1
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Chen JC, Jockusch RA. Protomers of DNA-binding dye fluoresce different colours: intrinsic photophysics of Hoechst 33258. Phys Chem Chem Phys 2019; 21:16848-16858. [DOI: 10.1039/c9cp02421b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new form of DNA-binder Hoechst 33258 is stabilised upon desolvation. Altered optical properties include a distinct green fluorescence.
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Affiliation(s)
- JoAnn C. Chen
- Department of Chemistry
- University of Toronto
- Toronto
- Canada M5S 3H6
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2
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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3
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Nakamura A, Tsukiji S. Ratiometric fluorescence imaging of nuclear pH in living cells using Hoechst-tagged fluorescein. Bioorg Med Chem Lett 2017; 27:3127-3130. [DOI: 10.1016/j.bmcl.2017.05.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 01/03/2023]
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4
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Paul S, Ahmed T, Samanta A. Influence of Divalent Counterions on the Dynamics in DNA as Probed by Using a Minor-Groove Binder. Chemphyschem 2017; 18:2058-2064. [DOI: 10.1002/cphc.201700251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Sneha Paul
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
| | - Tasnim Ahmed
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
| | - Anunay Samanta
- School of Chemistry; University of Hyderabad; Hyderabad 500046 India
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5
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Doan P, Pitter DRG, Kocher A, Wilson JN, Goodson T. A New Design Strategy and Diagnostic to Tailor the DNA-Binding Mechanism of Small Organic Molecules and Drugs. ACS Chem Biol 2016; 11:3202-3213. [PMID: 27668686 DOI: 10.1021/acschembio.6b00448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The classical model for DNA groove binding states that groove binding molecules should adopt a crescent shape that closely matches the helical groove of DNA. Here, we present a new design strategy that does not obey this classical model. The DNA-binding mechanism of small organic molecules was investigated by synthesizing and examining a series of novel compounds that bind with DNA. This study has led to the emergence of structure-property relationships for DNA-binding molecules and/or drugs, which reveals that the structure can be designed to either intercalate or groove bind with calf thymus dsDNA by modifying the electron acceptor properties of the central heterocyclic core. This suggests that the electron accepting abilities of the central core play a key role in the DNA-binding mechanism. These small molecules were characterized by steady-state and ultrafast nonlinear spectroscopies. Bioimaging experiments were performed in live cells to evaluate cellular uptake and localization of the novel small molecules. This report paves a new route for the design and development of small organic molecules, such as therapeutics, targeted at DNA as their performance and specificity is dependent on the DNA-binding mechanism.
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Affiliation(s)
- Phi Doan
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Demar R. G. Pitter
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Andrea Kocher
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James N. Wilson
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Theodore Goodson
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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6
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Mazzoli A, Spalletti A, Carlotti B, Emiliani C, Fortuna CG, Urbanelli L, Tarpani L, Germani R. Spectroscopic Investigation of Interactions of New Potential Anticancer Drugs with DNA and Non-Ionic Micelles. J Phys Chem B 2015; 119:1483-95. [DOI: 10.1021/jp510360u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Alessandra Mazzoli
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Anna Spalletti
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Benedetta Carlotti
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Carla Emiliani
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Cosimo G. Fortuna
- Department
of Chemical Sciences, University of Catania, 95124 Catania CT, Italy
| | - Lorena Urbanelli
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Luigi Tarpani
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
| | - Raimondo Germani
- Department
of Chemistry, Biology, and Biotechnology and Centro di Eccellenza
sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, 06100 Perugia, Italy
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7
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Chaudhuri S, Batabyal S, Polley N, Pal SK. Vitamin B2 in Nanoscopic Environments under Visible Light: Photosensitized Antioxidant or Phototoxic Drug? J Phys Chem A 2014; 118:3934-43. [DOI: 10.1021/jp502904r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Siddhi Chaudhuri
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Subrata Batabyal
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Nabarun Polley
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Department
of Chemical, Biological
and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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8
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Choudhury S, Batabyal S, Mondol T, Sao D, Lemmens P, Pal SK. Ultrafast dynamics of solvation and charge transfer in a DNA-based biomaterial. Chem Asian J 2014; 9:1395-402. [PMID: 24665050 DOI: 10.1002/asia.201400062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 02/19/2014] [Indexed: 12/27/2022]
Abstract
Charge migration along DNA molecules is a key factor for DNA-based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA-based materials for the intactness of the DNA structure and their dynamic role in the charge-transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA-cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well-known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as-prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature-dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2-ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge-transfer dynamics.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, SaltLake, Kolkata 700 098 (India)
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9
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Abstract
Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.
