Metal Ion-Directed Specific DNA Structures and Their Functions

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.

Electrochemical Molecular Beacon for Nucleic Acid Sensing in a Homogeneous Solution

Ferrocene (Fc) and β-cyclodextrin (βCyD) were modified at each end of stem-loop structured DNA as an electrochemical signal generator and its quencher, respectively, to give an electrochemical molecular beacon (eMB). A relatively high efficiency of signal quenching was achieved by an inclusion complex (βCyD ⊃ Fc) formation that was induced on the stem structure of the closed form (= stem-loop structure) of eMB. With the addition of target DNA, the structure of eMB opened to form a linear duplex, where the Fc dissociated from the βCyD to restore its intrinsic electrochemical signal. The signal contrast of the electric current for this off/on-type sensor was high, ca. 95. This technique did not require any modification of the electrode surface, and it realized the detection of the target nucleic acids in a homogeneous solution with a high sensitivity using high-performance liquid chromatography (HPLC) equipped with electrochemical detector.

Detection of prostate-specific antigen in semen using DNA aptamers: an application of nucleic acid aptamers in forensic body fluid identification

In forensics, body fluid identification plays an important role because it aids in reconstructing a crime scene. Therefore, it is essential to develop simple and reliable techniques for body fluid identification. Nucleic acid aptamers are useful tools in analytical chemistry that can be used to improve conventional forensic analytical techniques. They have numerous advantages over antibodies including their low cost, long shelf life, and applicability for chemical modification and PCR amplification. A DNA aptamer against a human prostate-specific antigen (PSA), which is a well-known protein marker for semen identification in forensics, has been reported previously. In this study, as a proof-of-concept for nucleic acid aptamer-based identification of body fluids, we developed a technique of aptamer-based PSA assays for semen identification that employed enzyme-linked oligonucleotide assay (ELONA) and real-time PCR. We evaluated their sensitivity and specificity for semen compared with those for blood, saliva, urine, sweat, and vaginal secretion. The assays have equivalent procedures compared to enzyme-linked immunosorbent assay; their results were consistent with those produced by the conventional immunochromatographic assay. The minimum volume of semen required for detection was 62.5 nL in ELONA and 5 nL in real-time PCR, making this assay applicable for semen detection in actual criminal investigation. Aptamers can be a cost-effective and versatile tool for forensic body fluid identification.

Luminescent and Chiroptical Properties of 1 : 1 Eu (III) : Tetracycline Species Probed by Circularly Polarized Luminescence

This study investigates the significantly different luminescent and chiroptical properties of tetracycline (TC) when coordinated to Eu(III). The approach involves understanding the 1) speciation of TC and 2) conformation and species formed between Eu(III) and TC in a ratio of 1 : 1 in a dimethylformamide (DMF) solution and as a function of the pH value. By identifying the conformational changes of the various 1 : 1 Eu(III) : TC species, the results from this study explain information on the local microenvironment about the Eu(III) metal center. In particular, ⁵ D₀ ←⁷ F₀ Eu(III) laser excitation spectroscopy was employed to distinguish the different types of species found in solution in order to understand the interaction between Eu(III) and TC. On the other hand, circularly polarized luminescence (CPL) spectroscopy was used to understand the structural changes within the 1 : 1 Eu(III) : TC complex that could be related to the chirality of the Eu(III)-containing species. The CPL spectrum serves as a "fingerprint" to indicate the conformational changes within the 1 : 1 Eu(III) : TC complex as a result of the chiroptical signal arising from the various Eu(III) : TC species.

Catalytic formation of luminescent lanthanide complexes using an entropy-driven DNA circuit

Luminescent lanthanide complexes were catalytically formed through an entropy-driven DNA circuit triggered by a target nucleic acid.

Cooperative recognition of a repetitive sequence through consecutive formation of triplex and duplex structures

Cooperative recognition of a repetitive sequence was performed with a short single DNA strand consisting of duplex- and triplex-forming regions modified with a ligand (benzoquinoquinoxaline) to stabilize a triplex structure. The former region was complementary with one unit of a repetitive sequence and the latter had a sequence that can bind with a cognate duplex formed by another DNA molecule bound on an adjacent site. The DNA binding to one unit of the repetitive sequence is expected to facilitate the second binding to an adjacent unit through cooperative triplex formation. The cooperativity was confirmed by evaluation of thermal stabilities of the complexes with a series of model repetitive sequences.

Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA

Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.

Metallo-regulation of the bimolecular triplex formation of a peptide nucleic acid

Peptide nucleic acid (PNA) conjugates incorporating a bipyridine unit were prepared. The bipyridine was built into the loop moiety of PNAs that were designed to specifically form a hairpin and a PNA/DNA bimolecular triplex. While the thermal stability of the hairpin structure was only minimally affected by Cu(2+) addition, the PNA/DNA bimolecular triplex structure was significantly destabilized by complexation with Cu(2+). The melting temperature of the bimolecular triplex decreased by 17.4 °C in the presence of Cu(2+). This corresponds to more than a 1000 fold decrease in the binding constant for bimolecular triplex formation. Upon complexation, the bipyridine unit underwent a drastic conformational change which accounts for the observed differences in the thermal stabilities of the triplex upon binding. The bipyridine-PNA conjugate may be useful as an allosteric DNA carrier that releases the DNA in response to a certain metal ion concentration.