1
|
Das M, Mukherjee S, Islam MM, Choudhuri I, Bhattacharyya N, Samanta BC, Dutta B, Maity T. Response of Ancillary Azide Ligand in Designing a 1D Copper(II) Polymeric Complex along with the Introduction of High DNA- and HAS-Binding Efficacy, Leading to Impressive Anticancer Activity: A Compact Experimental and Theoretical Approach. ACS OMEGA 2022; 7:23276-23288. [PMID: 35847281 PMCID: PMC9281303 DOI: 10.1021/acsomega.2c01403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new versatile azide-bridged polymeric Cu(II) complex, namely, [Cu(L)(μ1,3-N3)]∞ (1), was synthesized utilizing an N,N,O-donor piperidine-based Schiff base ligand (E)-4-bromo-2-((2-(-1-yl)imino)methyl)phenol (HL), obtained via the condensation reaction of 1-(2-aminoethyl) piperidine and 5-bromo salicylaldehyde. The single-crystal X-ray diffraction analysis reveals that complex 1 consists of an end-to-end azido-bridged polymeric network, which is further rationalized with the help of a density functional theory (DFT) study. After routine characterization with a range of physicochemical studies, complex 1 is exploited to evaluate its biomedical potential. Initially, theoretical inspection with the help of a molecular docking study indicated the ability of complex 1 to effectively bind with macromolecules such as DNA and the human serum albumin (HSA) protein. The theoretical aspect was further verified by adopting several spectroscopic techniques. The electronic absorption spectroscopic analysis indicates a remarkable binding efficiency of Complex 1 with both DNA and HSA. The notable fluorescence intensity reduction of the ethidium bromide (EtBr)-DNA adduct, 4',6-diamidino-2-phenylindole (DAPI)-DNA adduct, and HSA after the gradual addition of complex 1 authenticates its promising binding potential with the macromolecules. The retention of the canonical B form of DNA and α form of HSA during the association of complex 1 was confirmed by implementing a circular dichroism spectral study. The association ability of complex 1 with macromolecules further inspired us to inspect its impact on different cell lines such as HeLa (cervical cancer cell), PA1 (ovarian cancer cell), and HEK (normal cell). The dose-dependent and time-dependent in vitro 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay suggests an effective antiproliferative property of complex 1 with low toxicity toward the normal cell line. Finally, the anticancer activity of complex 1 toward carcinoma cell lines was analyzed by nuclear and cellular staining techniques, unveiling the cell death mechanism.
Collapse
Affiliation(s)
- Manik Das
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai 721404, India
| | - Somali Mukherjee
- School
of Chemical Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Kolkata 700064, India
| | - Indranil Choudhuri
- Department
of Chemistry, Panskura Banamali College, Panskura 721152, India
| | | | - Bidhan Chandra Samanta
- Department
of Chemistry, Mugberia Gangadhar Mahavidyalaya, Purba Medinipur 721425, India
| | - Basudeb Dutta
- Department
of Chemical Science, IISER Kolkata, Mohanpur, Kolkata 741246, India
| | - Tithi Maity
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai 721404, India
| |
Collapse
|
2
|
Satapathi D, Das M, Rajak K, Laha S, Islam MM, Choudhuri I, Bhattacharyya N, Das S, Samanta BC, Maity T. Development of DNA intercalative, HSA binder pyridine‐based novel Schiff base Cu(II), Ni(II) complexes with effective anticancer property: A combined experimental and theoretical approach. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Manik Das
- Department of Chemistry Prabhat Kumar College Contai West Bengal India
| | - Karunamoy Rajak
- Department of Chemistry Indian Institute of Technology Kharagpur Kharagpur West Bengal India
| | | | - Md. Maidul Islam
- Department of Chemistry Aliah University Kolkata West Bengal India
| | | | | | - Sinjan Das
- Department of Chemistry Jadavpur University Kolkata West Bengal India
| | | | - Tithi Maity
- Department of Chemistry Prabhat Kumar College Contai West Bengal India
| |
Collapse
|
3
|
