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Tian Z, Ding T, Niu H, Mu Y, Xu N, Kong M, Zhang Y, Tian Z, Wu Y, Wang C. The substituent group effect: investigation of naphthalimide-spermidine conjugates binding to DNA by spectroscopy, molecular docking and dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Tian Z, Cui H, Liu H, Dong J, Dong H, Zhao L, Li X, Zhang Y, Huang Y, Song L, Bian L, Wang Y, Xu X, Wang C. Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking. MEDCHEMCOMM 2017; 8:2079-2092. [PMID: 30108725 PMCID: PMC6072523 DOI: 10.1039/c7md00389g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/26/2017] [Indexed: 01/23/2023]
Abstract
The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Hailong Cui
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - He Liu
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Jun Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Huanyang Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Luyao Zhao
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xueting Li
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yan Zhang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yingying Huang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Lina Song
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Longxiang Bian
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Yuxia Wang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xuejun Xu
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
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Tian Z, Zhao L, Dong H, Zhang Y, Zhang Y, Ren Q, Shao S, Huang Y, Song L, Guo T, Xu X, Wang C. Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 169:27-34. [DOI: 10.1016/j.jphotobiol.2017.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 11/16/2022]
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4
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Tian Z, Huang Y, Zhang Y, Song L, Qiao Y, Xu X, Wang C. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:1-15. [PMID: 26926663 DOI: 10.1016/j.jphotobiol.2016.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yingying Huang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Zhang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Lina Song
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Qiao
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuejun Xu
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
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Funke A, Dickerhoff J, Weisz K. Towards the Development of Structure-Selective G-Quadruplex-Binding Indolo[3,2-b
]quinolines. Chemistry 2016; 22:3170-81. [DOI: 10.1002/chem.201504416] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Andrea Funke
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
| | - Klaus Weisz
- Institute of Biochemistry; Ernst-Moritz-Arndt University Greifswald; Felix-Hausdorff-Strasse 4 17487 Greifswald Germany
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Dickerhoff J, Riechert-Krause F, Seifert J, Weisz K. Exploring multiple binding sites of an indoloquinoline in triple-helical DNA: a paradigm for DNA triplex-selective intercalators. Biochimie 2014; 107 Pt B:327-37. [PMID: 25281796 DOI: 10.1016/j.biochi.2014.09.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/23/2014] [Indexed: 01/03/2023]
Abstract
Employing NMR spectroscopic methods preferred binding sites of a triplex-selective indoloquinoline drug were examined with three DNA triplex targets. To directly derive and evaluate number and type of the different sites of interaction, studies were performed on short triple-helical constructs specifically labeled with 3-(15)N thymidine probes. The detection and assignment of several coexisting species was enabled through the observation of slow exchange on the chemical shift timescale between complexes and free triplex. In general, the 5'-triplex-duplex junction constitutes the most favorable intercalation site, in particular when flanked by a TAT base triad. NMR data also revealed two different orientations for the intercalating indoloquinoline drug. Binding affinity significantly decreases with a C(+)GC triad bordering the junction but junction binding is still preferred over intercalation between TAT base triads within the triplex stem. In addition to the intercalation between two uncharged TAT triplets, intercalation between a TAT and a 3'-terminal C(+)GC triplet was also observed, indicating a non-protonated third strand cytosine at the triplex end position.
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Affiliation(s)
- Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Fanny Riechert-Krause
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Jenny Seifert
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany.
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7
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Spectroscopic study on the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:202-10. [PMID: 24976624 DOI: 10.1016/j.jphotobiol.2014.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/30/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
The interaction of naphthalimide-polyamine conjugates with herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The observed spectral quenching of compounds by DNA and the displacement of EB from DNA-EB complex by compounds indicated that these naphthalimide-polyamine conjugates could intercalate into the DNA base pairs. The UV test also showed that these compounds caused the conformational alteration of DNA. Further caloric fluorescent tests revealed that the quenching mechanism was a static type, which Ksv of 1-DNA, 2-DNA and 1-DNA-EB, 2-DNA-EB 3-DNA-EB was 1.208×10(4), 7.792×10(3) and 1.712×10(4), 1.287×10(4), 2.874×10(4), respectively, at room temperature. The obtained quenching constant, binding constant and thermodynamic parameters suggested that binding strength was associated with substituted groups on naphthalene backbone, and the type of interaction force included mainly hydrogen bonding and weak van der Waals. The binding process was mainly driven by hydrogen bond and van der Waals. Additionally, the effect of NaCl on compounds-DNA interaction provided further evidence that their interaction modes were dependent on substituted groups.
