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

α-D-2'-Deoxyadenosine, an irradiation product of canonical DNA and a component of anomeric nucleic acids: crystal structure, packing and Hirshfeld surface analysis

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.

Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation

Metal-mediated base pairs represent a topical alternative to canonical hydrogen-bonded base pairs. In this context, the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was introduced as an artificial nucleobase in a glycol nucleic acid-based nucleoside analogue into a DNA oligonucleotide in a way that the oligonucleotide contains a central block of six contiguous P residues. The ability to engage in Ag+-mediated base pairing was evaluated with respect to the four canonical nucleosides in positions complementary to P. Highly stabilizing Ag+-mediated base pairs were formed with cytosine and guanine (i.e., P-Ag+-C and P-Ag+-G base pairs), whereas the analogous base pairs with thymine and adenine were much less stable and hence formed incompletely. Surprisingly, the intermediate formation of a homodimeric duplex of the P-containing oligonucleotide was observed in all cases, albeit to a different extent. The homodimer is composed of P-Ag+-P base pairs and 18 overhanging mismatched canonical nucleobases. It demonstrates the obstacles present when designing metal-mediated base pairs as metal complexation may take place irrespective of the surrounding natural base pairs. Homodimer formation was found to be particularly prominent when the designated metal-mediated base pairs are of low stability, suggesting that homodimers and regular duplexes are formed in a competing manner.

Photoreactive silver-containing supramolecular polymers that form self-assembled nanogels for efficient antibacterial treatment

In this study, an efficient synthetic strategy and potential route to obtain a photo-reactive silver-containing cytosine-functionalized polypropylene glycol polymer (Ag-Cy-PPG) was developed by combining a hydrophilic oligomeric polypropylene glycol (PPG) backbone with dual pH-sensitive/photo-reactive cytosine-silver-cytosine (Cy-Ag-Cy) linkages. The resulting photo-responsive Ag-Cy-PPG holds great promise as a multifunctional biomedical material that generates spherical-like nanogels in water; the nanogels exhibit high antibacterial activity and thus may significantly enhance the efficacy of antibacterial treatment. Due to the formation of photo-dimerized Cy-Ag-Cy cross-linkages after UV irradiation, Ag-Cy-PPG converts into water-soluble cross-linked nanogels that possess a series of interesting chemical and physical properties, such as intense and stable fluorescence behavior, highly sensitive pH-responsive characteristics, on/off switchable phase transition behavior, and well-controlled release of silver ions (Ag+) in mildly acidic aqueous solution. Importantly, antibacterial tests clearly demonstrated that irradiated Ag-Cy-PPG nanogels exhibited strong antibacterial activity at low doses (MIC values of < 50 μg/mL) against gram-positive and gram-negative bacterial pathogens, whereas non-irradiated Ag-Cy-PPG nanogels did not inhibit the viability of bacterial pathogens. These results indicate that irradiated Ag-Cy-PPG nanogels undergo a highly sensitive structural change in the bacterial microenvironment due to their relatively unstable π-conjugated structures (compared to non-irradiated nanogels); this change results in a rapid structural response that promotes intracellular release of Ag+ and induces potent antibacterial ability. Overall, this newly created metallo-supramolecular system may potentially provide an efficient route to dramatically enhance the therapeutic effectiveness of antibacterial treatments.

Chiral-at-Metal Silver-Mediated Base Pairs: Metal-Centred Chirality versus DNA Helical Chirality

When covalently incorporating ligands capable of forming chiral metal complexes into a DNA oligonucleotide duplex, an enantiospecific formation of metal-mediated base pairs is possible. We have been investigating the chirality of the silver-mediated base pair P-Ag^I -P (P, 1H-imidazo[4,5-f][1,10]phenanthroline) depending on the number of consecutive P : P pairs within a series of duplexes. Towards this end, both enantiomers of the nucleoside analogue 3-(1H-imidazo[4,5-f][1,10]phenanthrolin-1-yl)propane-1,2-diol comprising an acyclic backbone were introduced into DNA duplexes, resulting in diastereomeric metal-mediated base pairs. The same chiral-at-metal complex is formed inside the duplex for up to five neighbouring P-Ag^I -P pairs, irrespective of whether (S)-P or (R)-P is used. With six silver-mediated base pairs, the chirality of the metal complex is inverted for (S)-P but not for (R)-P. This indicates an intricate balance of what determines the configuration of the metal complex, the intrinsically preferred metal-centred chirality or the DNA helical chirality.

Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration

DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.

Anomeric DNA: Functionalization of α-D Anomers of 7-Deaza-2'-deoxyadenosine and 2'-Deoxyuridine with Clickable Side Chains and Click Adducts in Homochiral and Heterochiral Double Helices

Anomeric base pairs in heterochiral DNA with strands in the α‐d and β‐d configurations and homochiral DNA with both strands in α‐d configuration were functionalized. The α‐d anomers of 2′‐deoxyuridine and 7‐deaza‐2′‐deoxyadenosine were synthesized and functionalized with clickable octadiynyl side chains. Nucleosides were protected and converted to phosphoramidites. Solid‐phase synthesis furnished 12‐mer oligonucleotides, which were hybridized. Pyrene click adducts display fluorescence, a few of them with excimer emission. T_m values and thermodynamic data revealed the following order of duplex stability α/α‐d≫β/β‐d≥α/β‐d. CD spectra disclosed that conformational changes occur during hybridization. Functionalized DNAs were modeled and energy minimized. Clickable side chains and bulky click adducts are well accommodated in the grooves of anomeric DNA. The investigation shows for the first time that anomeric DNAs can be functionalized in the same way as canonical DNA for potential applications in nucleic acid chemistry, chemical biology, and DNA material science.

Anomeric and Enantiomeric 2'-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions

Dodecamer duplex DNA containing anomeric (α/β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d-dC with enantiomeric β-l-dC is superior to the well-noted β-d/β-d-dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.

The α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis

β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.

The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration

Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.