Meng Y, Jiao Y, Zhang Y, Zhang H, Gong X, Liu Y, Shuang S, Dong C. One-step synthesis of red emission multifunctional carbon dots for label-free detection of berberine and curcumin and cell imaging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119432. [PMID: 33472136 DOI: 10.1016/j.saa.2021.119432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
In this work, the red emission multifunctional carbon dots (R-CDs) were prepared via one-pot hydrothermal strategy of neutral red (NR) and ethylenediamine (EDA) for the label-free detection of berberine and curcumin, cell imaging, and fluorescent flexible film. The as-fabricated R-CDs not only possess good water dispersibility and excellent fluorescence stability, but also were successfully employed as a photoluminescent nanoprobe for label-free monitoring of berberine (BRH) and curcumin (Cur) based on dynamic quenching and internal filter effect (IFE), respectively. More importantly, as-proposed R-CDs displayed outstanding cellular permeability and lower cytotoxicity for cellular applications, which was consistent with the results of confocal fluorescence imaging and cell viability measurement of SMMC7721 cells. Thus, the multifunctional R-CDs may provide a rich tool library for biosensing and cellular imaging reagent applications. Interestingly, R-CDs were also used to manufacture R-CDs/PVA composites as fluorescent flexible films. To the best of our knowledge, this is the first demonstration of a label-free multifunctional fluorescent nanoprobe for berberine and curcumin based on red emission CDs.
Collapse
Affiliation(s)
- Yating Meng
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Yuan Jiao
- College of Environmental Science and Engineering, Taiyuan University of Technology, Jinzhong 030600, China
| | - Yuan Zhang
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Huilin Zhang
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Xiaojuan Gong
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Yang Liu
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Shaomin Shuang
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Chuan Dong
- Institute of Environmental Science, and School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| |
Collapse
|
4
|
A spectroscopic deciphering of the differential interaction behavior of alkaloid drugs with native B-DNA and protonated DNA. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
5
|
Bhuiya S, Haque L, Dutta T, Chowdhury S, Das S. Binding aspects of dietary flavone, luteolin, with polymorphic forms of natural DNA: a spectroscopic and molecular docking approach. NEW J CHEM 2019. [DOI: 10.1039/c8nj04022b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Physicochemical studies on the interactions of small molecules with different polymorphs of DNA are relevant for elucidation at the molecular level of the processes occurringin vivo.
Collapse
Affiliation(s)
- Sutanwi Bhuiya
- Physical Chemistry Section, Department of Chemistry, Jadavpur University
- Jadavpur
- India
| | - Lucy Haque
- Physical Chemistry Section, Department of Chemistry, Jadavpur University
- Jadavpur
- India
| | - Taniya Dutta
- Physical Chemistry Section, Department of Chemistry, Jadavpur University
- Jadavpur
- India
| | - Susmita Chowdhury
- Physical Chemistry Section, Department of Chemistry, Jadavpur University
- Jadavpur
- India
| | - Suman Das
- Physical Chemistry Section, Department of Chemistry, Jadavpur University
- Jadavpur
- India
| |
Collapse
|
6
|
Basu A, Kumar GS. Nucleic acids binding strategies of small molecules: Lessons from alkaloids. Biochim Biophys Acta Gen Subj 2018; 1862:1995-2016. [DOI: 10.1016/j.bbagen.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 01/14/2023]
|
7
|
Banerjee S, Ghorai P, Brandão P, Ghosh D, Bhuiya S, Chattopadhyay D, Das S, Saha A. Syntheses, crystal structures, DNA binding, DNA cleavage, molecular docking and DFT study of Cu(ii) complexes involving N2O4 donor azo Schiff base ligands. NEW J CHEM 2018. [DOI: 10.1039/c7nj03293e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA binding and cleavage properties of three novel copper(ii) complexes involving azo Schiff base ligands have been studied.
