1
|
Agrawal P, Nair MS. Binding mechanism of andrographolide with intramolecular antiparallel G-quadruplexes of therapeutic importance: an in-silico analysis. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2023.2193647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
|
2
|
Yu Y, Zhang Q, Fei Y, Yan C, Ye T, Gao L, Gao H, Zhou X, Shao Y. Multicolorfully probing intramolecular G-Quadruplex tandem interface. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117655. [PMID: 31670046 DOI: 10.1016/j.saa.2019.117655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
A long guanine-rich oliogonucleotide sequence can form multiple G-quadruplex (G4) tandem individuals in a single molecule with internal G4-G4 (inG4-G4) interfaces. The interface can exist at the stacked (s-inG4-G4) or unstacked (us-inG4-G4) state, dependent of the G4 conformation and environment. Because of the vital bioactivity of the G4 interface state, there is a great demand for developing a reliable multicolor fluorescence method to identify the interface state using a fluorophore that can emit at the individual wavelength for a specific interface. Herein, we found that a porphyrin with four dihydroxyphenyl substituents (OH2PP) can multicolorfully recognize the s-inG4-G4 dimer interface against the us-inG4-G4 dimer one. The s-inG4-G4 dimer cause significant red shifts in the excitation and emission bands of OH2PP in contrast to the us-inG4-G4 dimer and G4 monomers. OH2PP adopts a 1:1 binding mode with the s-inG4-G4 dimer, whereas a 2:1 binding mode occurs to the us-inG4-G4 dimer. The limit of detection (LOD) for the s-inG4-G4 structure is about tens of nM level. The observed binding dependence of OH2PP on the linker length between the G4 individuals suggests the interface binding with the s-inG4-G4 dimer. Deformation of the porphyrin macrocycle within the s-inG4-G4 interface confinement most likely contributes to the multicolorful response with the hyperporphyrin effect. Our work demonstrates that OH2PP is a promising fluorophore to fluorescently recognize the G4 multimer with an ideal interface-sensitive multicolor response.
Collapse
Affiliation(s)
- Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, China.
| |
Collapse
|
3
|
Metabolomics methods to analyze full spectrum of amino acids in different domains of bovine colostrum and mature milk. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03385-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
4
|
Kim N. The Interplay between G-quadruplex and Transcription. Curr Med Chem 2019; 26:2898-2917. [PMID: 29284393 PMCID: PMC6026074 DOI: 10.2174/0929867325666171229132619] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
G4 DNA is a non-canonical DNA structure consisting of a stacked array of Gquartets held together by base pairing between guanine bases. The formation of G4 DNA requires a cluster of guanine-runs within a strand of DNA. Even though the chemistry of this remarkable DNA structure has been under investigation for decades, evidence supporting the biological relevance of G4 DNA has only begun to emerge and point to very important and conserved biological functions. This review will specifically focus on the interplay between transcription and G4 DNA and discuss two alternative but interconnected perspectives. The first part of the review will describe the evidence substantiating the intriguing idea that a shift in DNA structural conformation could be another layer of non-genetic or epigenetic regulator of gene expression and thereby an important determinant of cell fate. The second part will describe the recent genetic studies showing that those genomic loci containing G4 DNA-forming guanine-rich sequences are potential hotspots of genome instability and that the level and orientation of transcription is critical in the materialization of genome instability associated with these sequences.
