Mimic uracil–uracil base pairing: self-assembly and single crystal structure

Zhang, Menglei; Li, Zhongkui; Zhu, Yanhong; Yan, Li; Zhong, Xue; Zhang, Yijie; Li, Ziyao; Bai, Yixiang; Li, Hui

doi:10.1039/d3ce01056b

Cited by 1 publication

(2 citation statements)

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“…We are interested and have worked in this field for more than a decade. The crystal structures of the guanine–guanine base pairing (G-motif), the adenine–adenine base pair (A-motif), and the uracil–uracil base pair (U-motif) have been investigated. In this work, crystal structure data of thymine–thymine base pairing (T-motif) has been reported for the first time, although there are very rare theoretical studies. , …”

Section: Resultsmentioning

confidence: 99%

“…It helps to identify the protonation position of nucleobases, determine the hydrogen bond geometry, and understand the solid-state configuration of bases. We have studied the nonclassical base pairs, including cytosine and guanine base pairs, the cytosine− cytosine base pair (i-motif), adenine−adenine base pair (A-Motif), and the uracil−uracil base pair (U-motif) 29 by using Xray single-crystal diffraction. However, it is still a challenge to understand the cooperative interactions between base pairing, water helix, and strand helix skeleton in the DNA or RNA structure.…”

Section: Introductionmentioning

confidence: 99%

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Solidarity of the Coordination Helix and Water Helix in the Nucleotide Coordination Polymer

Zohaib,

Saqlain,

Khan

et al. 2024

Crystal Growth & Design

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Helix structure is a very important and fundamental structural feature of DNA and other biomaterials and is also one of the origins of chirality. Diversiform helix structures have been designed and constructed to understand the mechanism of helix formation. One of the challenges in this field is rationalizing single-stranded DNA and water helix. The possibility of water helix formation preceding the base pairing in DNA is an intriguing prospect. In this work, three coordination polymers based on the nucleotide dTMP have been designed and studied. Their single-crystal structures revealed that complexes 1 and 3 are 1D coordination polymers while complex 2 is a 2D coordination polymer. Complexes 1 and 2 are the coordination helixes. Importantly, the water helixes are enclosed in them. Both P and M water helixes exist in complex 1; only the M-water helix is in complex 2. It is worth noting that complex 3 exhibits the entanglement of coordination helixes and water helixes and then presents a pseudowater helix. The solidarity of the coordination helix and water helix in the crystal lattice has been investigated based on crystallography analysis. The building synthons limit the orientation of the nucleobase and lack adequate stereospace to confine the guest water molecules. A new type of nucleobase pairing, thymine−thymine, named T-motif, has been observed for the first time. The inherent and supramolecular chirality of these complexes have been discussed according to CD spectra in both solution and crystallized solid states. The water helix in complex 2 exhibits characteristic outcomes in the CD spectrum. The research results contribute to exploring and understanding the DNA structure and properties and the mechanism of helix formation.

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