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Purine‐2,6‐diamine and 8‐aza‐7‐deaza‐7‐bromopurine‐2,6‐diamine 2'‐deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA‐dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single‐stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The title compound 3‐phenyltetrahydropyrimido[4,5‐c]pyridazine 2′‐deoxyribonucleoside [systematic name: 6‐(2‐deoxy‐β‐d‐erythro‐pentofuranosyl)‐5,6,7,8‐tetrahydro‐3‐phenylpyrimido[4,5‐c]pyridazin‐7‐one monohydrate, C17H18N4O4·H2O, 1] shows two conformations in the crystalline state and the two conformers (1a and 1b) adopt different sugar puckers. The sugar residue of 1a shows a C2′‐endo S‐type conformation, while 1b displays a C3′‐endo N‐type sugar pucker. Both conformers adopt similar anti conformations around the N‐glycosylic bonds, with χ = −97.5 (3)° for conformer 1a and χ = −103.8 (3)° for conformer 1b. The extended crystalline network is stabilized by several intermolecular hydrogen bonds involving nucleoside and water molecules. The nucleobases and phenyl substituents of the two conformers (1a and 1b) are stacked and display a reverse alignment. A Hirshfeld surface analysis supports the hydrogen‐bonding pattern, while curvedness surfaces visualize the stacking interactions of neighbouring molecules. The recognition face of nucleoside 1 for base‐pair formation mimics that of 2′‐deoxythymidine. Nucleoside 1 shows two pKa values: 1.8 for protonation and 11.2 for deprotonation. DNA oligonucleotides containing nucleoside 1 were synthesized and hybridized with complementary DNA strands. Nucleoside 1 forms a stable base pair with dA which is as stable as the canonical dA–dT pair. The bidentate 1–dA base pair is strengthened by a third hydrogen bond provided by the dA analogue 3‐bromopyrazolo[3,4‐d]pyrimidine‐4,6‐diamine 2′‐deoxyribofuranoside (4). By this, duplex stability is increased and the suggested base‐pairing patterns are supported. [ABSTRACT FROM AUTHOR]

8‐Furylimidazolo‐2′‐deoxycytidine (furImidC), C14H14N4O5, is a fluorescent analogue of 2′‐deoxycytidine, also displaying the same recognition face. As a constituent of DNA, furImidC forms extraordinarily strong silver‐mediated self‐pairs. Crystal structure determination revealed that furImidC adopts two types of disordered residues: the sugar unit and the furyl moiety. The disorder of the sugar residue amounts to an 87:13 split. The disorder of the furyl ring results from axial chirality at the C8—C2′′ bond connecting the nucleobase to the heterocycle. The two atropisomers are present in unequal proportions [occupancies of 0.69 (2) and 0.31 (2)], and the nucleobase and the furyl moiety are coplanar. Considering the atomic sites with predominant occupancy, an anti conformation with χ = − 147.2 (7)° was found at the glycosylic bond and the 2′‐deoxyribosyl moiety shows a C2′‐endo (S, 2T1) conformation, with P = 160.0°. A 1H NMR‐based conformational analysis of the furanose puckering revealed that the S conformation predominates also in solution. In the solid state, two neighbouring furImidC molecules are arranged in a head‐to‐tail fashion, but with a notable tilt of the molecules with respect to each other. Consequently, one N—H...N hydrogen bond is found for neighbouring molecules within one layer, while a second N—H...N hydrogen bond is formed to a molecule of an adjacent layer. In addition, hydrogen bonding is observed between the nucleobase and the sugar residue. A Hirshfeld surface analysis was performed to visualize the intermolecular interactions observed in the X‐ray study. In addition, the fluorescence spectra of furImidC were measured in solvents of different polarity and viscosity. furImidC responds to microenvironmental changes (polarity and viscosity), which is explained by a hindered rotation of the furyl residue in solvents of high viscosity. [ABSTRACT FROM AUTHOR]

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. Tm 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. [ABSTRACT FROM AUTHOR]

The Watson–Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson–Crick and purine–purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5‐aza‐7‐deaza‐2′‐deoxyguanosine, its tripropargylamine derivative, and 2′‐deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine–purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5‐aza‐7‐deazaguanine–isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine–isoguanine base pair. Spacious residues are well accommodated in the large groove of purine–purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double‐helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable 'all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H...O and N—H...O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of 'all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy. [ABSTRACT FROM AUTHOR]

Nucleoside configuration (α‐d vs. β‐d), nucleobase substituents, and the helical DNA environment of silver‐mediated 5‐aza‐7‐deazaguanine‐cytosine base pairs have a strong impact on DNA stability. This has been demonstrated by investigations on oligonucleotide duplexes with silver‐mediated base pairs of α‐d and β‐d anomeric 5‐aza‐7‐deaza‐2′‐deoxyguanosines and anomeric 2′‐deoxycytidines incorporated in 12‐mer duplexes. To this end, a new synthetic protocol has been developed to access the pure anomers of 5‐aza‐7‐deaza‐2′‐deoxyguanosine by glycosylation of either the protected nucleobase or its salt followed by separation of the glycosylation products by crystallization and chromatography. Thermal stability measurements were performed on duplexes with α‐d/α‐d and β‐d/β‐d homo base pairs or α‐d/β‐d and β‐d/α‐d hybrid pairs within two sequence environments, positions 6 or 7, of oligonucleotide duplexes. The respective Tm stability increases observed after silver ion addition differ significantly. Homo base pairs with β‐d/β‐d or α‐d/α‐d nucleoside combinations are more stable than α‐d/β‐d hybrid base pairs. The positional switch of silver‐ion‐mediated base pairs has a significant impact on stability. Nucleobase substituents introduced at the 5‐position of the dC site of silver‐mediated base pairs affect base pair stability to a minor extent. Our investigation might lead to applications in the construction of bioinspired nanodevices, in DNA diagnostics, or metal‐DNA hybrid materials. [ABSTRACT FROM AUTHOR]