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Shahabadi N, Maghsudi M. Multi-spectroscopic and molecular modeling studies on the interaction of antihypertensive drug; methyldopa with calf thymus DNA. ACTA ACUST UNITED AC 2014; 10:338-47. [DOI: 10.1039/c3mb70340a] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Wey MT, Lyu PC, Kan LS. Thermodynamic and Kinetic Studies of a Stable Imperfect DNA Triplex by Spectroscopic and Calorimetric Methods. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Xiao Z, Guo X, Ling L. Sequence-specific recognition of double-stranded DNA with molecular beacon with the aid of Ag+ under neutral pH environment. Chem Commun (Camb) 2013; 49:3573-5. [DOI: 10.1039/c3cc40333e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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12
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Riechert-Krause F, Autenrieth K, Eick A, Weisz K. Spectroscopic and calorimetric studies on the binding of an indoloquinoline drug to parallel and antiparallel DNA triplexes. Biochemistry 2012; 52:41-52. [PMID: 23234257 DOI: 10.1021/bi301381h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
11-Phenyl-substituted indoloquinolines have been found to exhibit significant antiproliferative potency in cancer cells but to show only moderate affinity toward genomic double-helical DNA. In this study, parallel as well as antiparallel triple-helical DNA targets are employed to evaluate the triplex binding of these ligands. UV melting experiments with parallel triplexes indicate considerable interactions with the drug and a strong preference for TAT-rich triplexes in line with an increasing number of potential intercalation sites of similar binding strength between two TAT base triads. Via substitution of a singly charged aminoethylamine side chain by a longer and doubly charged bis(aminopropyl)amine substituent at the ligand, binding affinities increase and also start to exhibit long-range effects as indicated by a strong correlation between the binding affinity and the overall length of the TAT tract within the triplex stem. Compared to parallel triplexes, an antiparallel triplex with a GT-containing third strand constitutes a preferred target for the indoloquinoline drug. On the basis of pH-dependent titration experiments and corroborated by a Job analysis of continuous variation, binding of the drug to the GT triplex not only is strongly enhanced when the solution pH is lowered from 7 to 5 but also reveals a pH-dependent stoichiometry upon formation of the complex. Calorimetric data demonstrate that stronger binding of a protonated drug at acidic pH is associated with a more exothermic binding process. However, at pH 7 and 5, binding is enthalpically driven with additional favorable entropic contributions.
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Affiliation(s)
- Fanny Riechert-Krause
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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Eick A, Riechert-Krause F, Weisz K. Binding and NMR structural studies on indoloquinoline-oligonucleotide conjugates targeting duplex DNA. Bioconjug Chem 2012; 23:1127-37. [PMID: 22571630 DOI: 10.1021/bc200582u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
An 11-phenyl-indolo[3,2-b]quinoline (PIQ) was tethered through an aminoalkyl linker to the 5'-end of four pyrimidine oligonucleotides with T/C scrambled sequences at their two 5'-terminal positions. Binding to different double-helical DNA targets formed parallel triple helices with a PIQ-mediated stabilization that strongly depends on pH and the terminal base triad at the 5'-triplex-duplex junction. The most effective stabilization was observed with a TAT triplet at the 5'-junction under low pH conditions, pointing to a protonated ligand with a high triplex binding affinity and unfavorable charge repulsions in the case of a terminal C(+)GC triplet at the junction. The latter preference of the PIQ ligand for TAT over CGC is alleviated yet still preserved at higher pH. Intercalation of PIQ at the 5'-triplex-duplex junction as suggested by the triplex melting experiments was confirmed by homonuclear and heteronuclear NMR structural studies on a specifically isotope-labeled triplex. The NMR analysis revealed two coexisting species that only differ by a 180° rotation of the indoloquinoline within the intercalation pocket. NOE-derived molecular models indicate extensive stacking interactions of the indoloquinoline moiety with the TAT base triplet and CG base pair at the junction and a phenyl substituent that is positioned in the major groove and oriented almost perpendicular to the plane of the indoloquinoline.
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Affiliation(s)
- Andrea Eick
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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Fodor L, Csomós P, Csámpai A, Sohár P. Novel indole syntheses by ring transformation of β-lactam-condensed 1,3-benzothiazines into indolo[2,3-b][1,4]benzothiazepines and indolo[3,2-c]isoquinolines. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Neue B, Reiermann R, Gerdes K, Fröhlich R, Wibbeling B, Würthwein EU. Ring closure reactions of 2,6-diazaheptatrienyl metal compounds: synthesis of 3-aminoindole derivatives and 14-membered macrocyclic dimers. J Org Chem 2011; 76:8794-806. [PMID: 21988327 DOI: 10.1021/jo201521v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2,6-Diazaheptatrienyl metal compounds 6(-)K(+) are easily accessible from the corresponding diimines 6 by deprotonation using KO-t-Bu as base. According to quantum chemical calculations, they are, in comparison to other isomeric species with nitrogen atoms in other positions, highly reactive intermediates, which undergo in dilute solution at 50 °C ring closure reactions to form 3-aminoindole derivatives 8/10. In contrast, in more concentrated solution at room temperature, the formation of 14-membered macrocyclces 13 as a result of formal dimerization is observed. The 3-aminoindole derivatives obtained in this work possess rare substitution patterns, and the macrocyclic compounds are essentially unknown. Two-fold vinylogous derivatives 7 give rise to tricyclic systems with δ-carboline backbone 12. The experimental results are interpreted using high-level DFT calculations with regard to the possible reaction mechanism and the nature of the transition state of the five-membered ring formation. The molecular structures in the solid state of all types of compounds were elucidated by X-ray diffraction.
