The Research of G–Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes

Zhu, Yanhong; Li, Zhongkui; Wang, Pengfei; Qiu, Qi–Ming; Ma, Hongwei; Li, Hui

doi:10.3389/fchem.2021.709777

Cited by 4 publications

(4 citation statements)

References 67 publications

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“…In the solid-state CD spectrum of the IDP ligand, two peaks centered at 224 and 268 nm were attributed to the n−π* and π–π* transitions of the IDP ligand, respectively. Because in our previous research , different conformations of pentose rings can lead to differences in their CD spectra, the conformation of the pentose ring in the IDP ligand also has an E-type form according to the similarity of the CD spectra between IDP and IMP ligand ( P = 164°; E conformation).…”

Section: Resultsmentioning

confidence: 92%

Coordination Patterns of the Diphosphate in IDP Coordination Complexes: Crystal Structure and Chirality

Zhu

Zhong

et al. 2022

Inorg. Chem.

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The knowledge of accurate geometrical parameters from X-ray diffraction studies in the solid state of metal nucleotide is very important for understanding the relationship between structures and properties, including biochemical processes and even enzyme–metal–substrate interactions. The research is also very necessary to precisely and controllably design the functional materials. Here, seven types of coordination polymers of inosine 5′-diphosphate nucleotide (IDP) with transition metals, {[Zn(HIDP)(azpy)(H2O)2]·4H2O} n (1), {[Cd2(IDP)2(bpda)2]·[Cd(H2O)6]·11H2O} n (2), {[Cd3(IDP)2(4,4′-bipy)2(H2O)3]·6H2O} n (3), {[Cd2(IDP)2(bpe)2(H2O)2]·(H2bpe)·26H2O} n (4), {[Cu3(IDP)2(azpy)2(H2O)5]·5H2O} n (5), {[Cu3(IDP)2(bpe)2(H2O)5]·9H2O} n (6), and {[Co(HIDP)(azpy)(H2O)2]·7H2O} n (7) [4,4′-bipy = 4,4′-bipyridine, azpy = 4,4′-azopyridine, bpe = 1,2-bis(4-pyridyl)ethene, and bpda = 1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene], were designed, synthesized, and firmly characterized using single-crystal X-ray diffraction. The coordination patterns of the diphosphate group of IDP in these complexes were studied by crystallographic analysis, namely, open, close, and open–close hybrid types. We have investigated the diverse coordination patterns of the diphosphate group and its spatial relationship relative to the pentose ring on the basis of two conformational parameters, the pseudorotation phase angle and the degree of puckering. Crystallographic studies clearly reveal the correlation between the backbone torsion angle (ω′ and φ) of the sugar–diphosphate and the conformational preference of the pentose ring, i.e., the signs of the backbone torsion angles ω′ and φ are both plus (+) or minus (−), the conformation of the pentose ring is envelope form (E), while when one of the two signs is plus (+) and the other is minus (−), the pentose ring is in the twist form (T). This is the first time elucidation of the coordination pattern of diphosphate relative to the conformation of the pentose ring in nucleotide metal complexes, which are different from the other inorganic or organic diphosphate compounds. The chirality of these coordination polymers was examined by combining solid-state circular dichroism spectroscopy measurements with the explanation of their crystal structures. The results presented in this paper are very important for understanding their nucleotide coordination chemistry, their supramolecular chemistry, and even their biochemistry.

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Section: Resultsmentioning

confidence: 92%

Coordination Patterns of the Diphosphate in IDP Coordination Complexes: Crystal Structure and Chirality

Zhu

Zhong

et al. 2022

Inorg. Chem.

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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%

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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“…In this context, bipyridyl-type bridging ligands of differing sizes offer an ideal alternative because of their numerous features . First, they can precisely fix the orientation of purine bases via π–π stacking interactions.…”

Section: Resultsmentioning

confidence: 99%

“…Similar peaks appear at 228 and 271 nm in the spectrum of the dIMP ligand. In our previous research, the different conformation of pentose rings such as cytidine 5′-monophosphate (CMP)/2′-deoxycytidine 5′-monophosphate (dCMP) and guanosine 5′-monophosphate (GMP)/2′-deoxyguanosine 5′-monophosphate (dGMP) can lead to differences in their CD spectrum. Therefore, as per the similarity of the CD spectra of IMP ( P = 164°; E conformation) and dIMP, the deoxyribose ring of the dIMP ligand has an E-type structure.…”

Section: Resultsmentioning

confidence: 99%

Conformation Locking of the Pentose Ring in Nucleotide Monophosphate Coordination Polymers via π–π Stacking and Metal-Ion Coordination

Zhu

Song

et al. 2021

Inorg. Chem.

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The conformation of the pentose ring in nucleotides is extremely important and a basic problem in biochemistry and pharmaceutical chemistry. In this study, we used a strategy to regulate the conformation of pentose rings of nucleotides via the synergistic effect of metal-ion coordination and π–π stacking. Seven types of coordination complexes were developed and characterized using Fourier transform infrared spectroscopy, elemental analysis, thermogravimetric analysis, powder X-ray diffraction, ultraviolet–visible spectroscopy, 1H nuclear magnetic resonance spectroscopy, electrospray ionization mass spectrometry, and single-crystal X-ray diffraction. On the basis of two conformational parameters obtained from single-crystal structure analysis, i.e., the pseudorotation phase angle and degree of puckering, the exact conformation of the furanose ring in these coordination polymers was unequivocally determined. Crystallographic studies demonstrate that a short bridging ligand (4,4′-bipyridine) is conducive to the formation of a twist form, and long auxiliary ligands [1,2-bis(4-pyridyl)ethene and 4,4′-azopyridine] induce the formation of an envelope conformation. However, the longest auxiliary ligands [1,4-bis(4-pyridyl)-2,3-diaza-1,3-butadiene] cannot limit the flexibility of a nucleotide. Our results demonstrated that the proposed strategy is universal and controllable. Moreover, the chirality of these coordination polymers was examined by combining the explanation of their crystal structures with solid-state circular dichroism spectroscopy measurements.

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The Research of G–Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes

Cited by 4 publications

References 67 publications

Coordination Patterns of the Diphosphate in IDP Coordination Complexes: Crystal Structure and Chirality

Coordination Patterns of the Diphosphate in IDP Coordination Complexes: Crystal Structure and Chirality

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

Conformation Locking of the Pentose Ring in Nucleotide Monophosphate Coordination Polymers via π–π Stacking and Metal-Ion Coordination

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