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10
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Banerjee S, Tachiya M, Pal SK. Caffeine-Mediated Detachment of Mutagenic Ethidium from Various Nanoscopic Micelles: An Ultrafast Förster Resonance Energy Transfer Study. J Phys Chem B 2012; 116:7841-8. [DOI: 10.1021/jp302734e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soma Banerjee
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Masanori Tachiya
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Ibaraki 305-8565, Japan
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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11
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Batabyal S, Rakshit S, Kar S, Pal SK. An improved microfluidics approach for monitoring real-time interaction profiles of ultrafast molecular recognition. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:043113. [PMID: 22559521 DOI: 10.1063/1.4704839] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Our study illustrates the development of a microfluidics (MF) platform combining fluorescence microscopy and femtosecond/picosecond-resolved spectroscopy to investigate ultrafast chemical processes in liquid-phase diffusion-controlled reactions. By controlling the flow rates of two reactants in a specially designed MF chip, sub-100 ns time resolution for the exploration of chemical intermediates of the reaction in the MF channel has been achieved. Our system clearly rules out the possibility of formation of any intermediate reaction product in a so-called fast ionic reaction between sodium hydroxide and phenolphthalein, and reveals a microsecond time scale associated with the formation of the reaction product. We have also used the developed system for the investigation of intermediate states in the molecular recognition of various macromolecular self-assemblies (micelles) and genomic DNA by small organic ligands (Hoechst 33258 and ethidium bromide). We propose our MF-based system to be an alternative to the existing millisecond-resolved "stopped-flow" technique for a broad range of time-resolved (sub-100 ns to minutes) experiments on complex chemical∕biological systems.
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Affiliation(s)
- Subrata Batabyal
- Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700098, India
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12
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Rakshit S, Goswami N, Pal SK. Slow solvent relaxation dynamics of nanometer sized reverse micellar systems through tryptophan metabolite, kynurenine. Photochem Photobiol 2011; 88:38-45. [PMID: 21958420 DOI: 10.1111/j.1751-1097.2011.01007.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Exploration of environmental dynamics using intrinsic biological probe tryptophan is very important; however, it suffers from various difficulties. An alternative probe, kynurenine (KN), has been found to be an efficient probe for the ultrafast dynamics in the biological environment (Goswami et al., [2010] J. Phys. Chem. B., 114, 15236-15243). In the present study, we have investigated the efficacy of KN for the exploration of relatively slower dynamics of biologically relevant environments. A detailed investigation involving UV-Vis, steady-state/time-resolved fluorescence spectroscopy and Förster resonance energy transfer (FRET) studies on KN compared to a well-known solvation probe, H33258, a DNA-minor groove binder in a model nonionic reverse micelle reveals that ultrafast internal conversion associated with the hydrogen-bonding dynamics masks KN to become a dynamical reporter of the immediate environments of the probe.
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Affiliation(s)
- Surajit Rakshit
- Department of Chemical, Biological & Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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13
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Mondol T, Rajdev P, Makhal A, Pal SK. Interaction of an Antituberculosis Drug with a Nanoscopic Macromolecular Assembly: Temperature-Dependent Förster Resonance Energy Transfer Studies on Rifampicin in an Anionic Sodium Dodecyl Sulfate Micelle. J Phys Chem B 2011; 115:2924-30. [DOI: 10.1021/jp108115h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tanumoy Mondol
- Unit for Nano Science & Technology, Department of Chemical, Biological, and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Priya Rajdev
- Unit for Nano Science & Technology, Department of Chemical, Biological, and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Abhinandan Makhal
- Unit for Nano Science & Technology, Department of Chemical, Biological, and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Unit for Nano Science & Technology, Department of Chemical, Biological, and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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14
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Barooah N, Mohanty J, Pal H, Bhasikuttan AC. Supramolecular assembly of hoechst-33258 with cucurbit[7]uril macrocycle. Phys Chem Chem Phys 2011; 13:13117-26. [DOI: 10.1039/c1cp20493a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Barooah N, Mohanty J, Pal H, Sarkar SK, Mukherjee T, Bhasikuttan AC. pH and temperature dependent relaxation dynamics of Hoechst-33258: a time resolved fluorescence study. Photochem Photobiol Sci 2011; 10:35-41. [DOI: 10.1039/c0pp00215a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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16
