Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs

Islam, Md. Monirul; Fujii, Satoshi; Sato, Shinobu; Okauchi, Tatsuo; Takenaka, Shigeori

doi:10.1016/j.bmc.2015.05.046

Cited by 12 publications

(4 citation statements)

References 36 publications

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“…Moreover, the benzene part itself also prevents binding of 1 and 3 from threading intercalations with dsDNA. However, as we have reported earlier [33], 1 and 3 showed affinity to calf thymus DNA (CT-DNA), Poly[d(A-T)] 2 and Poly[d(G-C)] 2 due to hydrophobic interaction between cyclic NDI derivatives and dsDNA. Compound 1 showed lower binding affinity to CT-DNA, poly[d(A-T)] 2 and poly[d(G-C)] 2 than 3 perhaps because of steric reasons, whereas, according to the computer modeling, the NDI moiety site of cyclic NDI derivatives incorporated to end staking onto the G-quartet.…”

Section: Resultsmentioning

confidence: 63%

“…Guanine-rich telomere oligonucleotide sequence (5′-d-GGGTTAGGGTTAGGGTTAGGG3′), dual label with FAM (fluorescent donor) and TAMRA (fluorescent acceptor) at the 5′ and 3′ end, called ‘F21T’, respectively, were purchased from Sigma-Aldrich (St. Louis, MO, USA). The synthesis procedure of 1 was described in detail in a previous article [33]. Compound 2 was synthesized as described previously [44].…”

Section: Methodsmentioning

confidence: 99%

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A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative

et al. 2015

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A cyclic naphthalene diimide (cyclic NDI, 1), carrying a benzene moiety as linker chain, was synthesized and its interaction with G-quadruplex DNAs of a-core and a-coreTT as a human telomeric DNA, c-kit and c-myc as DNA sequence at promoter region, or thrombin-binding aptamer (TBA) studied based on UV-VIS and circular dichroism (CD) spectroscopic techniques, thermal melting temperature measurement, and FRET-melting assay. The circular dichroism spectra showed that 1 induced the formation of different types of G-quadruplex DNA structure. Compound 1 bound to these G-quadruplexes with affinities in the range of 10 6 -10 7 M −1 order and a 2:1 stoichiometry. Compound 1 showed 270-fold higher selectivity for a-core than dsDNA with a preferable a-core binding than a-coreTT, c-kit, c-myc and TBA in the presence of K + , which is supported by thermal melting studies. The FRET-melting assay also showed that 1 bound preferentially to human telomeric DNA. Compound 1 showed potent inhibition against telomerase activity with an IC50 value of 0.9 μM and preferable binding to G-quadruplexes DNA than our previously published cyclic NDI derivative 3 carrying a benzene moiety as longer linker chain.

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Section: Resultsmentioning

confidence: 63%

Section: Methodsmentioning

confidence: 99%

A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative

et al. 2015

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“…The Takenaka group reported on the design and synthesis of two cyclic NDI compounds (373, 374) specifically to target hybrid tetraplex DNA. , These cyclic NDIs are predicted to bind to active sites through stacking intercalation (Figure ). The cyclic derivative 373 bound to hybrid-type tetraplex DNA from 5′-AGGG(T TAGGG) 3 -3′ with binding constant K = 8.6 × 10 6 M –1 , which is a 260-fold greater affinity than binding to a double stranded oligonucleotide consisting of 5′-GGG AGG TTT CGC-3′ and 3′-CCC TCC AAA GCG-5′ with 0.5 μM of IC 50 for telomerase activity.…”

Section: Medicinal Applicationmentioning

confidence: 99%

Functional Naphthalene Diimides: Synthesis, Properties, and Applications

et al. 2016

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This comprehensive review surveys developments over the past decade in the field of naphthalene diimides (NDIs). It explores their application toward: supramolecular chemistry; sensors; host-guest complexes for molecular switching devices, such as catenanes and rotaxanes; ion-channels by ligand gating; gelators for sensing aromatic systems; catalysis through anion-π interactions; and NDI intercalations with DNA for medicinal applications. We have also explored new designs, synthesis, and progress in the field of core-substituted naphthalene diimides (cNDIs), and their implications in areas such as artificial photosynthesis and solar cell technology. Also presented are some interesting synthetic routes and procedures that can be used toward further development of NDI-bearing compounds for future applications. Finally, we conclude with our views on NDI chemistry for future research endeavors, and we outline what we believe are the key obstacles that need to be overcome for NDIs to see real world applications.

