Zn2+-cyclen-based complex enable a selective detection of single-stranded thymine-rich DNA in aqueous buffer

Zhu, Zece; Wang, Sheng; Wei, Danqing; Yang, Chuluo

doi:10.1016/j.bios.2016.05.085

Cited by 16 publications

(5 citation statements)

References 48 publications

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“…The destabilizing effect of U C is additive and increases with increasing number of cyclen moieties attached to a single strand and their total number in the duplex, with ∆T m averaging −6 • C for each U C introduced. However, there are two exceptions to this regularity; one of which is DU28, where some selectivity against mismatch TT was observed, as evidenced by ∆T m of +1 • C. This result is not necessarily surprising, as previous work on Zn(II)-cyclen complexes has shown that cyclen is able to selectively recognize thymine by forming hydrogen bonds between the carbonyl oxygens of thymine and the cyclen amino groups [25,26]. The second exception is DU19, where two U C units are adjacent on complementary strands of the duplex, however, their destabilizing effect is not additive.…”

Section: Ultraviolet Thermal Melting Studiesmentioning

confidence: 81%

Polyamine–Oligonucleotide Conjugates: 2′-OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes

et al. 2021

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Oligonucleotides with the sequences 5′-GTG AUPA TGC, 5′-GCA TAUP CAC and 5′-GUPG ATA UPGC, where UP is 2′-O-propargyl uridine, were subjected to post-synthetic Cu(I)-catalyzed azide–alkyne cycloaddition to attach 1,4,7,10-tetraazacyclododecane (cyclen) and two well-known DNA intercalating dyes: thioxanthone and 1,8-naphthalimide. We propose a convenient cyclen protection–deprotection strategy that allows efficient separation of the resulting polyamine–oligonucleotide conjugates from the starting materials by RP-HPLC to obtain high-purity products. In this paper, we present hitherto unknown macrocyclic polyamine–oligonucleotide conjugates and their hybridization properties reflected in the thermal stability of thirty-two DNA duplexes containing combinations of labeled strands, their unmodified complementary strands, and strands with single base pair mismatches. Circular dichroism measurements showed that the B-conformation is retained for all dsDNAs consisting of unmodified and modified oligonucleotides. An additive and destabilizing effect of cyclen moieties attached to dsDNAs was observed. Tm measurements indicate that placing the hydrophobic dye opposite to the cyclen moiety can reduce its destabilizing effect and increase the thermal stability of the duplex. Interestingly, the cyclen-modified U showed significant selectivity for TT mismatch, which resulted in stabilization of the duplex. We conclude the paper with a brief review and discussion in which we compare our results with several examples of oligonucleotides labeled with polyamines at internal strand positions known in the literature.

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Section: Ultraviolet Thermal Melting Studiesmentioning

confidence: 81%

Polyamine–Oligonucleotide Conjugates: 2′-OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes

et al. 2021

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“…[42] Thes igmoidal profile of Figure 4B could be hence the result of cooperative binding and not cooperative catalysis between metal ions.I n this scenario each metal complex would be involved in the binding of ad ifferent, single phosphate with az ipper-like interaction. [43] Thecoordination of two Zn(II) ions to asingle phosphate,a sr equired by ac ooperative,d inuclear catalytic mechanism, would be hence impossible.T his could explain why AuNP1-3-Zn(II) show very low or no activity at all. All of them require ad inuclear catalytic site for activity.…”

Section: Cleavage Of Pbr322 and Bnp By Aunp4 Occurs With Different Mechanismsmentioning

confidence: 99%

A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex

et al. 2020

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Similarly to enzymes,f unctionalized gold nanoparticles efficiently catalyze chemical reactions,hence the term nanozymes.H erein, we present our results showing how surface-passivated gold nanoparticles behave as synthetic nanonucleases,a ble to cleave pBR322 plasmid DNAwith the highest efficiency reported so far for catalysts based on asingle metal ion mechanism. Experimental and computational data indicate that we have been successful in creating acatalytic site precisely mimicking that suggested for natural metallonucleases relying on as ingle metal ion for their activity.I tc omprises one Zn(II) ion to which ap hosphate diester of DNAi s coordinated. Importantly,a si nn ucleic acids-processing enzymes,apositively charged arginine playsakey role by assisting with transition state stabilization and by reducing the pK a of the nucleophilic alcohol of as erine.O ur results also show howd esigning ac atalyst for am odel substrate (bis-pnitrophenylphosphate) may provide wrong indications as for its efficiency when it is tested against the real target (plasmid DNA).

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“…Deoxyribonucleic acid (DNA) is one of the most important biomolecules encoding genetic information and controlling gene expression in biological systems. − It has been recognized that DNA expression is highly variable among different cells (e.g., cancer cells, neuron) or the same type of cell under a different status (e.g., differentiation, apoptosis). Aberrant DNA levels can generally indicate disease states.…”

Section: Introductionmentioning

confidence: 99%

Activatable QD-Based Near-Infrared Fluorescence Probe for Sensitive Detection and Imaging of DNA

Shen

Zhang

Sun

et al. 2017

ACS Appl. Mater. Interfaces

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Accurate detection of DNA is essential for the precise diagnosis of diseases. Here we report an activatable near-infrared (NIR) fluorescence nanoprobe (QD-Al-GFLX) composed of NIR quantum dots (QDs) and Al(III)-gatifloxacin (Al-GFLX) complexes for the sensitive detection of double-stranded DNA (dsDNA) both in aqueous solution and in living cells. We demonstrated that the initial strong NIR fluorescence of QDs in QD-Al-GFLX was quenched by the Al-GFLX complex via a photoinduced electron transfer (PET) mechanism. Upon interaction with dsDNA, the high binding affinity between dsDNA and Al-GFLX complex could trigger QD-Al-GFLX dissociation, which could eliminate the PET process, resulting in significant enhancement of NIR fluorescence. QD-Al-GFLX was sensitive and specific to detect dsDNA in aqueous solution, with a detection limit of 6.83 ng/mL. The subsequent fluorescence imaging revealed that QD-Al-GFLX holds a high ability to enter into live cells, generating strong NIR fluorescence capable of reporting on dsDNA levels. This study highlighted the potential of using QD-Al-GFLX nanoprobe for the real-time detection and imaging of dsDNA in living cells.

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Zn2+-cyclen-based complex enable a selective detection of single-stranded thymine-rich DNA in aqueous buffer

Cited by 16 publications

References 48 publications

Polyamine–Oligonucleotide Conjugates: 2′-OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes

Polyamine–Oligonucleotide Conjugates: 2′-OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes

A Gold Nanoparticle Nanonuclease Relying on a Zn(II) Mononuclear Complex

Activatable QD-Based Near-Infrared Fluorescence Probe for Sensitive Detection and Imaging of DNA

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