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

Zhang, Aigui; Kondhare, Dasharath; Leonard, Peter; Seela, Frank

doi:10.1002/chem.202201294

Cited by 4 publications

(3 citation statements)

References 72 publications

(36 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, strands are in a parallel and not an antiparallel orientation as in natural DNA. Moreover, �-oligonucleotides were used as invader strands in DNA displacement reactions (Zhang et al, 2022b) or implemented in the construction of �/�-heterochiral DNA duplexes containing silver-mediated base pairs (Chai et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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

Leonard,

Zhang,

Budow-Busse

et al. 2024

Acta Crystallogr C

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Leonard,

Zhang,

Budow-Busse

et al. 2024

Acta Crystallogr C

Self Cite

View full text Add to dashboard Cite

show abstract

“…Toehold‐free displacement was recently reported for anomeric DNA. [3d] In this protocol, different stabilities of heterochiral vs. homochiral DNA were applied.…”

Section: Introductionmentioning

confidence: 99%

“…For this, FRET quencher systems are commonly applied. [3d] Recently, our laboratory used the fluorescence of ethidium bromide fluorescence as external sensor. For this work, the two new environmental sensitive fluorescence pyrene sensors 4 and 5 were developed and were implemented in the displacement systems.…”

Section: Introductionmentioning

confidence: 99%

DNA Strand Displacement with Base Pair Stabilizers: Purine‐2,6‐Diamine and 8‐Aza‐7‐Bromo‐7‐Deazapurine‐2,6‐Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction

Zhang

Kondhare

Leonard

et al. 2022

Chemistry A European J

View full text Add to dashboard Cite

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.

show abstract

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

Zhang

Kondhare

Leonard

et al. 2022

Chemistry A European J

View full text Add to dashboard Cite

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.

show abstract

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

Cited by 4 publications

References 72 publications

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

DNA Strand Displacement with Base Pair Stabilizers: Purine‐2,6‐Diamine and 8‐Aza‐7‐Bromo‐7‐Deazapurine‐2,6‐Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction

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

Contact Info

Product

Resources

About