Structural insights into the recognition of DNA defects by small molecules

Dayanidhi, P. David; Vaidyanathan, V. G.

doi:10.1039/d0dt04289g

Cited by 9 publications

(10 citation statements)

References 81 publications

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“…In DNA-free aqueous solution, [Ru(bpy) 2 (dppz)] 2+ shows no luminescence, but it becomes strongly emissive upon intercalating with DNA base pairs by ligand dppz. Since then, many efforts have been devoted to improving the selectivity and accuracy of DNA sensing using TMCs . However, new probes with good selectivity and accuracy and superb photophyscial properties are still in great demand for DNA recognition.…”

Section: Introductionmentioning

confidence: 99%

Dual-Emissive Tris-Heteroleptic Ruthenium Complexes: Tuning the DNA-Triggered Ratiometric Emission Response by Ancillary Ligands

Yang

Sun

et al. 2021

Inorg. Chem.

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Three tris-heteroleptic mononuclear Ru(II) complexes with dual fluorescence and phosphorescence[Ru(dpma)(bpy)(phen)]2+ (1 2+), [Ru(dpma)(bpy)(dppz)]2+ (2 2+), and [Ru(dpma)(phen)(dppz)]2+ (3 2+)have been designed and used as ratiometric light-response probes for DNA, where dpma is di(pyrid-2-yl)(methyl)-amine, bpy is 2,2′-bipyridine, phen is 1,10-phenanthroline, and dppz is dipyridophenazine, respectively. Single crystals of complex 2(PF6)2 have been obtained and studied by X-ray analysis. The interactions of these complexes with different DNAs are investigated by means of spectroscopic methods, viscosity measurements, and molecular modeling. In the presence of calf thymus DNA, complexes 2(PF6)2 and 3(PF6)2 show the emergence of a new lower-energy phosphorescence emission band; meanwhile, the higher-energy fluorescence emission band is essentially unchanged, functioning as an intrinsic internal reference. These two complexes exhibit stronger preference for calf thymus DNA over single-strand DNA (d(A)16 and d(C)16). In contrast, no binding interaction between 1(PF6)2 and calf thymus DNA is observed. The intrinsic binding constants (K b) of 2(PF6)2 and 3(PF6)2 with calf thymus DNA are determined to be (1.4 ± 0.4) × 105 and (9.5 ± 0.15) × 104 M–1, respectively. In addition, these spectroscopic results are compared with those of the prototype complex [Ru(bpy)2(dppz)]2+ (4 2+), and density functional theory and time-dependent density functional theory calculations are employed to elucidate these experimental findings.

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Section: Introductionmentioning

confidence: 99%

Dual-Emissive Tris-Heteroleptic Ruthenium Complexes: Tuning the DNA-Triggered Ratiometric Emission Response by Ancillary Ligands

Yang

Sun

et al. 2021

Inorg. Chem.

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“…Therefore, the search for new compounds that selectively bind to DNA and thereby significantly affect its biological activity is still an intensively investigated field of interdisciplinary research projects. In this context, duplex DNA that contains apurinic/apyrimidinic (AP) sites, that is, in which one regular DNA base is missing, is also an important target [3–5] . Such DNA with AP sites (AP‐DNA) is generated in a cell during base‐excision repair (BER) processes when enzymes recognize chemically modified bases and remove them by cleavage of the glycosidic bond [6] .…”

Section: Introductionmentioning

confidence: 99%

“…Such AP‐DNA ligands are intended to suppress BER by blocking the binding site for the enzymes and thus increase the efficiency of antitumor agents. According to this concept, ligands have been developed that bind to AP with high affinity and selectivity [3–5] . And the viability of this concept to block AP‐DNA during enzymatic repair by complexation with exogenous substances has been demonstrated with AP‐DNA ligands that inhibit the enzyme APE1 when bound to the AP site [10] …”

Section: Introductionmentioning

confidence: 99%

“…In this context, duplex DNA that contains apurinic/ apyrimidinic (AP) sites, that is, in which one regular DNA base is missing, is also an important target. [3][4][5] Such DNA with AP sites (AP-DNA) is generated in a cell during base-excision repair (BER) processes when enzymes recognize chemically modified bases and remove them by cleavage of the glycosidic bond. [6] Notably, these DNA repair processes occur also in cancer cells, which may significantly limit the effect of DNA-targeting agents.…”

Section: Introductionmentioning

confidence: 99%

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Photoinduced Reactions of Styrylpyridine Derivatives for the In Situ Formation of Selective Ligands for Apyrimidinic DNA

Schlosser,

Stötzel,

Fedorov

et al. 2023

ChemPhotoChem

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The photocyclization reaction of sterically demanding styrylpyridine derivatives was investigated and shown to depend on the type of substituent. With this method, a 2,2‐diphenyl‐1,3‐benzodioxolo‐annelated benzo[c]quinolizinium was synthesized, and its association with regular and abasic site‐containing DNA (AP‐DNA) was investigated by absorption, fluorescence, circular and linear dichroism spectroscopy. Specifically, this ligand binds preferentially to AP‐DNA relative to regular duplex DNA, and the AP‐DNA/ligand complex is formed in situ upon irradiation of the styrylpyridine substrate in the presence of the DNA.

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“…6 On the other hand, synthetic DNA binders that can selectively recognize specific sites in DNA duplexes have significant potential for analyzing non-canonical DNA structures. 7 Of particular interest are fluorescence-responsive binders, which can be used to selectively detect abasic sites, mismatched base pairs and damaged nucleobases through the binding-induced fluorescence response; 8 however, fluorescent binders for Tg-containing DNA duplexes have yet to be developed due to the challenge of selectively recognizing Tg-DNAs.…”

mentioning

confidence: 99%

Synthetic DNA binders for fluorescent sensing of thymine glycol-containing DNA duplexes and inhibition of endonuclease activity

et al. 2023

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Structural insights into the recognition of DNA defects by small molecules

Abstract: Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural...

Cited by 9 publications

References 81 publications

Dual-Emissive Tris-Heteroleptic Ruthenium Complexes: Tuning the DNA-Triggered Ratiometric Emission Response by Ancillary Ligands

Dual-Emissive Tris-Heteroleptic Ruthenium Complexes: Tuning the DNA-Triggered Ratiometric Emission Response by Ancillary Ligands

Photoinduced Reactions of Styrylpyridine Derivatives for the In Situ Formation of Selective Ligands for Apyrimidinic DNA

Synthetic DNA binders for fluorescent sensing of thymine glycol-containing DNA duplexes and inhibition of endonuclease activity

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