strand is most likely to be released into the solvent because of the weaker Hoogsteen H-bonding interaction and the presence of the highly mobile hydration waters within the third strand. Additionally, it is confirmed through Fourier transform infrared spectroscopy that the deprotonation of A^•+ results in the dissociation of the third strand and disruption of the secondary structure of the triplex. These results provide valuable kinetic data and in-depth mechanistic insights for understanding the adenine oxidative DNA damage in the triplex.