Collapse
Affiliation(s)
- Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston; The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
5
|
Kudrev AG. Scheme of the Complex Formation of DNA Telomeric Sequence with TMPyP4 Porphyrine. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218120198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Mandal P, Sahoo D, Saha S, Chowdhury J. Sensing of Different Human Telomeric G-Quadruplex DNA Topologies by Natural Alkaloid Allocryptopine Using Spectroscopic Techniques. J Phys Chem B 2018; 122:10279-10290. [PMID: 30346761 DOI: 10.1021/acs.jpcb.8b07856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Paulami Mandal
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Dibakar Sahoo
- School of Physics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Saumen Saha
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Joydeep Chowdhury
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| |
Collapse
|
7
|
Keane PM, Kelly JM. Transient absorption and time-resolved vibrational studies of photophysical and photochemical processes in DNA-intercalating polypyridyl metal complexes or cationic porphyrins. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.02.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
Mongwaketsi N, Mayedwa N, Matinise N, Kaviyarasu K, Sparrow R, Maaza M. Polymer matrices for porphyrin nanorods incorporation. Artificial light harvesting applications. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618500268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This contribution is focused on the supramolecular approach in exploration of aggregates formation by two different porphyrins wherein self-assembly plays an important role. Spectroscopic and microscopic studies usually provide information on investigations regarding the effects of various parameters on the fabrication of porphyrin aggregates by ionic self- assembly. Various properties of ionic self-assembled porphyrin nanorods have been investigated, including nonlinear optical (NLO) properties, and these studies were influenced by the fact that porphyrins have great thermal stability and extended [Formula: see text]conjugated macro cyclic rings which give them large nonlinear optical effects. The major reasons limiting porphyrin nanorods photonic applications include the difficulty of handling them in liquid solutions and their degradation with long exposure to light. This necessitates the use of appropriate solid matrices to host the nanorods. Inspired by the precise organization and orientation of the chromophores in natural systems, attention has been on the design of nanometer sized chromophoric assemblies, which may find applications in the field of molecular photonics. However, it is challenging to design multicomponent systems with controlled structural arrangement at the molecular level. A lack of precise arrangement may have a negative impact on the construction of an efficient artificial light harvesting system. This review is focused on exploring the possibility of incorporating nanorods into polymer matrices to overcome the limiting factors of applications of these materials in photonic devices.
Collapse
Affiliation(s)
- Nametso Mongwaketsi
- National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West Cape Town, 7129, South Africa
| | - Noluthando Mayedwa
- UNESCO-UNISA Africa Chair in Nanosciences-Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P.O. Box 392, Pretoria 0001, South Africa
| | - Nolubabalo Matinise
- National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West Cape Town, 7129, South Africa
| | - Kasinathan Kaviyarasu
- UNESCO-UNISA Africa Chair in Nanosciences-Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P.O. Box 392, Pretoria 0001, South Africa
| | - Raymond Sparrow
- Council for Scientific & Industrial Research (CSIR), Bioscience, P.O. Box 395, Pretoria 0001, South Africa
| | - Malik Maaza
- National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West Cape Town, 7129, South Africa
- UNESCO-UNISA Africa Chair in Nanosciences-Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P.O. Box 392, Pretoria 0001, South Africa
| |
Collapse
|
9
|
Qin T, Liu K, Song D, Yang C, Su H. Porphyrin Bound to i-Motifs: Intercalation versus External Groove Binding. Chem Asian J 2017; 12:1578-1586. [DOI: 10.1002/asia.201700398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/05/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Tingxiao Qin
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Kunhui Liu
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Chunfan Yang
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
| | - Hongmei Su
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
| |
Collapse
|
10
|
Gao Y, Guang T, Ye X. Sedimentation velocity analysis of TMPyP4-induced dimer formation of human telomeric G-quadruplex. RSC Adv 2017. [DOI: 10.1039/c7ra07758k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Analytical ultracentrifugation sedimentation velocity (AUC-SV) was used to study the interactions between TMPyP4 and AGGG(TTAGGG)3 (Tel22) and the TMPyP4-induced dimer formation of G-quadruplex.
Collapse
Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Tianlei Guang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| |
Collapse
|
11
|
Chakraborty B, Sengupta C, Pal U, Basu S. Acridone in a biological nanocavity: detailed spectroscopic and docking analyses of probing both the tryptophan residues of bovine serum albumin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02454a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AD initially gets hooked to Trp 212 housed in domain IIA, inducing conformational changes in the protein and paving the way for the ligand to reach Trp 134 located in domain IB.
