Exceptionally Selective and Tunable Sensing of Guanine Derivatives and Analogues by Structural Complementation in a G‐Quadruplex

Li, Xinmin; Zheng, Ke-wei; Hao, Yu-hua; Tan, Zheng

doi:10.1002/anie.201607195

Cited by 20 publications

(18 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The effect of o 8 dG has been well demonstrated to depend on the secondary structure of nucleic acids [ 26 , 285 , 286 ]. Recent studies provided additional results, such as the comparison of the effect of o 8 dG in triplexes and GQs [ 100 ], the involvement of o 8 dG in the stabilization of “guanine-vacancy-bearing” GQs [ 287 ], or a comprehensive study on the complex effect of metal ions and cosolutes on the topology of the A(htel-21) GQ when both o 8 G and xanthine were contained in the tetrads [ 288 ]. 8-Oxoguanine in GQ loops accommodated well and did not have much effect on the stability [ 281 ].…”

Section: Natural Base Lesions and Epigenetic Modifications In Gq Dmentioning

confidence: 99%

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Sági¹

2017

Journal of Nucleic Acids

View full text Add to dashboard Cite

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.

show abstract

Section: Natural Base Lesions and Epigenetic Modifications In Gq Dmentioning

confidence: 99%

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Sági¹

2017

Journal of Nucleic Acids

View full text Add to dashboard Cite

show abstract

“…Considering that a guanine vacancy in one of the G‐quartet layers (GVBQ) can be filled by a guanine base from GTP or GMP to complete an intact G‐quartet , the number of potential G4s was increased from 52 to 356 (Table ), corresponding to a G4 occurrence frequency of 1.96‰, higher than that of canonical 3‐G4 DNAs. The above analysis and prediction indicate that G4 DNAs exist in the E. coli genome and may be roadblocks for Pols in genome transaction processes.…”

Section: Resultsmentioning

confidence: 99%

Escherichia coli DNA polymerase I can disrupt G‐quadruplex structures during DNA replication

et al. 2017

View full text Add to dashboard Cite

Non-canonical four-stranded G-quadruplex (G4) DNA structures can form in G-rich sequences that are widely distributed throughout the genome. The presence of G4 structures can impair DNA replication by hindering the progress of replicative polymerases (Pols), and failure to resolve these structures can lead to genetic instability. In the present study, we combined different approaches to address the question of whether and how Escherichia coli Pol I resolves G4 obstacles during DNA replication and/or repair. We found that E. coli Pol I-catalyzed DNA synthesis could be arrested by G4 structures at low protein concentrations and the degree of inhibition was strongly dependent on the stability of the G4 structures. Interestingly, at high protein concentrations, E. coli Pol I was able to overcome some kinds of G4 obstacles without the involvement of other molecules and could achieve complete replication of G4 DNA. Mechanistic studies suggested that multiple Pol I proteins might be implicated in G4 unfolding, and the disruption of G4 structures requires energy derived from dNTP hydrolysis. The present work not only reveals an unrealized function of E. coli Pol I, but also presents a possible mechanism by which G4 structures can be resolved during DNA replication and/or repair in E. coli.

show abstract

“…8-Oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG) is one of the biomarkers in DNA oxidative damage [ 21 ], and plays a major role in mutagenesis, aging and carcinogenesis [ 22 ]. 8-oxoG is a problematic lesion to detect in nucleic acid [ 23 ], and could be further oxidized to the labile products-dGh [ 24 ], which are sensitive to hot piperidine.…”

Section: Resultsmentioning

confidence: 99%

Application of Ammonium Persulfate for Selective Oxidation of Guanines for Nucleic Acid Sequencing

et al. 2017

View full text Add to dashboard Cite

Nucleic acids can be sequenced by a chemical procedure that partially damages the nucleotide positions at their base repetition. Many methods have been reported for the selective recognition of guanine. The accurate identification of guanine in both single and double regions of DNA and RNA remains a challenging task. Herein, we present a new, non-toxic and simple method for the selective recognition of guanine in both DNA and RNA sequences via ammonium persulfate modification. This strategy can be further successfully applied to the detection of 5-methylcytosine by using PCR.

show abstract

Exceptionally Selective and Tunable Sensing of Guanine Derivatives and Analogues by Structural Complementation in a G‐Quadruplex

Cited by 20 publications

References 30 publications

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

Escherichia coli DNA polymerase I can disrupt G‐quadruplex structures during DNA replication

Application of Ammonium Persulfate for Selective Oxidation of Guanines for Nucleic Acid Sequencing

Contact Info

Product

Resources

About