Studies on the structure and chirality of A-motif in adenosine monophosphate nucleotide metal coordination complexes

Iqbal, Muhammad Javed; Li, Zhongkui; Khan, Maroof Ahmad; Zhu, Yanhong; Hussain, Wajid; Su, Hao; Qiu, Qi–Ming; Shoukat, Rizwan; Lĭ, Hui

doi:10.1039/d1ce00276g

Cited by 4 publications

(3 citation statements)

References 45 publications

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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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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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“…5 In contrast to B-DNA, a typical right-handed double helix with Watson-Crick base-pairing, repetitive DNA sequences can adopt non-B structures, including Hoogsteen base-paring, 6 Gquadruplex, 7 left-handed Z-DNA, 8 triplex (H-DNA), 9 tetraplex, 10 cruciform, 11 hairpin, 12 i-motif (cytosine-cytosine base-pair mismatch), 13 and A-motif (adenine-adenine base-pair mismatch). 14 Metal-nucleotide coordination complexes involve significant (M-L) supramolecular interactions. Such complexes serve as valuable biomimetic techniques, aiding the comprehension of metal ion-nucleic acid interactions.…”

Section: Introductionmentioning

confidence: 99%

“…5 In contrast to B-DNA, a typical right-handed double helix with Watson–Crick base-pairing, repetitive DNA sequences can adopt non-B structures, including Hoogsteen base-paring, 6 G-quadruplex, 7 left-handed Z-DNA, 8 triplex (H-DNA), 9 tetraplex, 10 cruciform, 11 hairpin, 12 i-motif (cytosine–cytosine base-pair mismatch), 13 and A-motif (adenine–adenine base-pair mismatch). 14…”

Section: Introductionmentioning

confidence: 99%

Sugar–nucleobase hydrogen bonding in cytidine 5′-monophosphate nucleotide-cadmium coordination complexes

Khan,

Ismail,

et al. 2024

CrystEngComm

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The Full Cytosine‐Cytosine Base Paring: Self‐Assembly and Crystal Structure

Song

Zhu

et al. 2023

Chemistry A European J

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The synthesis of self‐assembly systems that can mimic partial biological behaviours require ingenious and delicate design. For decades, scientists are committed to exploring new base pairing patterns using hydrogen bonds directed self‐assembly of nucleotides. A fundamental question is the adaptive circumstance of the recognition between base pairs, namely, how solvent conditions affect the domain of base pairs. Towards this question, three nucleotide complexes based on 2’‐deoxycytidine‐5’‐monophosphate (dCMP) and cytidine‐5’‐monophosphate (CMP) were synthesized in different solvents and pH values, and an unusual cytosine‐cytosine base paring pattern (named full C : C base pairing) has been successfully obtained. Systematic single crystal analysis and 1H NMR titration spectra have been performed to explore factors influencing the formation of base paring patterns. Moreover, supramolecular chirality of three complexes were studied using circular dichroism (CD) spectroscopy in solution and solid‐state combined with crystal structure analysis.

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Studies on the structure and chirality of A-motif in adenosine monophosphate nucleotide metal coordination complexes

Abstract: Nucleotide constructs the B-DNA and non-B DNA. Non-B DNA leads to the genetic instability, genetic diseases and rearrangement of bases. Adenine-Adenine base pair mismatch (A-motif) is considered to be the...

Cited by 4 publications

References 45 publications

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

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

Sugar–nucleobase hydrogen bonding in cytidine 5′-monophosphate nucleotide-cadmium coordination complexes

The Full Cytosine‐Cytosine Base Paring: Self‐Assembly and Crystal Structure

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