Collapse
Affiliation(s)
| | | | - Uttam Pal
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata
- India
- Homi Bhaba National Institute
| |
Collapse
|
12
|
Boschi E, Davis S, Taylor S, Butterworth A, Chirayath LA, Purohit V, Siegel LK, Buenaventura J, Sheriff AH, Jin R, Sheardy R, Yatsunyk LA, Azam M. Interaction of a Cationic Porphyrin and Its Metal Derivatives with G-Quadruplex DNA. J Phys Chem B 2016; 120:12807-12819. [PMID: 27936741 DOI: 10.1021/acs.jpcb.6b09827] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
G-quadruplex (GQ) structures formed from guanine-rich sequences are found throughout the genome and are overrepresented in the promoter regions of some oncogenes, at the telomeric ends of eukaryotic chromosomes, and at the 5'-untranslated regions of mRNA. Interaction of small molecule ligands with GQ DNA is an area of great research interest to develop novel anticancer therapeutics and GQ sensors. In this paper we examine the interactions of TMPyP4, its isomer TMPyP2 (containing N-methyl-2-pyridyl substituents, N-Me-2Py) as well as two metal derivatives ZnTMPyP4 and CuTMPyP4 with GQs formed by dT4G4 and dT4G4T in 100 mM K+ or Na+ conditions. The DNA sequences were chosen to elucidate the effect of the 3'-T on the stabilization effect of porphyrins, binding modes, affinities, and stoichiometries determined via circular dichroism melting studies, UV-vis titrations, continuous variation analysis, and fluorescence studies. Our findings demonstrate that the stabilizing abilities of porphyrins are stronger toward (dT4G4)4 as compared to (dT4G4T)4 (ΔTm is 4.4 vs -6.4 for TMPyP4; 12.7 vs 5.7 for TMPyP2; 16.4 vs 12.1 for ZnTMPyP4; and 1.9 vs -8.4 °C for CuTMPyP4) suggesting that the 3'G-tetrad presents at least one of the binding sites. The binding affinity was determined to be moderate (Ka ∼ 106-107 μM-1) with a typical binding stoichiometry of 1:1 or 2:1 porphyrin-to-GQ. In all studies, ZnTMPyP4 emerged as a ligand superior to TMPyP4. Overall, our work contributes to clearer understanding of interactions between porphyrins and GQ DNA.
Collapse
Affiliation(s)
- Eric Boschi
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Supriya Davis
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Scott Taylor
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Andrew Butterworth
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Lilyan A Chirayath
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Vaishali Purohit
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Laura K Siegel
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Janesha Buenaventura
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Alexandra H Sheriff
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| | - Rowen Jin
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Richard Sheardy
- Department of Chemistry & Biochemistry, Texas Woman's University , 324 Ann Stuart Science Center, P.O. Box 425859, Denton, Texas 76204-5859, United States
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College , 500 College Avenue, Swarthmore, Pennsylvania 19081, United States
| | - Mahrukh Azam
- Department of Chemistry, West Chester University of Pennsylvania , West Chester, Pennsylvania 19383, United States
| |
Collapse
|
13
|
|
14
|
Mandal P, Bhattacharya M, Chowdhury J. Targeting G-quadruplex DNA and B-DNA with a natural alkaloid: a comparative spectroscopic study. RSC Adv 2016. [DOI: 10.1039/c6ra22776g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Different modes of binding of natural alkaloid harmine with G-quadruplex DNA and B-DNA: key roles in molecular recognition.
Collapse
Affiliation(s)
- Paulami Mandal
- Department of Biochemistry
- University of Calcutta
- Kolkata-700019
- India
| | | | | |
Collapse
|
15
|
Liu B, Xiao X, Yu J, Mao D, Lu G. Influence of synthesis conditions on the morphologies of ReBO 3 microstructures and white light emission of YBO 3:Eu 3+ phosphors prepared by an oleic acid-assisted hydrothermal method. RSC Adv 2016. [DOI: 10.1039/c6ra13370c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
YBO3:5%Eu3+ phosphor prepared by the OA-assisted hydrothermal method displays the white color under excitation at 394 nm, and the light color of YBO3:Eu3+ can be varied with the Eu3+ dopant concentration or the excitation wavelength.
