DNA duplex as a scaffold for a ground state complex formation between a zinc cationic porphyrin and phenylethynylpyren-1-yl

Mutsamwira, Saymore; Ainscough, Eric W.; Partridge, Ashton; Derrick, Peter J.; Filichev, Vyacheslav V.

doi:10.1016/j.jphotochem.2014.04.026

Cited by 11 publications

(13 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such DNA-binding small molecules have long been of interest due to their widespread applications. They are often used as therapeutic drugs [27][28][29][30][31][32] or as building blocks in creating functional assemblies [33][34][35][36][37]. They are most frequently used in molecular biology as DNA-labeling agents that can also perturb enzymatic reactions [38].…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Mechanics in Ligand Concentration Gradient

et al. 2020

View full text Add to dashboard Cite

Single-molecule experiments provide unique insights into the mechanisms of biomolecular phenomena. However, because varying the concentration of a solute usually requires the exchange of the entire solution around the molecule, ligand-concentration-dependent measurements on the same molecule pose a challenge. In the present work we exploited the fact that a diffusion-dependent concentration gradient arises in a laminar-flow microfluidic device, which may be utilized for controlling the concentration of the ligand that the mechanically manipulated single molecule is exposed to. We tested this experimental approach by exposing a λ-phage dsDNA molecule, held with a double-trap optical tweezers instrument, to diffusionally-controlled concentrations of SYTOX Orange (SxO) and tetrakis(4-N-methyl)pyridyl-porphyrin (TMPYP). We demonstrate that the experimental design allows access to transient-kinetic, equilibrium and ligand-concentration-dependent mechanical experiments on the very same single molecule.

show abstract

Section: Introductionmentioning

confidence: 99%

Single-Molecule Mechanics in Ligand Concentration Gradient

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The interactions of these constructs with [Ru(bpy) 3 ] 2 + and with the Zn 2 + derivative of 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21 H,23H-porphine (ZnTMpyP4, Figure 1 C) were investigated. Even though we never observed PUC in solutions containing TINA monomer and ZnTMpyP4, [18,39] this porphyrin represents a class of photosensitizers based on porphyrin and phthalocyanine derivatives, which are commonly used in PUC in combination with polycyclic aromatic chromophores. [16] This prompted us to investigate the interaction of ZnTMpyP4 with TINA-modified G4-DNAs.…”

mentioning

confidence: 73%

“…We propose that unmodified G4-DNA similar to DNA duplexes protects the porphyrin from water quenching, but TINA quenching of the porphyrin counters the protection provided by the G-quadruplex. [39] Upon G4-DNA formation all TINA-modified sequences exhibited monomeric fluorescence with maxima at 395-400 nm as well as excited dimer (excimer) fluorescence centred at 517 nm for TG4 TX and TG4 XT and 490 nm for TG3 XG3 T.…”

mentioning

confidence: 97%

“…In contrast, drastic differences in fluorescence intensity of ZnTMpyP4 were observed in the presence of G4-DNAs. The unmodified TG4 T enhanced fluorescence emission of the porphyrin, [39] whereas TINA-containing G4-DNAs quenched porphyrin fluorescence with the largest reduction in fluorescence intensity of ca. 3.5 times in the presence of TG3 XG3 T (SI, Figure S9B).…”

mentioning

confidence: 99%

See 1 more Smart Citation

G‐Quadruplex Supramolecular Assemblies in Photochemical Upconversion

Mutsamwira

Ainscough

Partridge

et al. 2016

Chemistry A European J

Self Cite

View full text Add to dashboard Cite

Parallel, tetramolecular G-quadruplex (G4) DNA possessing TINA monomer, (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol, were synthesised and evaluated in complexes with tris(2,2'-bipyridine)ruthenium(II), [Ru(bpy)3 ](2+) , and the Zn(2+) derivative of 5,10,15,20-tetrakis-(1-methyl-4-pyridyl)-21 H,23H-porphine, ZnTMpyP4. UV/Vis, fluorescence, and circular dichroism (CD) spectroscopy showed that the use of G4-DNA as a template resulted in the effective communication between the ligands and the TINA molecule that was covalently attached to the 5'-end and between T and dG at the 5'-end of the dTG4 T sequence. Only one G4-DNA possessing the TINA molecule at the 5'-end of the dTG4 T sequence was able to yield a green-to-blue photochemical upconversion (PUC, λem =420 nm) in the presence of [Ru(bpy)3 ](2+) upon excitation at 500 nm. Different DNA secondary structures can thus be used in DNA-based assemblies for PUC and the way of attachment of chromophores to DNA plays a pivotal role for the creation of a photosynthetic centre.

show abstract

“…For example, TINA monomers being inserted at terminal position of DNA duplexes can form supramolecular complexes with cationic porphyrin. Formation of these complexes results in TINA fluorescence quenching due to ground state complex formation [ 234 ]. More recently, the authors of [ 228 , 235 ] have shown that TINA monomers attached at the terminal positions of DNA complexes (duplexes or G-quadruplexes) can act as acceptor of energy in photochemical upconvertion.…”

Section: Agents For Targeting Of Dsdnasmentioning

confidence: 99%

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

View full text Add to dashboard Cite

In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

show abstract

DNA duplex as a scaffold for a ground state complex formation between a zinc cationic porphyrin and phenylethynylpyren-1-yl

Cited by 11 publications

References 40 publications

Single-Molecule Mechanics in Ligand Concentration Gradient

Single-Molecule Mechanics in Ligand Concentration Gradient

G‐Quadruplex Supramolecular Assemblies in Photochemical Upconversion

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

Contact Info

Product

Resources

About