Effects of Bis(aromatic) Pendants on Recognition of Nucleobase Thymine by Zn<sup>2+</sup> -1,4,7,10-tetraazacyclododecane (Zn<sup>2+</sup> -cyclen)

Kimura, Eiichi; Katsube, Naomi; Koike, Takao; Shiro, Motoo; Aoki, Shin

doi:10.1080/10610270290025997

Cited by 21 publications

(18 citation statements)

References 30 publications

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“…Zn(II) complexes with pendents containing two fused rings show increased binding for non-canonical thymine over duplex DNA. [9,27] In contrast, a pendent with a simple benzene derivative did not increase binding strength significantly. [35] Pendent groups with three fused rings are not selective for unpaired thymines because they typically bind through intercalation into the DNA duplex.…”

Section: Introductionmentioning

confidence: 89%

“…Selective binding of the Zn(II) cyclen macrocycle to unpaired thymine bases is maintained for several different types of aromatic pendent groups. [9,27] The development of Zn(II) complexes for selective binding of unpaired thymine bases which are in unusual DNA structures is more complicated. For example, the interaction of Zn(II) complexes with unpaired thymines in non-canonical context including those in bulged DNA and quadruplex DNA has been reported.…”

Section: Introductionmentioning

confidence: 99%

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Zn(II) complexes that trigger a DNA conformational switch

Sander

Morrow

2016

Inorganica Chimica Acta

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Several Zn(II) complexes are shown to produce a DNA conformational switch that involves dissociation of a fully complementary duplex into two hairpins. Of the three different pendent groups studied, a Zn(II) complex with a planar pendent connected directly to the macrocycle is the most effective at promoting the conformational switch. DNA duplexes of varying length and sequence are studied in order to examine the effect of lengthening AT tracts on conversion of duplex to hairpins. The role of hairpin structure in dissociated strands is also examined and shown to be a necessary component of an effective switch. Insight into the conformation switch is obtained through binding studies of the different Zn(II) complexes to DNA oligonucleotides that contain unpaired thymines by using surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC).

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Section: Introductionmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Zn(II) complexes that trigger a DNA conformational switch

Sander

Morrow

2016

Inorganica Chimica Acta

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“…Previously, Shionoya et al [14] reported that a macrocyclic tetraamine zinc(II) complex (Zn 2+ -cyclen, cyclen = 1,4,7,10-tetraazacyclododecane) selectively binds to deoxythymidine (dT) in aqueous solution with a dissociation constant K d = [free dT][free Zn 2+ -cyclen]/[dT-Zn 2+ -cyclen] = 0.3 mM at pH 8. We have also found that the derivative of Zn 2+ -cyclen-attached aromatic rings,Zn 2+ -1,7-bis(4-quinolylmethyl)-1,4,7,10-tetraazacyclododecane (Zn 2+ -Q 2 -cyclen), binds to dT (K d = 10 µM at pH 8.0) much more strongly due to additional double π-π stacking interactions between the two quinoline rings and the nucleobase [15,16]. The macrocyclic tetraamine zinc(II) complexes preferentially bind to dT in double-stranded DNA to dissociate -), as described previously [15].…”

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confidence: 85%

“…Zn 2+ -1,7-bis(4-quinolylmethyl)-1,4,7,10-tetraazacyclododecane (Zn 2+ -Q 2 -cyclen), binds to dT (K d = 10 µM at pH 8.0) much more strongly due to additional double π-π stacking interactions between the two quinoline rings and the nucleobase [15,16]. The macrocyclic tetraamine zinc(II) complexes preferentially bind to dT in double-stranded DNA to dissociate -), as described previously [15].…”

Section: Introductory Statementmentioning

confidence: 99%

A heteroduplex-preferential Tm depressor for the specificity-enhanced DNA polymerase chain reactions

Kinoshita

Kinoshita–Kikuta

Koike

2005

Analytical Biochemistry

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A macrocyclic tetraamine zinc(II) complex appended with two quinoline groups, Zn(2+)-1,7-bis(4-quinolylmethyl)-1,4,7,10- tetraazacyclododecane (Zn(2+)-Q2-cyclen), was successfully used as a novel additive to suppress nonspecific products in DNA polymerase chain reaction (PCR). In the presence of Zn(2+)-Q2-cyclen, the Tm drop of 20-bp heteroduplexes containing a noncomplementary basepair was greater than that of the corresponding homoduplex (i.e., primer DNA). Here, we applied such preferential DNA melting to a specificity-enhanced PCR using micromolar concentrations of Zn(2+)-Q2-cyclen. We demonstrated the selective amplification of target DNA fragments (i.e., the human heart sodium channel Nav1.5 gene) from genomic DNA or a cDNA library. The optimum condition for the specificity-enhanced PCR could be determined in the concentration range of 1-50muM of Zn(2+)-Q2-cyclen.

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“…The biochemical and pharmacological properties of macrocyclic polyamines have been partially exploited. Important DNA-recognizing behavior and anti-human immunodeficiency virus activity of some derivatives of these macrocycles have been reported (1,8,10). However, owing to their unique capacity to bind some of the biologically significant metals, including Zn, these macrocyclic polyamines have opened a new era in bioorganic and medicinal chemistry research.…”

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confidence: 99%