A unified computational view of DNA duplex, triplex, quadruplex and their donor–acceptor interactions

Abstract

DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.

TripDesign: A DNA Triplex Design Approach Based on Interaction Forces

“…For the stability of the DNA triplex, the interaction of hydrogen bonds between bases is only one of the influencing factors, and another important factor is the stacking interaction between the layers of the triplex; that is, the stacking force of the DNA triplex helix structure. 35 The π−π stacking force is one of the most important intermolecular interactions in DNA. 36 Usually, between adjacent base pairs, π−π stacking interactions cause the order of base pairs to stack.…”

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

“…Taking advantage of precise hybridization between two DNA strands with complementary sequences, DNA can easily form different nano-sized simple structures, including linear double-stranded helices, hairpin structures, kissing complexes, Holliday junctions, and DNA tiles (Figure 3A). In some cases, DNA can also form triplex or quadruplex structures, due to different hydrogen bonding patterns of nucleobases (Rosu et al, 2002;Park et al, 2021). To construct more complicated DNA structures, these simple structural units can be assembled in a defined order, either by hybridizing different DNA strands, or by integrating parts of different structural units into the same strand of DNA.…”

DNA‐Encoded Nanomaterials with Controllable Properties

“…[27] A classical right-handed helical duplex structure (B-DNA) is generated via Watson-Crick hydrogen bonds (AÀ T and CÀ G) (Figure 1A-B), and also with existence of electrostatic and π-π stacking interactions. [28] Apart from B-DNA, DNA sequences could fold into non-B DNA structures, such as triplex, G-quadruplex and i-motif, etc., under certain conditions. [29] A DNA triplex found in homopurine-homopyrimidine chains is stabilized by both Watson-Crick hydrogen bonds and Hoogsteen hydrogen bonds (TÀ A•T, CÀ G * C + ) (Figure 1C), and dissociates into a duplex and a homopyrimidine chain at alkaline pH, due to deprotonation of C and T bases.…”

“…DNA is a polydeoxynucleotide containing bases (adenine (A), thymine (T), cytosine (C), guanine (G)), phosphate groups and sugar rings [27] . A classical right‐handed helical duplex structure (B‐DNA) is generated via Watson‐Crick hydrogen bonds (A−T and C−G) (Figure 1A–B), and also with existence of electrostatic and π‐π stacking interactions [28] . Apart from B‐DNA, DNA sequences could fold into non‐B DNA structures, such as triplex, G‐quadruplex and i‐motif, etc., under certain conditions [29] .…”