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Banerjee D, Makhal A, Pal SK. Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes. J Fluoresc 2009; 19:1111-8. [PMID: 19565329 DOI: 10.1007/s10895-009-0512-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
Abstract
Understanding the sequence dependent molecular recognition of DNA is crucial for the rational design of many drugs. Femtosecond resolved studies on the hydration dynamics of the dodecamer duplexes having sequences (CGCGAATTCGCG)2 and (CGCAAATTTGCG)2, and their complexes with the nucleic protein histone 1 (H1) reveal significant correlation of the molecular recognition of the DNA and DNA-protein complexes with the dynamics of hydration. The different molecular recognition of DNA and DNA-protein complexes is also borne out by circular dichroism (CD) and fluorescence detected CD measurements.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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17
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Molecular recognition of plant DNA: does it differ from conventional animal DNA? Int J Biol Macromol 2009; 44:133-7. [PMID: 19059281 DOI: 10.1016/j.ijbiomac.2008.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 10/07/2008] [Accepted: 11/05/2008] [Indexed: 11/20/2022]
Abstract
The recognition mechanism of DNA with small drugs/ligands is an important field of research from pharmacological point of view. Such studies are ample with DNAs extracted from animal cells, but are rare for those extracted from plant cells. However, such a study is strongly demanding for the formulation of pesticides and other agrochemicals. In this contribution, for the first time, we report the interaction of two well-known DNA binder ethidium bromide (EB) and Hoechst 33258 (H33258) with two genomic DNAs extracted from the leaves of Ricinus communis L. (castor bean) and Mangifera indica (mango) using steady-state and picosecond-resolved fluorescence spectroscopy. The purity of the extracted DNAs is confirmed from gel electrophoresis and optical absorption studies. As evidenced from the circular dichroism (CD) measurements the DNAs retain physiologically relevant B forms. The well-known DNA intercalator EB has been found to show an additional electrostatic mode of binding with the DNAs, which is not present in the conventional animal DNAs. The binding affinity of EB is found to be even weaker for the DNA extracted from M. indica compared to that in R. communis L. On the other hand, the binding affinity of H33258 with the plant DNAs is found to be comparable to that of animal DNAs. The difference in interaction could be rationalized from the possible differences in the base sequences.
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18
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Ban G, Dong R, Li K, Han H, Yan X. Study on the Electric Conductivity of Ag-Doped DNA in Transverse Direction. NANOSCALE RESEARCH LETTERS 2009; 4:321-326. [PMID: 20596459 PMCID: PMC2893934 DOI: 10.1007/s11671-008-9245-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Accepted: 12/30/2008] [Indexed: 05/29/2023]
Abstract
In this article, we reported a novel experiment results on Ag-doped DNA conductor in transverse direction. I-V characteristics were measured and the relative conductances were calculated for different silver ions concentrations. With the increase of the concentration of silver ions, the conductive ability of DNA risen rapidly, the relative conductance of DNA enhanced about three magnitudes and reached a stable value when Ag(+) concentration was up to 0.005 mM. In addition, Raman spectra were carried out to analyse and confirm conduction mechanism.
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Affiliation(s)
- Ge Ban
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Ruixin Dong
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Ke Li
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Hongwen Han
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, Shandong, 252059, China
| | - Xunling Yan
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, Shandong, 252059, China
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19
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Banerjee D, Pal SK. Excited-State Solvation and Proton Transfer Dynamics of DAPI in Biomimetics and Genomic DNA. J Phys Chem A 2008; 112:7314-20. [DOI: 10.1021/jp801778e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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20
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Sando S, Narita A, Hayami M, Aoyama Y. Tuning the Hoechst Dye into Color-changing Fluorescent pH Indicator in an Acidic Range. CHEM LETT 2008. [DOI: 10.1246/cl.2008.246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Banerjee D, Pal SK. Dynamics in the DNA recognition by DAPI: exploration of the various binding modes. J Phys Chem B 2008; 112:1016-21. [PMID: 18171050 DOI: 10.1021/jp077090f] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo1 using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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22
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Berg MA, Coleman RS, Murphy CJ. Nanoscale structure and dynamics of DNA. Phys Chem Chem Phys 2008; 10:1229-42. [DOI: 10.1039/b715272h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Banerjee D, Sinha SS, Pal SK. Interplay between Hydration and Electrostatic Attraction in Ligand Binding: Direct Observation of Hydration Barrier at Reverse Micellar Interface. J Phys Chem B 2007; 111:14239-43. [DOI: 10.1021/jp076392e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Sudarson Sekhar Sinha
- Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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24
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Sarkar R, Pal SK. Interaction of Hoechst 33258 and Ethidium with Histone1−DNA Condensates. Biomacromolecules 2007; 8:3332-9. [PMID: 17902690 DOI: 10.1021/bm700690p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report structural and dynamical aspects of DNAs from various sources including synthetic oligonucleotides in bulk buffer and as a complex with histone1 (H1). High-resolution transmission electron microscopic (HRTEM) studies reveal the structural change of the DNAs upon complexation with H1 leading to formation of compact-globular and hollow-toroidal particles. In order to explore the functionality of ligand binding of the DNAs and their complexes with H1, we have used two biologically common fluorescent probes Hoechst 33258 (H33258) and Ethidium (EB) as model ligands. Picosecond resolved fluorescence and polarization gated anisotropy studies examined that the minor groove binding of H33258 to the genomic DNA-H1 complex remains almost unaltered. However, the intercalative interaction of EB with the DNA in the complex is severely perturbed compared to that with the DNA in bulk buffer. Time-dependent solvochromic effect of the probe H33258 further elucidates the dynamical solvation, which is reflective of the overall environmental relaxation of the DNAs upon condensation by H1. We have also performed circular dichroism (CD) studies on the DNAs and their complexes with H1, which reveal the change in conformation of the DNAs in the complexes. Our studies in the ligand-binding mechanisms of the DNA-H1 complex are important to understand the mechanism of drug binding to linker DNA in condensed chromatin.
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Affiliation(s)
- Rupa Sarkar
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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Banerjee D, Pal SK. Direct Observation of Essential DNA Dynamics: Melting and Reformation of the DNA Minor Groove. J Phys Chem B 2007; 111:10833-8. [PMID: 17676797 DOI: 10.1021/jp074697n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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Banerjee D, Pal SK. Simultaneous binding of minor groove binder and intercalator to dodecamer DNA: importance of relative orientation of donor and acceptor in FRET. J Phys Chem B 2007; 111:5047-52. [PMID: 17455977 DOI: 10.1021/jp0715427] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the present study, steady-state, picosecond time-resolved fluorescence and polarization gated anisotropy have been used to establish simultaneous binding of an intercalator (ethidium bromide, EtBr) and a minor groove binder (Hoeschst 33258, H258) to a dodecamer DNA of specific sequence. The Förster resonance energy transfer (FRET) studies between the dyes H258 (donor) and EtBr (acceptor) in the dodecamer, where the ligands have a particular relative orientation of the transition dipoles, in contrast to the cases in sodium dodecyl sulfate (SDS) micelles and larger genomic DNA, where the orientations are random, reveal the effect of the binding geometry of the ligands in the constrained environment. Our study establishes that reconsideration of the value of the orientation factor (kappa2) is crucial for correct estimation of the donor-acceptor distance when the ligands are simultaneously bound to a specific region of biological macromolecules.
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Shaw AK, Pal SK. Fluorescence Relaxation Dynamics of Acridine Orange in Nanosized Micellar Systems and DNA. J Phys Chem B 2007; 111:4189-99. [PMID: 17394304 DOI: 10.1021/jp067156r] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we report a detailed study of the fluorescence relaxation dynamics of a well-known fluorescent DNA intercalator, acridine orange (AO), in reverse micelles (RM), micelles, and DNA using picosecond resolved fluorescence spectroscopy. Solvation studies of AO in AOT reverse micelles (RM) containing water indicate the locations of AO close to the interface and those in RM containing NaOH; there are two types of AO--one in the nonpolar oil phase and the other at the interface. The bound water at the reverse micellar interface is found to be much more rigid than that at the micellar interface of sodium dodecyl sulfate (SDS) micelles. Dynamic light scattering (DLS) studies allow for the determination of the hydrodynamic radius and the overall tumbling motion of the macromolecules. Wobbling-in-cone data analysis of the temporal fluorescence anisotropy decay allows for determination of restriction on the motion of fluorophores attached to the macromolecules. This model further applied to AO-intercalated genomic DNA and synthetic oligonucleotides within their structural integrity (as confirmed through circular dichroism (CD) studies) shows that AO experiences less restriction in genomic salmon sperm DNA compared with that in synthetic oligonucleotides, and among the oligonucleotides, the ones with AT base pairs are much more rigid. This study would invoke further research on the dynamical nature of AO in restricted environments.
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Affiliation(s)
- Ajay Kumar Shaw
- Unit for Nanoscience and Technology, Department of Chemical, Biological, and Macromolecular Sciences, Satyendra Nath Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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