Collapse
Affiliation(s)
- Saikat Banerjee
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Pravat Ghorai
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Paula Brandão
- Departamento de Química
- CICECO
- Universidade de Aveiro
- 3810-193 Aveiro
- Portugal
| | | | - Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | | | - Suman Das
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Amrita Saha
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| |
Collapse
|
8
|
Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM. Robust IR-based detection of stable and fractionally populated G-C + and A-T Hoogsteen base pairs in duplex DNA. FEBS Lett 2017; 591:1770-1784. [PMID: 28524232 PMCID: PMC5584567 DOI: 10.1002/1873-3468.12681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 11/11/2022]
Abstract
Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
Collapse
Affiliation(s)
- Allison L Stelling
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Seung H Choi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Mary C Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
| |
Collapse
|
9
|
A sensitive spectrofluorometric method for detection of berberine hydrochloride using Ag nanoclusters directed by natural fish sperm DNA. Biosens Bioelectron 2016; 85:758-763. [DOI: 10.1016/j.bios.2016.05.070] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/15/2016] [Accepted: 05/21/2016] [Indexed: 11/23/2022]
|
10
|
Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
11
|
Basu A, Kumar GS. Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid. J Mol Recognit 2016; 29:363-9. [DOI: 10.1002/jmr.2536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/26/2015] [Accepted: 12/26/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Anirban Basu
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| |
Collapse
|
12
|
Khan AY, Suresh Kumar G. Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:417-425. [PMID: 26241827 DOI: 10.1016/j.saa.2015.07.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/08/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.
Collapse
Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| |
Collapse
|
13
|
Pradhan AB, Haque L, Bhuiya S, Ganguly A, Das S. Deciphering the Positional Influence of the Hydroxyl Group in the Cinnamoyl Part of 3-Hydroxy Flavonoids for Structural Modification and Their Interaction with the Protonated and B Form of Calf Thymus DNA Using Spectroscopic and Molecular Modeling Studies. J Phys Chem B 2015; 119:6916-29. [PMID: 25978104 DOI: 10.1021/acs.jpcb.5b02827] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ankur Bikash Pradhan
- Department
of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Lucy Haque
- Department
of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Sutanwi Bhuiya
- Department
of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Aniruddha Ganguly
- University of Calcutta, Senate House,
87/1, College Street, Kolkata, West Bengal 700073, India
| | - Suman Das
- Department
of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| |
Collapse
|
14
|
Pradhan AB, Haque L, Bhuiya S, Das S. Exploring the mode of binding of the bioflavonoid kaempferol with B and protonated forms of DNA using spectroscopic and molecular docking studies. RSC Adv 2015. [DOI: 10.1039/c4ra14553d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mode of binding of kaempferol with B and protonated form of calf thymus DNA.
Collapse
Affiliation(s)
| | - Lucy Haque
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Suman Das
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| |
Collapse
|
15
|
Khan AY, Saha B, Kumar GS. Interaction of phenazinium dyes with double-stranded poly(A): spectroscopy and isothermal titration calorimetry studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:615-624. [PMID: 24861262 DOI: 10.1016/j.saa.2014.04.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/19/2014] [Accepted: 04/14/2014] [Indexed: 06/03/2023]
Abstract
A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.