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Affiliation(s)
- Benedikt Neue
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstrasse 40, 48149 Münster, Germany
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Miao XM, Xiong C, Wang WW, Ling LS, Shuai XT. Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles. Chemistry 2011; 17:11230-6. [PMID: 21922555 DOI: 10.1002/chem.201003010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 06/21/2011] [Indexed: 11/08/2022]
Abstract
An ultrasensitive and simple dynamic-light-scattering (DLS) assay for the sequence-specific recognition of double-stranded DNA (dsDNA) was developed based on detection of the average diameter change of Au nanoparticle (AuNP) probes modified with oligonucleotides 5'-TTTCTCTTCCTT- CTCTTC-(T)(12)-SH-3' (Oligo 1) and 5'-TTCTTTCTTTTCTTTTTC-(T)(12)- SH-3' (Oligo 2). The target dsDNA was composed of two complementary oligonucleotides: 5'-AAAGAGAAGGAAGAGAAGAAGAAAGAAAAGAAAAAG-3' (Oligo 3) and 3'-TTTCTCTTCCTTCTCTTCTTCTTTCTTTTCTTTTTC-5' (Oligo 4). Hybridization of the two AuNPs-Oligo probes with the target dsDNA induced aggregation of the target dsDNA by forming triplex DNA, which accordingly increased the average diameter. This diameter change could then be detected by DLS. The average diameter was proportional to the target dsDNA concentration over the range from 593 fM to 40 pM, with a detection limit of 593 fM. Moreover, the assay had good sequence specificity for the target dsDNA.
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Affiliation(s)
- Xiang-Min Miao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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In vitro anticancer activity and evaluation of DNA duplex binding affinity of phenyl-substituted indoloquinolines. Bioorg Med Chem Lett 2011; 21:2380-3. [DOI: 10.1016/j.bmcl.2011.02.088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 02/18/2011] [Accepted: 02/20/2011] [Indexed: 11/19/2022]
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18
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Wu C, Zhou Y, Miao X, Ling L. A novel fluorescent biosensor for sequence-specific recognition of double-stranded DNA with the platform of graphene oxide. Analyst 2011; 136:2106-10. [PMID: 21442091 DOI: 10.1039/c1an15061h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A fluorescent biosensor for sequence-specific recognition of double-stranded DNA (dsDNA) was developed based upon the DNA hybridization between dye-labeled single-stranded DNA (ssDNA) and double-stranded DNA. The fluorescence of FAM-labeled single-stranded DNA was quenched when it adsorbed on the surface of graphene oxide (GO). Upon addition of the target dsDNA, a homopyrimidine·homopurine part of dsDNA on the Simian virus 40 (SV40) (4424-4440, gp6), hybridization occurred between the dye-labeled DNA and the target dsDNA, which induced the dye-labeled DNA desorbed from the surface of GO, and turned on the fluorescence of the dye. Under the optimum conditions, the enhanced fluorescence intensity was proportional to the concentration of target dsDNA in the range 40.0-260 nM, and the detection limit was found to be 14.3 nM alongside the good sequence selectivity.
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Affiliation(s)
- Chengke Wu
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, PR China
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N-[2(3-Carboxyl-9-benzyl-carboline-1-yl)ethyl-1-yl]-amino acids: correlation of spectral property with in vivo anti-tumor activity. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9504-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Kolevzon N, Yavin E. Site-Specific DNA Photocleavage and Photomodulation by Oligonucleotide Conjugates. Oligonucleotides 2010; 20:263-75. [DOI: 10.1089/oli.2010.0247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Netanel Kolevzon
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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Eick A, Riechert-Krause F, Weisz K. Spectroscopic and calorimetric studies on the triplex formation with oligonucleotide-ligand conjugates. Bioconjug Chem 2010; 21:1105-14. [PMID: 20481559 DOI: 10.1021/bc100107n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several triplex-forming 9-mer oligonucleotide (TFO) conjugates with a methyl- or methoxy-substituted 5-phenyl-6H-indolo[3,2-b]quinoline (PIQ) attached at the 5'-terminus or 3'-terminus or at an internal C5 thymine position were synthesized and tested for their ability to form and stabilize a triple helix with a double-helical DNA target employing UV melting experiments, fluorescence titrations, and isothermal titration calorimetry (ITC). A considerable thermal stabilization by up to 14 degrees C at pH 6.0 was observed for the 5'- and 3'-conjugates with little influence on the type of substituent but also for a conjugate with the ligand tethered by a short linker to the interior of the 9-mer TFO. A detailed thermodynamic characterization of the unmodified TFO and its 5'-conjugate with a methyl-substituted ligand by ITC experiments yielded a DeltaDeltaG degrees of -1.8 kcal mol(-1) at pH 6.0 for the TFO-attached PIQ-triplex interaction and also revealed a favorable entropic contribution as the major determinant for the free energy of PIQ binding in the conjugate. The pH dependence of triplex thermal stability highlights the importance of ring protonation of the triplex-bound ligand for its effective interaction and triplex stabilization near physiological conditions.
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Affiliation(s)
- Andrea Eick
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Germany
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