Collapse
Affiliation(s)
- Baobao Liu
- Research Institute of Applied Catalysis
- Shanghai Institute of Technology
- Shanghai 201418
- P. R. China
| | - Xiuzhen Xiao
- Research Institute of Applied Catalysis
- Shanghai Institute of Technology
- Shanghai 201418
- P. R. China
| | - Jun Yu
- Research Institute of Applied Catalysis
- Shanghai Institute of Technology
- Shanghai 201418
- P. R. China
| | - Dongsen Mao
- Research Institute of Applied Catalysis
- Shanghai Institute of Technology
- Shanghai 201418
- P. R. China
| | - Guanzhong Lu
- Research Institute of Applied Catalysis
- Shanghai Institute of Technology
- Shanghai 201418
- P. R. China
- Key Laboratory for Advanced Materials and Research Institute of Industrial Catalysis
| |
Collapse
|
16
|
Zhao D, Fan Y, Gao F, Yang TM. “Turn-off-on” fluorescent sensor for (N-methyl-4-pyridyl) porphyrin -DNA and G-quadruplex interactions based on ZnCdSe quantum dots. Anal Chim Acta 2015; 888:131-7. [DOI: 10.1016/j.aca.2015.06.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/05/2015] [Accepted: 06/26/2015] [Indexed: 12/29/2022]
|
17
|
Jeon SH, Moon J, Lee MW, Kim SK. Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin. Biophys Chem 2015; 205:9-15. [PMID: 26057195 DOI: 10.1016/j.bpc.2015.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
The thermal stability of the G-quadruplex formed from the thrombin-binding aptamer, 5'G2T2G2TGTG2T2G2, in which the guanine (G) base at the central loop was replaced with an adenine (A) or inosine (I) base, was examined to determine the role of the central G base in stabilizing the quadruplex. Replacement of the central G base by the I base resulted in a slight decrease in thermal stability. On the other hand, the stability of the G-quadruplex decreased to a significant extent when it was replaced with the A base. The optimized structure of the G-quadruplex, which was obtained by a molecular dynamic simulation, showed that the carbonyl group of the C5 position of the central G base could form hydrogen bonds with the G1 amine group at the C7 position on the upper G-quartet. This formation of a hydrogen bond contributes to the stability of the G-quadruplex. The spectral property of meso-tetrakis(N-methylpyridium-4yl)porphyrin (TMPyP) associated with the G-quadruplex was characterized by a moderate red shift and hypochromism in the absorption spectrum, a positive CD signal, and two emission maxima in the fluorescence emission spectrum, suggesting that TMPyP binds at the exterior of the G-quadruplex. Spectral properties were slightly altered when the G base at the central loop was replaced with A or I, while the fluorescence decay times of TMPyP associated with the G-quadruplex were identical. Observed spectral properties removes the possibility of intercalation binding mode for TMPyP. TMPyP binds at the exterior of the quadruplex. Whether it stacks on the central loop or binds at the side of the quadruplex is unclear at this stage.
Collapse
Affiliation(s)
- Sun Hee Jeon
- Department of Chemistry, Yeungnam University, 214 Dae-dong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea
| | - Jihye Moon
- Department of Chemistry, Yeungnam University, 214 Dae-dong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea
| | - Myung Won Lee
- Department of Chemistry, Yeungnam University, 214 Dae-dong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea; Department of Chemistry, Pukyoung National University, Pusan, 608-737, Republic of Korea
| | - Seog K Kim
- Department of Chemistry, Yeungnam University, 214 Dae-dong, Gyeongsan City, Gyeong-buk, 712-749, Republic of Korea.
| |
Collapse
|
18
|
Mongwaketsi NP, Kotsedi L, Nuru ZY, Sparrow R, Garab G, Maaza M. Porphyrin nanorods-polymer composites for solar radiation harvesting applications. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424614500941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The interest in exploring porphyrin-based nanostructures for artificial solar radiation harvesting stems from their structural similarity to chlorophylls. In nature, the precise organization and orientation of the chlorophylls result in efficient absorption of light energy. Inspired by these naturally occurring architectures relevant optical studies including the dynamics of intermolecular and intra-molecular processes of the porphyrin nanorods were investigated. The design of artificial light harvesting systems requires several key factors, such as absorption in the UV-visible and near-infrared wavelengths, energy transfer ability and the selection of light absorbing pigments. Another key factor is the organizational structure through which the components will interact. We attempted to accomplish this by incorporating porphyrin nanorods into polymer matrices and this will also aid in achieving an arrangement where they can be directly used as devices. The nanorods were embedded in a polymeric matrix, using latex technology and electrospinning which gave the possibility of investigating the orientation of nanorods in the polymer. Spectroscopic and microscopic studies were conducted to investigate the optical and morphological properties of the porphyrin nanorods-polymer composites for applications in artificial solar radiation harvesting systems.