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“…In addition, 24d was found to have a good telomerase inhibition (EC 50 =0.35 μM) . Further studies revealed affinities in the range 10 5 –10 6 M −1 , for the interaction of 24d with different dsDNA sequences. In all cases, derivative 24d showed about 10 times higher affinities and more favourable interactions with dsDNA compared to compound 24b with shorter bridges between the aromatic rings.…”

Section: Cyclophanes and Macrocyclesmentioning

confidence: 90%

Naphthalenediimide – A Unique Motif in Macrocyclic and Interlocked Supramolecular Structures

et al. 2018

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This review presents as urvey through macrocyclic andi nterlocked structures containing 1,4,5,8-naphthalendiimide residues from the synthetic point of view and also illustrates the structural particularities that dictate their main applications in supramolecular, biological and materials chemistry. Thep aper is organised as ac omprehensived escription of macrocycles,c yclophanes,c atenanes,r otaxanes and metallamacrocyclesa long with other types of supramolecular interlockeda rchitectures.F or each category,w ep resent the synthetic approach, the structural investigation of their properties and the developed applications as semiconductors, energy storage devices,p hotovoltaics,a rtificial photosystems,sensors,catalysts or molecular machines. 1I ntroduction 2C yclophanes andMacrocycles 3C atenanes andRotaxanes 4M etallamacrocyclic andI nterlocked Structures 5O ther Complex Interlocked Structures 6C onclusions 1I ntroductionArylenediimides (ADIs) are ac lass of aromatic, redox-active compounds showing good thermal, chemical and photochemicals tability that found importanta pplications in various fields ranging from biological chemistry to supramolecular chemistry and materials sciences. [1][2][3][4][5][6][7][8] Pyrromelliticdiimides (PMDIs), naphthalenediimides (NDIs) and perylenediimides (PDIs) are the most studied compounds of this class.Althought he first reports regarding the synthesis and photoelectronic properties of NDI derivatives can be found in the early 1970s, [9] the real potentialo f these compounds was recognized only at the endo f the last century.T he NDI derivatives have lately emerged as the hottest topic among the arylenediimides and became the most investigated in this class. This is reasoned by their enhanced photophysical and redox properties,c omparedt oP MDIsa sw ell as their improved solubility comparedtoP DIs. [6] Structurally,N DI is ap lanar molecule containinga hydrophobic naphthalene core functionalized at positions 1, 4, 5a nd 8w ith twoe lectron-withdrawing imide groups that decrease the charge density on the naphthalene moiety,r esulting in highly acidic p-sur-face.T hese structural elements made NDI an appealing building block for the construction of complex supramoleculara rchitectures associated by p-p stacking, charge-transfer (CT) and van derW aals interactions that involve the naphthalene residue,h ydrogen bonding involving aromatic C-H and C=Og roups,a s well as metal-coordination to the imide groups. [10][11][12][13] N,N-Functionalized NDI derivatives are readily accessible by treatment of 1,4,5,8-naphthalenetetracarboxylic acid dianhydride (NDA) with aliphatic or aromatic amines,i np olars olvents such as DMF or N,Ndimethylacetamide,a th igh temperatures. [14] Simple NDI chromophores display intense absorption bands, in DCM, at wavelengths lower than 400 nm, and weak emission bands,w ith shortS tokes shifts and low quantum yields.M oreover, NDI derivatives have low LUMO energy levels (i.e., À3.7eVf or N,N-dioctylnaphthalenediimide) andc an easily undergo two oneelectronr ev...

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Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs

Cited by 12 publications

References 36 publications

A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative

A Selective G-Quadruplex DNA-Stabilizing Ligand Based on a Cyclic Naphthalene Diimide Derivative

Functional Naphthalene Diimides: Synthesis, Properties, and Applications

Naphthalenediimide – A Unique Motif in Macrocyclic and Interlocked Supramolecular Structures

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