Collapse
Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| |
Collapse
|
16
|
Sarkar S, Bhadra K. Binding of alkaloid harmalol to DNA: Photophysical and calorimetric approach. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:272-80. [DOI: 10.1016/j.jphotobiol.2013.11.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022]
|
17
|
Seo YJ, Kim BH. Ethynylpyrene induces pH-dependent, fluorescence-detectable, reversible DNA condensation and decondensation. RSC Adv 2013. [DOI: 10.1039/c3ra41502c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
18
|
Bhowmik D, Hossain M, Buzzetti F, D’Auria R, Lombardi P, Kumar GS. Biophysical Studies on the Effect of the 13 Position Substitution of the Anticancer Alkaloid Berberine on Its DNA Binding. J Phys Chem B 2012; 116:2314-24. [DOI: 10.1021/jp210072a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Maidul Hossain
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Franco Buzzetti
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Rosaria D’Auria
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio, 70 - 20026 - Novate Milanese (MI), Italy
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry
Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| |
Collapse
|
19
|
Wu F, Shao Y, Ma K, Cui Q, Liu G, Xu S. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site. Org Biomol Chem 2012; 10:3300-7. [DOI: 10.1039/c2ob00028h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
20
|
Das A, Bhadra K, Achari B, Chakraborty P, Kumar GS. Interaction of aristololactam-β-D-glucoside and daunomycin with poly(A): spectroscopic and calorimetric studies. Biophys Chem 2011; 155:10-9. [PMID: 21392880 DOI: 10.1016/j.bpc.2011.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 01/11/2011] [Accepted: 01/30/2011] [Indexed: 11/19/2022]
Abstract
The binding of two sugar containing antibiotics viz. aristololactam-β-D-glucoside and daunomycin with single and double stranded poly(A) was investigated by spectroscopic and calorimetric studies. The binding affinity of daunomycin to ss poly(A) was of the order of 10⁶ M⁻¹ and that to ds poly(A) was of the order of 10⁵ M⁻¹. Aristololactam-β-D-glucoside showed a relatively weaker binding with an affinity of the order of 10⁴ M⁻¹ with both the conformations of poly(A). Fluorescence studies showed maximum quenching for daunomycin-ss poly(A) complexes. The binding constants calculated from fluorescence spectroscopy were in good agreement with that obtained from UV spectroscopy. Moderate perturbation of circular dichroic spectra of both the conformations of poly(A) in presence of these molecules with concomitant formation of prominent extrinsic CD bands in the 300-450 nm region further revealed the association. Isothermal titration calorimetry results showed an overall entropy driven binding in all the four systems though the entropy change was maximum in daunomycin-ss poly(A) binding. The binding affinity was also maximum for daunomycin-ss poly(A) and varied as daunomycin-ds poly(A) > aristololactam-β-D-glucoside-ds poly(A) > aristololactam-β-D-glucoside-ss poly(A). A 1:1 binding stoichiometry was observed in all the cases, as confirmed by Job plot analysis, indicating the interaction to consist of a single binding mode. Ferrocyanide quenching studies showed good stacking interaction in all cases but was best for daunomycin-ss poly(A) interaction. No self-structure formation was observed in poly(A) with both daunomycin and aristololactam-β-D-glucoside suggesting the hindrance of the sugar moiety for such structural organization.
Collapse
Affiliation(s)
- Abhi Das
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, CSIR, Kolkata 700032, India
| | | | | | | | | |
Collapse
|
21
|
Bhadra K, Kumar GS. Therapeutic potential of nucleic acid-binding isoquinoline alkaloids: Binding aspects and implications for drug design. Med Res Rev 2010; 31:821-62. [DOI: 10.1002/med.20202] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
22
|
Bhadra K, Maiti M, Kumar GS. Interaction of isoquinoline alkaloids with polymorphic DNA structures. Chem Biodivers 2010; 6:1323-42. [PMID: 19774594 DOI: 10.1002/cbdv.200900017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The interaction of berberine, palmatine, and coralyne with the B, Z, and H(L) form of poly[d(G-C)] was studied. Berberine and palmatine showed moderate binding to the B form, while coralyne showed higher binding, as revealed from spectroscopic and thermodynamic data. Berberine and coralyne binding to the B form was exothermic and enthalpy-driven, while palmatine showed exothermic binding which was favored by both negative enthalpy and negative entropy changes. Berberine and palmatine neither bind nor converted the Z-form structure to B form. Coralyne, on the other hand, exhibited a strong binding affinity to Z DNA structure that was enthalpy-driven. Berberine binding to the H(L) form was cooperative, exothermic, and favored by both negative enthalpy and negative entropy changes with the formation of an induced CD band. Palmatine showed weak binding, while coralyne showed a strong binding with the H(L) form. The structural differences in the isoquinoline alkaloids appear to influence the affinity and mode of interactions with these polymorphic DNA structures.
