Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases

Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration

DNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and those available were obtained from a limited set of melting temperature at high sodium concentration. To our knowledge, there is currently no NN set of parameters for up to three mismatches covering all configurations at low sodium concentrations. Here, we are applying the NN model to a large set of 4096 published melting temperatures, covering all combinations of single, double and triple mismatches. Dealing with such a large set of temperature is challenging in several ways, bringing new methodological problems. Here, optimizing a large number of 252 independent parameters has required the development of a new method where we readjust the seed parameters using the definition of the Gibbs free energy. The new parameters predict the training set within 1.1 °C and the validation set to 2.7 °C.

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs

The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

Importance of isothermal titration calorimetry for the detection of the direct binding of metal ions to mismatched base pairs in duplex DNA

Metal ion-nucleic acid interactions contribute substantially to the structure and biological activity of nucleic acids and have a wide range of potential applications in nanotechnology. In this study, we examined the interactions between metal ions and mismatched base pairs in duplex DNA to reveal the underlying molecular mechanism. UV melting analyses showed that the melting temperature (Tm) of a 21-base pair duplex DNA with each of the C-A, C-C and C-T mismatched base pairs increased upon the addition of Ag+. However, isothermal titration calorimetry (ITC) demonstrated that Ag+ only bound to the C-C mismatched base pair of the duplex DNA to form C-Ag-C bonds, without binding to the C-A and C-T mismatches. These results showed that Tm increased even when metal ions did not bind to the mismatched base pairs of the duplex DNA. Although the increase in Tm upon the addition of the metal ions is often used to detect metal ion binding to mismatched base pairs of duplex DNA, these results indicated that UV melting analyses are unable to detect the direct binding of metal ions to the mismatched base pairs. Because ITC analyses directly detect the heat derived from metal ion binding to mismatched base pairs of duplex DNA, we concluded that this may be an effective detection approach.

Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition

Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (^PhedU). The crosslinking ability of ^PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a ^PhedU dimer after short irradiation times of a few seconds. A ^PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.

Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs

Polymerase-mediated synthesis of RNA-DNA metal base pairs.

Enzymatic construction of metal-mediated nucleic acid base pairs

Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.

Differentiating a Least-Stable Single Nucleotide Mismatch in DNA Via Metal Ion-Mediated Base Pairing and Using Thioflavin T as an Extrinsic Fluorophore

Monitoring the DNA dynamics in solution has great potential to develop new nucleic acid-based sensors and devices. With spectroscopic approaches, both at the ensemble average and single-molecule resolution, this study is directed to differentiate a single nucleotide mismatch (SNM) via a metal ion-stabilized mismatched base-pairing (C-Ag⁺-C/C-Cu²⁺-T) (C = cytosine, T = thymine) and site-selective extrinsic fluorophore, specifically, Thioflavin T (ThT). This is the first approach of its kind where dynamic quantities like molecular diffusion coefficients and diffusion times have been utilized to distinguish the least-stable SNM (CC & CT) formed by the most discriminating nucleobase, specifically, cytosine in a 20-mer duplex DNA. Additionally, this work also quantifies metal ions (Ag⁺ and Cu²⁺) at lower concentrations using fluorescence correlation spectroscopy. Our results can provide greater molecular-level insights into the mismatch-dependent metal-DNA interactions and also illuminate ThT as a new fluorophore to monitor the dynamics involved in DNA-metal composites.

Crystallographic Structure of Novel Types of AgI -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids

Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of Ag^I ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of Ag^I -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing Ag^I -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of Ag^I -mediated base pairs in the central region. The bent duplex structure induced by the addition of Ag^I ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.

Electronic Level Structure of Silver-Intercalated Cytosine Nanowires

Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag⁺-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity. However, a high-resolution morphological characterization of long Ag⁺-intercalated polycytosine DNA has hitherto not been carried out. Furthermore, the electronic level structure of this molecule has not been studied before. Here we present a scanning tunneling microscopy and spectroscopy study of this intriguing nanowire. Its temperature-independent morphological and electronic properties suggest substantial stability, while its emergent electronic levels and energy gap provide the basis for its high conductivity.

Enzymatic formation of consecutive thymine–HgII–thymine base pairs by DNA polymerases

Ten consecutive T–Hg^II–T base pairs were successfully formed by DNA polymerase-catalyzed primer extension reactions.

Enzymatic Synthesis of Cu(II)-Responsive Deoxyribozymes through Polymerase Incorporation of Artificial Ligand-Type Nucleotides

Metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, have shown promise as functional units to develop stimuli-responsive DNA materials. Although a variety of metal-mediated base pairs have been constructed with artificial ligand-type nucleotides and various metal ions, the application of such metal-mediated base pairs has been relatively poorly explored mainly due to the cumbersome chemical synthesis of artificial DNA strands. Herein we report a facile enzymatic method to synthesize DNA strands containing a ligand-type hydroxypyridone (H) nucleotide, which forms a Cu^II-mediated base pair (H-Cu^II-H). A two-step primer extension reaction using two commercially available polymerases enabled the incorporation of a H nucleotide at an internal position of oligonucleotides. The polymerase synthesis was subsequently applied to the development of metal-responsive deoxyribozymes (DNAzymes), whose catalytic activity was regulated by the formation of a single H-Cu^II-H base pair in its stem region. The DNAzyme activity was reversibly switched by the alternate addition and the removal of Cu^II ions. Furthermore, metal-dependent orthogonal activation of a Cu^II-responsive H-DNAzyme and a Hg^II-responsive T-DNAzyme was experimentally demonstrated by utilizing both H-Cu^II-H as well as widely explored T-Hg^II-T base pairs. These results suggest that the incorporation of H-Cu^II-H base pairs would facilitate the rational design of metal-responsive functional DNAs. Accordingly, the facile enzymatic synthesis of artificial ligand-bearing DNAs developed in this study would significantly expand the toolbox of DNA-based supramolecular chemistry and DNA nanotechnology.