Collapse
Affiliation(s)
- Nametso P. Mongwaketsi
- iThemba LABS, Materials Research Department, National Research Foundation, P. O. Box 722 Somerset West 7129, South Africa
| | - Lebogang Kotsedi
- iThemba LABS, Materials Research Department, National Research Foundation, P. O. Box 722 Somerset West 7129, South Africa
- UNESCO-UNISA Africa Chair in Nanosciences/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P. O. Box 392, Pretoria 0001, South Africa
| | - Zebib Y. Nuru
- iThemba LABS, Materials Research Department, National Research Foundation, P. O. Box 722 Somerset West 7129, South Africa
- UNESCO-UNISA Africa Chair in Nanosciences/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P. O. Box 392, Pretoria 0001, South Africa
| | - Raymond Sparrow
- Council for Scientific & Industrial Research, Biosciences, P. O. Box 395, Pretoria 0001, South Africa
| | - Gyozo Garab
- Institute of Plant Biology, Biological Research Center, P. O. Box 521, Szeged H-6701, Hungary
| | - Malik Maaza
- iThemba LABS, Materials Research Department, National Research Foundation, P. O. Box 722 Somerset West 7129, South Africa
- UNESCO-UNISA Africa Chair in Nanosciences/Nanotechnology, College of Graduate Studies, University of South Africa, Muckleneuk Ridge, P. O. Box 392, Pretoria 0001, South Africa
| |
Collapse
|
19
|
Wang Y, Hu Y, Wu T, Liu H, Zhang L, Zhou X, Shao Y. Specific G-quadruplex structure recognition of human telomeric RNA over DNA by a fluorescently activated hyperporphyrin. Analyst 2015; 140:5169-75. [DOI: 10.1039/c5an00937e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Selective recognition of the G-quadruplex structure of human telomeric RNA (TERRA) over DNA was achieved using an activated hyperporphyrin as a fluorescent probe.
Collapse
Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Hua Liu
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Lihua Zhang
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry
- Zhejiang Normal University
- Jinhua 321004
- Zhejiang, People's Republic of China
| |
Collapse
|
20
|
Song D, Yang W, Qin T, Wu L, Liu K, Su H. Explicit Differentiation of G-Quadruplex/Ligand Interactions: Triplet Excited States as Sensitive Reporters. J Phys Chem Lett 2014; 5:2259-2266. [PMID: 26279544 DOI: 10.1021/jz501040a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a new transient spectral method utilizing triplet excited state as sensitive reporters to monitor and differentiate the multiplex G-quadruplex/ligand interactions in a single assay, which is a difficult task and usually requires a combination of several techniques. From a systematic study on the interactions of porphyrin (TMPyP4) with each telomeric G-quadruplex: AG3(T2AG3)3, G2T2G2TGTG2T2G2, (G4T4G4)2, and (TG4T)4, it is convincingly shown that the ligand triplet decay lifetimes are sensitive to the local bound microenvironment within G-quadruplexes, from which the coexisting binding modes of end-stacking, intercalation, and sandwich are distinguished and their respective contribution are determined. The complete scenario of mixed interaction modes is thus revealed, shedding light on the past controversial issues. Additional control experiments demonstrate the sensitivity of this triplet reporter method, which can even capture the binding behavior change as the G-quadruplex structures are adjusted by Na(+) or K(+).