Collapse
Affiliation(s)
- Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4 Raja S.C. Mullick Road, Kolkata 700032, India.
| | | | | |
Collapse
|
23
|
Islam MM, Chowdhury SR, Kumar GS. Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides. J Phys Chem B 2009; 113:1210-24. [PMID: 19132839 DOI: 10.1021/jp806597w] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine and a synthetic derivative coralyne to three double stranded ribonucleic acids, poly(A). poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical techniques. Absorbance and fluorescence studies showed that the alkaloids bound cooperatively to these RNAs with the binding affinities of the order 10(4) M(-1). Circular dichroic results suggested that the conformation of poly(A). poly(U) was perturbed by all the three alkaloids, that of poly(I).poly(C) by coralyne only and that of poly(C).poly(G) by none. Fluorescence quenching studies gave evidence for partial intercalation of berberine and palmatine and complete intercalation of coralyne to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity from spectral data. The binding of all the three alkaloids considerably stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of the alkaloids to these double stranded RNAs varied in the order, berberine = palmatine < coralyne. The temperature dependence of the enthalpy changes afforded large negative values of heat capacity changes for the binding of palmatine and coralyne to poly(A).poly(U) and of coralyne to poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation was also seen in almost all the systems that showed binding. These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.
Collapse
Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata 700 032, India
| | | | | |
Collapse
|
24
|
Saha B, Mukherjee A, Santra CR, Chattopadhyay A, Ghosh AN, Choudhuri U, Karmakar P. Alprazolam Intercalates into DNA. J Biomol Struct Dyn 2009; 26:421-9. [DOI: 10.1080/07391102.2009.10507257] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
25
|
Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
26
|
Berberine-DNA complexation: new insights into the cooperative binding and energetic aspects. Biochim Biophys Acta Gen Subj 2008; 1780:1054-61. [PMID: 18549823 DOI: 10.1016/j.bbagen.2008.05.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/16/2008] [Accepted: 05/16/2008] [Indexed: 01/31/2023]
Abstract
The equilibrium binding of the cytotoxic plant alkaloid berberine to various DNAs and energetics of the interaction have been studied. At low ratios of bound alkaloid to base pair, the binding exhibited cooperativity to natural DNAs having almost equal proportions of AT and GC sequences. In contrast, the binding was non-cooperative to DNAs with predominantly high AT or GC sequences. Among the synthetic DNAs, cooperative binding was observed with poly(dA).poly(dT) and poly(dG).poly(dC) while non-cooperative binding was seen with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Both cooperative and non-cooperative bindings were remarkably dependent on the salt concentration of the media. Linear plots of ln K(a) versus [Na(+)] for poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) showed the release of 0.56 and 0.75 sodium ions respectively per bound alkaloid. Isothermal titration calorimetry results revealed the binding to be exothermic and favoured by both enthalpy and entropy changes in all DNAs except the two AT polymers and AT rich DNA, where the same was predominantly entropy driven. Heat capacity values (DeltaCp(o)) of berberine binding to poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), Clostridium perfringens and calf thymus DNA were -98, -140, -120 and -110 cal/mol K respectively. This study presents new insights into the binding dependent base pair heterogeneity in DNA conformation and the first complete thermodynamic profile of berberine binding to DNAs.
