Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore

Abstract

Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore. Furthermore, the accurate isomerization efficiency between the trans and cis form was obtained with single molecule resolution.

Light‐Induced Reversible Reconfiguration of DNA‐Based Constitutional Dynamic Networks: Application to Switchable Catalysis

“…Forexample,the K + -ion-induced formation of G-quadruplexes and their separation by crown ethers, [17] the pH-stimulated formation and dissociation of i-motif or triplex structures, [18,19] and the metal-ion cooperative binding of duplex nucleic acids (for example,byT -Hg 2+ -T or C-Ag + -C bridges) and their ligand-induced separation (for example,by cysteine). [21] Thec ontrol over the functions,s tructures,a nd stimuli-responsive reconfiguration properties of oligonucleotides have turned nucleic acids into an ideal material to develop the area of DNAn anotechnology, [22] and particularly to use oligonucleotides for the assembly of DNA-based switches and machines, [23] DNA sensors, [24] stimuli-responsive drug carriers, [25] and DNAbased computing circuits. [21] Thec ontrol over the functions,s tructures,a nd stimuli-responsive reconfiguration properties of oligonucleotides have turned nucleic acids into an ideal material to develop the area of DNAn anotechnology, [22] and particularly to use oligonucleotides for the assembly of DNA-based switches and machines, [23] DNA sensors, [24] stimuli-responsive drug carriers, [25] and DNAbased computing circuits.…”

“…[20] Additionally,l ight was used as an auxiliary trigger for the switchable stabilization and separation of duplex nucleic acids in the presence of photoisomerizable units (for example,the stabilization of duplex nucleic acids by trans-azobenzene units and destabilization of the duplexes in the presence of cis-azobenzene). [21] Thec ontrol over the functions,s tructures,a nd stimuli-responsive reconfiguration properties of oligonucleotides have turned nucleic acids into an ideal material to develop the area of DNAn anotechnology, [22] and particularly to use oligonucleotides for the assembly of DNA-based switches and machines, [23] DNA sensors, [24] stimuli-responsive drug carriers, [25] and DNAbased computing circuits. [26] These properties of oligonucleotides have been recently applied to construct CDNs.…”

Synthetically Diversified Protein Nanopores: Resolving Click Reaction Mechanisms

“…Although modification of α-HL via mutagenesis is possible, 9,20,21,31,32 the commercial availability of α-HL means that it is often used in its wild-type form. 4,8,[10][11][12][13][14][15]22,23,34 Furthermore, cysteine mutants may sometimes present purification or misfolding issues arising from disulfide formation. Recently, fully assembled wild-type α-HL nanopores have been modified in situ through direct chemical functionalization of lysine residues.…”

Single‐Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions

“…Molecules with photoresponsive groups can undergo photoisomerization process due to steric hindrance upon light stimulus, resulting in a change in their molecular structures . Recently, the unzipping kinetic stability of DNA duplexes modified with single azobenzene (azo‐DNA) has been examined by α‐HL nanopores . The photoresponsive azo‐DNA undergoes a reversible conversion between trans form and cis form under photoirradiation (Figure b).…”

“…[38] Recently,t he unzipping kinetic stabilityo fD NA duplexes modified with singlea zobenzene (azo-DNA) has been examined by a-HL nanopores. [39] The photoresponsive azo-DNA undergoes ar eversible conversion between trans form and cis form under photoirradiation ( Figure 2b). The trans forms of azo-DNA showed al ongeru nzipping time compared with cis forms of azo-DNA, which demonstrated that the azo-DNA in trans form is much more stable than that in cis form (Figure 2c).…”