Collapse
Affiliation(s)
- Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wen Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Tingxiao Qin
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lidan Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Kunhui Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| |
Collapse
|
21
|
Kim YH, Lee C, Kim SK, Jeoung SC. Interaction of Metallo- and free base meso-tetrakis(N-methylpyridium-4-yl)porphyrin with a G-quadruplex: Effect of the central metal ions. Biophys Chem 2014; 190-191:17-24. [DOI: 10.1016/j.bpc.2014.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 02/07/2023]
|
22
|
Calculation of cooperativity and equilibrium constants of ligands binding to G-quadruplex DNA in solution. Talanta 2013; 116:541-7. [DOI: 10.1016/j.talanta.2013.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/03/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022]
|
23
|
Sun EJ, Wang BB, Yang XY, Zhang SQ, Cheng XL, Shi TS. Synthesis and Raman, Electrochemical, Fluorescence Studies of Free-Base and Transition Metal Porphyrin-Nicacid Dyads With Different Substituent Groups. ACTA ACUST UNITED AC 2012. [DOI: 10.1080/15533174.2012.680145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Er-Jun Sun
- a Department of Chemistry , Changchun Normal University , Changchun , P. R. China
- b College of Chemistry , Jilin University , Changchun , P. R. China
| | - Bin-Bin Wang
- a Department of Chemistry , Changchun Normal University , Changchun , P. R. China
- b College of Chemistry , Jilin University , Changchun , P. R. China
| | - Xiang-Yu Yang
- a Department of Chemistry , Changchun Normal University , Changchun , P. R. China
| | - Si-Qi Zhang
- a Department of Chemistry , Changchun Normal University , Changchun , P. R. China
| | - Xiu-Li Cheng
- b College of Chemistry , Jilin University , Changchun , P. R. China
| | - Tong-Shun Shi
- b College of Chemistry , Jilin University , Changchun , P. R. China
| |
Collapse
|
24
|
Jäger K, Bats JW, Ihmels H, Granzhan A, Uebach S, Patrick BO. Polycyclic azoniahetarenes: assessing the binding parameters of complexes between unsubstituted ligands and G-quadruplex DNA. Chemistry 2012; 18:10903-15. [PMID: 22807262 DOI: 10.1002/chem.201103019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 05/02/2012] [Indexed: 12/22/2022]
Abstract
Polycyclic azoniahetarenes were employed to determine the effect of the structure of unsubstituted polyaromatic ligands on their quadruplex-DNA binding properties. The interactions of three isomeric diazoniadibenzo[b,k]chrysenes (4 a-c), diazoniapentaphene (5), diazoniaanthra[1,2-a]anthracene (6), and tetraazoniapentapheno[6,7-h]pentaphene (3) with quadruplex DNA were examined by DNA melting studies (FRET melting) and fluorimetric titrations. In general, penta- and hexacyclic azoniahetarenes bind to quadruplex DNA (K(b) ≈10(6) M(-1)) even in the absence of additional functional side chains. The binding modes of 4 a-c and 3 were studied in more detail by ligand displacement experiments, isothermal titration calorimetry, and CD and NMR spectroscopy. All experimental data indicate that terminal π stacking of the diazoniachrysenes to the quadruplex is the major binding mode; however, because of different electron distributions of the π systems of each isomer, these ligands align differently in the binding site to achieve ideal binding interactions. It is proposed that tetraazonia ligand 3 binds to the quadruplex by terminal stacking with a small portion of its π system, whereas a significant part of the bulky ligand most likely points outside the quadruplex structure, and is thus partially placed in the grooves. Notably, 3 and the known tetracationic porphyrin TMPyP4 exhibit almost the same binding properties towards quadruplex DNA, with 3 being more selective for quadruplex than for duplex DNA. Overall, studies on azonia-type hetarenes enable understanding of some parameters that govern the quadruplex-binding properties of parent ligand systems. Since unsubstituted ligands were employed in this study, complementary and cooperative effects of additional substituents, which may interfere with the ligand properties, were eliminated.
Collapse
Affiliation(s)
- Katharina Jäger
- Department Chemie-Biologie, Universität Siegen, Siegen, Germany
| | | | | | | | | | | |
Collapse
|
25
|
Santoro AM, Lo Giudice MC, D’Urso A, Lauceri R, Purrello R, Milardi D. Cationic Porphyrins Are Reversible Proteasome Inhibitors. J Am Chem Soc 2012; 134:10451-7. [DOI: 10.1021/ja300781u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Anna Maria Santoro
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| | - Maria Cristina Lo Giudice
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Rosaria Lauceri
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A.
