Reviewed by Louis CastelJan 27 2025
In a recent study published in the journal Intelligent Computing, researchers from Peking University showed how nuclear electric resonance can be used to manipulate DNA artificially for computational purposes by controlling the nuclear spins of nitrogen atoms in DNA through electric field gradients.
Red arrows indicate the nuclear spin axes at the positions of the N3 nitrogen atoms on the guanine (G) bases. Due to the helical structure of DNA, there is an angular deviation in the orientation of adjacent bases, resulting in a corresponding angular deviation in the axes. Image Credit: Yu Zheng and Quansheng Ren.
Through molecular dynamics simulations, quantum chemical computations, and theoretical analyses, recent research reveals how differences in the orientation patterns of electric field gradients across DNA bases and nitrogen atom sites influence the alignment of nitrogen nuclear spins, encoding both genetic and structural information.
“Our research has unveiled the patterns of the principal axis directions of the electric field gradient at the nitrogen atom sites in DNA molecules, demonstrating that these directions are closely associated with the types of bases and the 3D structure of DNA,” the authors said.
Thus, the base sequence and three-dimensional structure information of DNA molecules are encoded by these nitrogen nuclear spin patterns. Consequently, bases may one day be employed as a storage mechanism in a DNA-based quantum computing device by manipulating their sequence.
A computation mechanism would also be necessary for such a device. Because of their more intricate and diverse characteristics, proton nuclear spins can interact with nitrogen nuclear spins to obtain information and perform computational functions. This process makes it possible to use DNA for quantum computing.
The electric field gradient orientations of the nitrogen atoms in DNA vary depending on whether they are bonded to three or two atoms. In the former, the principal axis is always perpendicular to the base plane, whereas in the latter, depending on the type of base and nitrogen, the principal axis either aligns with or is nearly perpendicular to the bisector of the bonds. The four bases adenine, guanine, cytosine, and thymine have different orientations.
Additionally, spin system simulations analyzing the electric field gradient data from neighboring bases showed a consistent alignment between the structural deflection angles of the bases and the deflection angles of nitrogen nuclear spin orientations in adenine -and guanine-bound nitrogen atoms. In contrast, thymine and cytosine show greater variability, with no fixed rules for nitrogen orientations.
The authors modeled the atomic coordinates of the DNA molecule over time using molecular dynamics simulations to study the electric field gradients in DNA. Using strict equilibration and simulation procedures, they employed a solvated DNA system with additional ions to guarantee neutrality.
The positions of the nitrogen atoms within the DNA bases were then the focus of quantum chemical calculations performed on specific nucleotide subsets. Principal axis directions and eigenvalues were extracted from the analysis of the electric field gradient components.
The authors investigated how nitrogen nuclear spins influence the spin directions of nearby proton nuclei under the electric field gradient. They analyzed how DNA structure affects the deflection angles of nuclear spin orientations by comparing the electric field gradient deflection angles of the nuclei to the structural deflection angles of two adjacent, identical DNA bases.
The study builds on the authors' earlier work, which examined how nuclear electric resonance might be used to manipulate sodium ion nuclear spins on phospholipid membranes through the use of electric field gradients.
This study reveals the complex interplay between electric field gradients, nitrogen atom orientations, and DNA base structures, enhancing the understanding of DNA computation through molecular-level artificial intervention and opening new avenues for advancements in quantum computing and genetic information processing.
Journal Reference:
Zheng, Y., et al. (2024) Encoding Genetic and Structural Information in DNA Using Electric Field Gradients and Nuclear Spins. Intelligent Computing. doi.org/10.34133/icomputing.0094.