Collapse
|
27
|
Giri P, Kumar GS. Self-structure induction in single stranded poly(A) by small molecules: Studies on DNA intercalators, partial intercalators and groove binding molecules. Arch Biochem Biophys 2008; 474:183-92. [PMID: 18387354 DOI: 10.1016/j.abb.2008.03.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/13/2008] [Accepted: 03/15/2008] [Indexed: 11/17/2022]
Abstract
Self-structure induction in single stranded poly(A) has been one typical example of the various ways that could be used to modulate nucleic acid structural aspects through binding of small molecules. For the first time, the interaction between a series of small molecules and poly(A) has been investigated to understand the nature of the structural features in DNA binding small molecules that could be responsible for the formation of self-structure in single stranded poly(A) molecules. Classical intercalators like ethidium, coralyne, quinacrine and proflavine, partial intercalators like berberine and palmatine and classical minor groove binders like hoechst 33258 and DAPI have been chosen for this study. The binding of each of these molecules to poly(A) has been characterized by absorption spectral titration, job plot and isothermal titration calorimetry. Self-structure formation was monitored from circular dichroic melting, optical melting and differential scanning calorimetry. The results revealed that while all the intercalators studied induced self-structure formation, partial intercalators did not induce the same in poly(A). Of the two classical DNA minor groove binding molecules investigated, hoechst was effective in inducing self-structure while DAPI was ineffective. Self-structure induction in poly(A) was observed to be directly linked to the cooperative binding of the molecules to poly(A) in that all the molecules that bound cooperatively induced self-structure in poly(A). Structural and thermodynamic aspects of the interaction leading to self-structure formation are described.
Collapse
Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | | |
Collapse
|
28
|
Islam MM, Suresh Kumar G. RNA targeting by small molecule alkaloids: Studies on the binding of berberine and palmatine to polyribonucleotides and comparison to ethidium. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.05.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
29
|
Bhadra K, Maiti M, Kumar GS. Thermodynamics of the binding of cytotoxic protoberberine molecule coralyne to deoxyribonucleic acids. Biochim Biophys Acta Gen Subj 2008; 1780:298-306. [DOI: 10.1016/j.bbagen.2007.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 11/14/2007] [Accepted: 11/30/2007] [Indexed: 11/15/2022]
|
30
|
Hossain M, Giri P, Kumar GS. DNA Intercalation by Quinacrine and Methylene Blue: A Comparative Binding and Thermodynamic Characterization Study. DNA Cell Biol 2008; 27:81-90. [PMID: 17924822 DOI: 10.1089/dna.2007.0652] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maidul Hossain
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| |
Collapse
|
31
|
Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug–DNA binding. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.02.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
32
|
Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M. Alkaline titrations of poly(dG-dC).poly(dG-dC): microemulsion versus solution behavior. J Biomol Struct Dyn 2007; 24:561-70. [PMID: 17508778 DOI: 10.1080/07391102.2007.10507145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
PolyGC was titrated with a strong base in the presence of increasing concentrations of NaCl (from 0.00 to 0.60M) either in water solution or with the polynucleotide solubilized in the aqueous core of reverse micelles, i.e., the cationic quaternary water-in-oil microemulsion CTAB/n-hexane/n-pentanol/water. The results for matched samples in the two media were compared. CD and UV spectroscopies and, for the solution experiments, pH measurements were used to follow the course of deprotonation. In both media the primary effect of the addition of base was denaturation of the polynucleotide, reversible by back-titration with a strong acid. In solution, the apparent pK(a) of the transition decreases with increasing the salt concentration and a roughly linear dependence of pK(a) on p[NaCl] has been found. A parallel monotonic decay with ionic strength has been found in solution for R(OH), defined as the number of hydroxyl ions required per monomeric unit of polyGC to reach half-transition. By contrast, in microemulsion, R(OH) has been found to be independent of the NaCl concentration (and 10 to 50 times lower than in solution). This result is proposed as an indirect evidence of the independence of pK(a) on the salt concentration in microemulsion, where the pH cannot be measured. A sort of buffering effect of the positive charges on the micellar wall and of their counter-ions on the ionic strength could well explain this discrepancy of behavior in the two media.