Doria 6 - 95125 Catania
| | - Danilo Milardi
- IBB-CNR, Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche Viale A. Doria 6 - 95125 Catania
| |
Collapse
|
26
|
Liu W, Fu Y, Zheng B, Cheng S, Li W, Lau TC, Liang H. Kinetics and mechanism of conformational changes in a G-quadruplex of thrombin-binding aptamer induced by Pb2+. J Phys Chem B 2011; 115:13051-6. [PMID: 21950308 DOI: 10.1021/jp2074489] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It has been shown that guanine-rich DNA can fold into a G-quadruplex with certain metal cations. The spectral characteristics, thermostability, and kinetics for the formation of a Pb(2+)-driven G-quadruplex of thrombin-binding aptamer (TBA) were measured in the current work using a combination of ultraviolet (UV) and circular dichroism (CD) spectroscopy along with stopped-flow technique. CD spectra demonstrated that TBA could fold into a unique G-quadruplex with a strong positive peak at 312 nm. Analysis of the titration data reveals that the binding stoichiometry is 1:1 for the titration of TBA with Pb(NO(3))(2), which is in accordance with the localization of the Pb(2+) ion between the adjacent G-quartets. Thermal denaturation profiles indicate that the Pb(2+)-induced intramolecular G-quadruplex is more stable than those driven by Na(+) or K(+) ions. Kinetic studies suggest that the Pb(2+)-induced folding G-quadruplex of TBA probably proceeds through the rapid formation of an intermediate Pb(2+)-TBA complex, which then isomerizes to the fully folded structure. Conformational changes transpire after the addition of Pb(NO(3))(2) to the Na(+)- or K(+)-induced G-quadruplexes, which may be attributed to the replacement of Na(+) or K(+) ions by Pb(2+) ions and the generation of a more compact structure of the Pb(2+)-TBA structure. The relaxation time, τ, of folding the G-quadruplex is reduced from 1.05 s in the presence of Pb(2+) ions alone to 0.34 s under the cooperation of initially added Na(+) ions, while τ is increased to 8.33 s under the competition of initially added K(+) ions.
Collapse
Affiliation(s)
- Wei Liu
- Hefei National Laboratory for Physics Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, P R China
| | | | | | | | | | | | | |
Collapse
|
27
|
Binding properties of human telomeric quadruplex multimers: A new route for drug design. Biochimie 2011; 93:1392-400. [DOI: 10.1016/j.biochi.2011.04.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 04/05/2011] [Indexed: 12/21/2022]
|
28
|
Murat P, Singh Y, Defrancq E. Methods for investigating G-quadruplex DNA/ligand interactions. Chem Soc Rev 2011; 40:5293-307. [PMID: 21720638 DOI: 10.1039/c1cs15117g] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.
Collapse
Affiliation(s)
- Pierre Murat
- Department of Chemistry, The University of Cambridge, Cambridge CB2 1EW, UK.
| | | | | |
Collapse
|
29
|
Romera C, Bombarde O, Bonnet R, Gomez D, Dumy P, Calsou P, Gwan JF, Lin JH, Defrancq E, Pratviel G. Improvement of porphyrins for G-quadruplex DNA targeting. Biochimie 2011; 93:1310-7. [PMID: 21689723 DOI: 10.1016/j.biochi.2011.06.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 06/07/2011] [Indexed: 01/17/2023]
Abstract
G-quadruplex nucleic acids are emerging as therapeutic targets for small molecules referred to as small-molecule G-quadruplex ligands. The porphyrin H(2)-TMPyP4 was early reported to be a suitable motif for G-quadruplex DNA recognition. It probably binds to G-quadruplex nucleic acid through π-π stacking with the external G-quartets. We explored chemical modifications of this porphyrin such as insertion of various metal ions in the centre of the aromatic core and addition of bulky substituents that may improve the specificity of the compound toward G-quadruplex DNA. Porphyrin metallation, affording a G4-ligand with two symmetric faces, allowed the conclusion that the presence of an axial water molecule perpendicular to the aromatic plane lowered but did not hamper π-π stacking interactions between the aromatic parts of the ligand on the one hand and the external G-quartet on the other. The charge introduced in the centre of the porphyrin had little influence on binding. Thus, the ionic channel in the centre of G-quadruplex nucleic acids was not found to provide clear additional molecular clues for G-quadruplex nucleic acids targeting by porphyrins tested in the present study. Furthermore, we confirmed the unique G-quadruplex selectivity of a porphyrin modified with four bulky substituents at the meso positions and showed that although the compound is not "drug-like" it was capable of entering cells in culture and mediated some of the typical cellular effects of small-molecule G-quadruplex ligands.
