Metal Ion-Directed Specific DNA Structures and Their Functions

Abstract

Various DNA structures, including specific metal ion complexes, have been designed based on the knowledge of canonical base pairing as well as general coordination chemistry. The role of metal ions in these studies is quite broad and diverse. Metal ions can be targets themselves in analytical applications, essential building blocks of certain DNA structures that one wishes to construct, or they can be responsible for signal generation, such as luminescence or redox. Using DNA conjugates with metal chelators, one can more freely design DNA complexes with diverse structures and functions by following the simple HSAB rule. In this short review, the authors summarize a part of their DNA chemistries involving specific metal ion coordination. It consists of three topics: (1) significant stabilization of DNA triple helix by silver ion; (2) metal ion-directed dynamic sequence edition through global conformational change by intramolecular complexation; and (3) reconstruction of luminescent lanthanide complexes on DNA and their analytical applications.

Keywords: ATP sensor; DNA conjugate; DNAzyme; aptamer; lanthanide; metal ion; sequence edition; silver ion; terpyridine; triple helix.

Figure 1

Triplex stabilization by silver ion. (a) Structure of the triplex and CG.CAg⁺ base triplet; (b) upper left: UV melting curves in the presence of Ag⁺ with various feeding ratios. Only the temperature of the triplex–duplex transition increased with the addition of Ag⁺. Bottom left: pH dependence of the melting temperatures of triplex in the absence and presence of Ag⁺. The melting temperature in the presence of Ag⁺ consists of two pH-independent regions. Right: Phase diagram of the structure of Ag⁺-mediated nucleobase complexes.

Figure 2

Metal ion-directed reversible edition of the DNA sequence. The sequence of terpy₂DNA is edited by intramolecular complexation with appropriate metal ions through Ω-shaped global conformational change.

Figure 3

Metal ion-directed regulation of DNAzyme activity. (a) Allosteric regulation of split DNAzyme activity by metal ion-directed dynamic sequence edition of the template, terpy₂DNA. (b) Left: Time courses of the ABTS oxidation by the split DNAzyme with terpy₂DNA in the presence of Fe²⁺ and Ni²⁺. Red, split DNAzyme/terpy₂DNA + Fe²⁺; blue, split DNAzyme/terpy₂DNA + Ni²⁺; black, split DNAzyme/terpy₂DNA, no metal ions. Right: Images of reaction solutions shown in the time courses.

Figure 4

Multicolored allele typing using time-resolved luminescence from lanthanide complexes (Tb³⁺ and Eu³⁺) cooperatively formed with a pair of split probes. (a) The structure of the Ln³⁺ complex formed on tandem duplex of the split probes with target sequence. (b) Allele typing of thiopurine S-methyltransferase gene.

Figure 5

ATP sensing using LCMB and iATP. (a) operating principle of ATP sensing using competitive reaction over iATP between ATP and LCMB; (b) luminescence signal response of ATP sensor to NTPs.

Figure 6

Nonenzymatic signal amplification by DNA circuits: (a) Luminous DNA wire was produced by target-initiated HCR; (b) Luminous cruciform DNA was produced by CHA.

Figure 6

Nonenzymatic signal amplification by DNA circuits: (a) Luminous DNA wire was produced by target-initiated HCR; (b) Luminous cruciform DNA was produced by CHA.