Collapse
Affiliation(s)
- Marta Airoldi
- Dipartimento di Chimica Inorganica e Analitica Stanislao Cannizzaro, Universita di Palermo, Viale delle Scienze, Pad. 17, 90128 Palermo, Italy
| | | | | | | | | |
Collapse
|
33
|
Bhadra K, Maiti M, Kumar GS. Molecular recognition of DNA by small molecules: AT base pair specific intercalative binding of cytotoxic plant alkaloid palmatine. Biochim Biophys Acta Gen Subj 2007; 1770:1071-80. [PMID: 17434677 DOI: 10.1016/j.bbagen.2007.03.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 02/27/2007] [Accepted: 03/03/2007] [Indexed: 11/28/2022]
Abstract
The base dependent binding of the cytotoxic alkaloid palmatine to four synthetic polynucleotides, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) was examined by competition dialysis, spectrophotometric, spectrofluorimetric, thermal melting, circular dichroic, viscometric and isothermal titration calorimetric (ITC) studies. Binding of the alkaloid to various polynucleotides was dependent upon sequences of base pairs. Binding data obtained from absorbance measurements according to neighbour exclusion model indicated that the intrinsic binding constants decreased in the order poly(dA).poly(dT)>poly(dA-dT).poly(dA-dT)>poly(dG-dC).poly(dG-dC)>poly(dG).poly(dC). This affinity was also revealed by the competition dialysis, increase of steady state fluorescence intensity, increase in fluorescence quantum yield, stabilization against thermal denaturation and perturbations in circular dichroic spectrum. Among the polynucleotides, poly(dA).poly(dT) showed positive cooperativity at binding values lower than r=0.05. Viscosity studies revealed that in the strong binding region, the increase of contour length of DNA depended strongly on the sequence of base pairs being higher for AT polymers and induction of unwinding-rewinding process of covalently closed superhelical DNA. Isothermal titration calorimetric data showed a single entropy driven binding event in the AT homo polymer while that with the hetero polymer involved two binding modes, an entropy driven strong binding followed by an enthalpy driven weak binding. These results unequivocally established that the alkaloid palmatine binds strongly to AT homo and hetero polymers by mechanism of intercalation.
Collapse
Affiliation(s)
- Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India
| | | | | |
Collapse
|
34
|
Giri P, Kumar GS. Specific binding and self-structure induction to poly(A) by the cytotoxic plant alkaloid sanguinarine. Biochim Biophys Acta Gen Subj 2007; 1770:1419-26. [PMID: 17600625 DOI: 10.1016/j.bbagen.2007.05.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2007] [Revised: 05/17/2007] [Accepted: 05/21/2007] [Indexed: 11/24/2022]
Abstract
The cytotoxic plant alkaloid sanguinarine was found to bind preferentially and strongly to single stranded poly(A) with an association constant (K(a)) in the range 3.6-4.6 x 10(6) M(-1) in comparison to several nucleic acids. The binding induced unique self-structure formation in poly(A) that showed cooperative melting transition in circular dichroism, absorbance, and differential scanning calorimetry studies. The alkaloid binding was characterized to be intercalation as revealed from fluorescence quenching experiments and was predominantly enthalpy driven as revealed from isothermal titration calorimetry. Sanguinarine is the first and only natural product so far known to induce a self-structure formation in poly(A).
Collapse
Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700032, India
| | | |
Collapse
|
35
|
Islam MM, Sinha R, Kumar GS. RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium. Biophys Chem 2007; 125:508-20. [PMID: 17156912 DOI: 10.1016/j.bpc.2006.11.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 11/03/2006] [Accepted: 11/03/2006] [Indexed: 11/30/2022]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine with t-RNA(phe) was studied using various biophysical techniques and the data was compared with the binding of the classical DNA intercalator, ethidium. The results of optical thermal melting, differential scanning calorimetry and circular dichroism characterized the native cloverleaf structure of t-RNA under the conditions of the study. The strong binding of the alkaloids and ethidium to t-RNA was revealed from the absorption and fluorescence studies. The salt dependence of the binding constants enabled the dissection of the binding free energy to electrostatic and non-electrostatic contributions. This analysis revealed a surprisingly large favourable component of the non-electrostatic contribution to the binding of these charged alkaloids and ethidium to t-RNA. Isothermal titration calorimetric studies revealed that the binding of both the alkaloids is driven by a moderately favourable enthalpy decrease and a moderately favourable entropy increase while that of ethidium is driven by a large favourable enthalpy decrease. Taken together, the results suggest that the binding of these alkaloid molecules on the t-RNA structure appears to be mostly by partial intercalation while ethidium intercalates to the t-RNA. These results reveal the molecular aspects on the interaction of these alkaloids to t-RNA.
