The Complementarity of the Loop to the Stem in DNA Pseudoknots Gives Rise to Local TAT Base-Triplets

Reiling-Steffensmeier, Calliste; Marky, Luis A.

doi:10.1016/bs.mie.2015.07.029

Cited by 3 publications

(2 citation statements)

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“…Hexagonal packing of DNA and RNA was observed for DNA and RNA complexes with Cetyltrimethyl Ammonium Bromide (CTBA) and for Dimethyldioctadecyl Ammonium Bromide (DDAB) complexes is observed lamellar structure. Variations in the internal spacing and degree of long-range ordering are dependent on both surfactant type and concentrations of added salt [19][20][21][22][23][24][25][26][27][28][29]. When we increased the amount of salt into our complexes, we observed that the d spacing (d=2Π/r) are increased.…”

mentioning

confidence: 68%

A Thermodynamic Study on Hydration and Dehydration of DNA and RNA −Amphiphile Complexes

Heidari¹

2016

J Bioengineer & Biomedical Sci

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confidence: 68%

A Thermodynamic Study on Hydration and Dehydration of DNA and RNA −Amphiphile Complexes

Heidari¹

2016

J Bioengineer & Biomedical Sci

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“…Adenine (A) is oxidized and can be used as a hole carrier, while thymine (T) is reduced and regarded as an electron carrier [17,18]. T and A form a dimer through the Watson-Crick structure, and the third base T is parallel to A and connected by hydrogen bonds to form a stable base triplet structure [19][20][21][22]. At present, the charge transfer of TAT base triplets at short-range is thought to be caused by superexchange [23,24].…”

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confidence: 99%

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

Zhu,

Li,

Wan

et al. 2023

Molecules

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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.

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

Zhu¹,

Li²,

Wan³

et al. 2023

Preprint

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The Complementarity of the Loop to the Stem in DNA Pseudoknots Gives Rise to Local TAT Base-Triplets

Cited by 3 publications

References 48 publications

A Thermodynamic Study on Hydration and Dehydration of DNA and RNA −Amphiphile Complexes

A Thermodynamic Study on Hydration and Dehydration of DNA and RNA −Amphiphile Complexes

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

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

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