Collapse
Affiliation(s)
- Carmen Romera
- CNRS, Laboratoire de Chimie de Coordination, 205 Route de Narbonne, Toulouse Cedex 4, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Jensen TJ, H. Vicente MG, Luguya R, Norton J, Fronczek FR, Smith KM. Effect of overall charge and charge distribution on cellular uptake, distribution and phototoxicity of cationic porphyrins in HEp2 cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2010; 100:100-11. [PMID: 20558079 PMCID: PMC3161426 DOI: 10.1016/j.jphotobiol.2010.05.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 04/26/2010] [Accepted: 05/15/2010] [Indexed: 10/19/2022]
Abstract
Five cationic porphyrins bearing one to four -N(CH(3))(3)(+) groups linked to the p-phenyl positions of 5,10,15,20-tetraphenylporphyrin (TPP) were synthesized in order to study the effect of overall charge and its distribution on the cellular uptake, phototoxicity and intracellular localization using human carcinoma HEp2 cells. The di-cationic porphyrins DADP-o and DADP-a accumulated the most within cells and preferentially localize within vesicular compartments and in mitochondria. Of these two only DADP-a was phototoxic to the cells (IC(50)=3 microM at 1 J/cm(2)). The mono-cationic porphyrin MAP was found to be the most phototoxic of the series, and it localized mainly in lipid membranes, including the plasma membrane, ER, mitochondria, and Golgi. Both the tri-cationic porphyrin TRAP and the tetra-cationic porphyrin TEAP localized subcellularly mainly in the mitochondria, but of the two only TEAP showed moderate phototoxicity (IC(50)=8 microM at 1 J/cm(2)). Our results suggest that MAP is the most promising PDT photosensitizer, and that both DADP-o and TRAP might find application as transport vehicles for therapeutics into cells.
Collapse
Affiliation(s)
- Timothy J. Jensen
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| | - M. Graça H. Vicente
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| | - Raymond Luguya
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| | - Jolanna Norton
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| | - Frank R Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| | - Kevin M. Smith
- Department of Chemistry, Louisiana State University, Baton Rouge LA, 70803, USA
| |
Collapse
|
31
|
Monchaud D, Granzhan A, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition. J Nucleic Acids 2010; 2010. [PMID: 20725629 PMCID: PMC2915875 DOI: 10.4061/2010/525862] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/01/2023] Open
Abstract
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
Collapse
Affiliation(s)
- David Monchaud
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Batiment 110, 91405 Orsay, France
| | | | | | | | | | | |
Collapse
|
32
|
Wei C, Wang J, Zhang M. Spectroscopic study on the binding of porphyrins to (G(4)T(4)G(4))4 parallel G-quadruplex. Biophys Chem 2010; 148:51-5. [PMID: 20202738 DOI: 10.1016/j.bpc.2010.02.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 01/19/2010] [Accepted: 02/10/2010] [Indexed: 11/19/2022]
Abstract
The binding mode and stoichiometry of the cationic porphyrin TMPyP4 to G-quadruplex structure are still controversial to date, mainly due to the intricate polymorphism of G-rich sequences in the different conditions of solution. Here in the presence of the molecular crowding agent PEG, the binding interaction of TMPyP4 and another porphyrin derivative TPrPyP4 with four-stranded parallel (G(4)T(4)G(4))4 G-quadruplex was studied systematically using circular dichroism, visible absorption titration, and steady-state and time-resolved fluorescence spectroscopies. The results show that each (G(4)T(4)G(4))4 molecule is able to bind four TMPyP4 or TPrPyP4 molecules. Two types of independent and nonequivalent binding sites with the higher and lower binding affinity are confirmed, and the stronger and weaker binding constants are 2.74 x 10(8) and 8.21 x 10(5)M(-1) for (G(4)T(4)G(4))4-TMPyP4, 2.05 x 10(8) and 1.05 x 10(6)M(-1) for (G(4)T(4)G(4))4-TPrPyP4, respectively. The two porphyrin molecules stack on the two ends of G-quadruplex with the higher binding affinity, another two porphyrins bind weakly to the two external grooves.
Collapse
Affiliation(s)
- Chunying Wei
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.
| | | | | |
Collapse
|