Collapse
Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | | | | |
Collapse
|
36
|
Protoberberine Alkaloids: Physicochemical and Nucleic Acid Binding Properties. TOPICS IN HETEROCYCLIC CHEMISTRY 2007. [DOI: 10.1007/7081_2007_071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
37
|
Maiti M, Kumar GS. Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives. Med Res Rev 2007; 27:649-95. [PMID: 16894530 DOI: 10.1002/med.20087] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.
Collapse
Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India.
| | | |
Collapse
|
38
|
Douki T. Low ionic strength reduces cytosine photoreactivity in UVC-irradiated isolated DNA. Photochem Photobiol Sci 2006; 5:1045-51. [PMID: 17077901 DOI: 10.1039/b604517k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Exposure of DNA to far-UV radiation leads to the formation of several types of dimeric lesions, including cyclobutane dimers and (6-4) photoproducts. In order to gain insights into the main parameters driving DNA photochemistry, the effect of ionic strength on the yield of formation of these photoproducts was investigated in UVC-irradiated samples of isolated genomic DNA. The main consequence of lowering the ionic strength was a decrease in the UVC-induced formation of thymine-cytosine and cytosine-cytosine photoproducts. The reactivity of thymine-thymine and cytosine-thymine doublets was hardly affected. Evidence was obtained against a major role played by duplex denaturation in these observations. A more likely explanation is a change in the DNA structure as the result of a larger extent of protonation at low counter-ions concentration.
Collapse
Affiliation(s)
- Thierry Douki
- Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique UMR-E 3 CEA-UJF, CEA/DSM/Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 38054, Grenoble Cedex 9, France.
| |
Collapse
|
39
|
Sinha R, Islam MM, Bhadra K, Kumar GS, Banerjee A, Maiti M. The binding of DNA intercalating and non-intercalating compounds to A-form and protonated form of poly(rC).poly(rG): spectroscopic and viscometric study. Bioorg Med Chem 2005; 14:800-14. [PMID: 16202606 DOI: 10.1016/j.bmc.2005.09.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Revised: 08/31/2005] [Accepted: 09/01/2005] [Indexed: 11/20/2022]
Abstract
Polymorphic RNA conformations may serve as potential targets for structure specific antiviral agents. As an initial step in the development of such drugs, the interaction of a wide variety of compounds which are characterized to bind to DNA through classical or partial intercalation or by mechanism of groove binding, with the A-form and the protonated form of poly(rC).poly(rG), been evaluated by multifaceted spectroscopic and viscometric techniques. Results of this study suggest that (i) ethidium intercalates to the A-form of RNA, but does not intercalate to the protonated form, (ii) methylene blue intercalates to the protonated form of the RNA but does not intercalate to the A-form, (iii) actinomycin D does not bind to either conformations of the RNA, and (iv) berberine binds to the protonated form by partial intercalation process, while its binding to the A-form is very weak. The DNA groove binder distamycin A has much higher affinity to the protonated form of the RNA compared to the A-form and binds to both structures by non-intercalative mechanism. We conclude that the binding affinity characteristics of these DNA binding molecules to the RNA conformations are vastly different and may serve as data for the development of RNA based antiviral drugs.
Collapse
Affiliation(s)
- Rangana Sinha
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India
| | | | | | | | | | | |
Collapse
|