Silver(I) ions modulate the stability of DNA duplexes containing cytosine, methylcytosine and hydroxymethylcytosine at different salt concentrations

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

Unexpected cytosine-AuCl4- interaction under electrospray ionization mass spectrometry conditions-Formation of cytosine-Au(I) complexes

The interaction of cytosine with AuCl₄^-, under electrospray ionization mass spectrometric conditions, is discussed. On the basis of respective full scan mass spectra and product ion spectra, obtained in positive and negative ion mode, it has been deduced that cytosine is very prone to form Au(I)-containing complexes. The complexes may be formed in the gas phase by decomposition of Au(III)-containing complexes and also in the electrospray ionization source as a result of the occurrence of redox process. It has also been found that the interaction of cytosine with Au⁺ is stronger than that with Cu⁺ or Ag⁺, although taking into account the electrostatic attraction, it is not expected.

HgII binds to C-T mismatches with high affinity

Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.

Metal-Mediated Base Pairs: From Characterization to Application

The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA

A method for identifying and differentiating DNA duplexes containing the mismatched base pairs CC and CA at single molecule resolution with the protein pore α-hemolysin (αHL) is presented. Unique modulating current signatures are observed for duplexes containing the CC and CA mismatches when the mismatch site in the duplex is situated in proximity to the latch constriction of αHL during DNA residence inside the pore. The frequency and current amplitude of the modulation states are dependent on the mismatch type (CC or CA) permitting easy discrimination of these mismatches from one another, and from a fully complementary duplex that exhibits no modulation. We attribute the modulating current signatures to base flipping and subsequent interaction with positively charged lysine residues at the latch constriction of αHL. Our hypothesis is supported by the extended residence times of DNA duplexes within the pore when a mismatch is in proximity to the latch constriction, and by the loss of the two-state current signature in low pH buffers (<6.3), where the protonation of one of the cytosine bases increases the stability of the intrahelical state.

Exploring a DNA Sequence for the Three-Dimensional Structure Determination of a Silver(I)-Mediated C-C Base Pair in a DNA Duplex By (1)H NMR Spectroscopy

Recently, we discovered novel silver(I)-mediated cytosine-cytosine base pair (C-Ag(I)-C) in DNA duplexes. To understand the properties of these base pairs, we searched for a DNA sequence that can be used in NMR structure determination. After extensive sequence optimizations, a non-symmetric 15-base-paired DNA duplex with a single C-Ag(I)-C base pair flanked by 14 A-T base pairs was selected. In spite of its challenging length for NMR measurements (30 independent residues) with small sequence variation, we could assign most non-exchangeable protons (254 out of 270) and imino protons for structure determination.