Regulated Incorporation of Two Different Metal Ions into Programmed Sites in a Duplex by DNA Polymerase Catalyzed Primer Extension

Abstract

Metal-mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag I ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C-Ag I -T base pair, as well as the previously reported C-Ag I -A base pair. The comparative susceptibility of dNTPs to Ag I -mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP > dTTP @ dCTP. Furthermore, two kinds of metal ions, Ag I and Hg II, selectively mediate the incorporation of thymidine 5'-triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.

A label-free G-quadruplex-based mercury detection assay employing the exonuclease III-mediated cleavage of T–Hg2+–T mismatched DNA

“…In 2004, Ono and co-workers discovered that Hg 2+ is able to coordinate with thymine nucleobases [ 9 – 12 ]. This discovery has sparked a wave of novel Hg 2+ detection methods, such as oligonucleotide-based luminescence [ 13 – 28 ], colorimetric [ 29 – 40 ], electrochemical [ 41 , 42 ] and surface-enhanced Raman scattering methods [ 43 – 46 ].…”

“…This discovery has sparked a wave of novel Hg 2+ detection methods, such as oligonucleotide-based luminescence [ 13 – 28 ], colorimetric [ 29 – 40 ], electrochemical [ 41 , 42 ] and surface-enhanced Raman scattering methods [ 43 – 46 ]. Later on, they reported the crystal structure of a DNA duplex containing the T−Hg II −T mismatch, which showed that the T−Hg II −T bond largely distorts DNA structure and also stabilizes B-form DNA [ 12 ]. Moreover, C−Ag I −A [ 47 ] and C−Ag I −T mismatches have also been reported [ 11 ].…”

Heterochiral DNA with Complementary Strands with α‐d and β‐d Configurations: Hydrogen‐Bonded and Silver‐Mediated Base Pairs with Impact of 7‐Deazapurines Replacing Purines

“…[25] silver-mediated base pairs of dC with dA or dT was in the same range as that of the dC-Ag + -dC pair.A lso, successful DNA polymerase-catalyzed primer extension mediated by silver ions by the formation of dC-Ag + pairs with dA, dT,o rd C has been reported. [37] According to the findings on silver ion binding in homochiral DNA duplexesa nd the observation of metal-mediated base pairing in parallel DNA, [38] we anticipated that heterochiral DNA formed by complementary a-d/b-d strandsw ould be capable of forming silver-mediated base pairs when containing mismatches. Consequently,t he formation of silver-mediated base pairs involving a-dC opposite dC, dT,d A, and a-dC (b strand)w as investigated in heterochiral duplexes.…”

Enzymatic construction of metal-mediated nucleic acid base pairs

“…However, a few years later, PEX studies performed on this system revealed that a C-Ag I -C base pair could not be formed. 49,50 Scheme 2. PCR amplification using a C-C mismatch A) in the absence of Ag I cations and B) in the presence of Ag I cations.…”