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Bubble Relaxation Dynamics in Homopolymer DNA Sequences. Molecules 2023; 28:molecules28031041. [PMID: 36770707 PMCID: PMC9920605 DOI: 10.3390/molecules28031041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.
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2
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Rabiul Islam M, Warsi F, Sayem Alam M, Ali M. Solvatochromic behaviour of coumarin 102 in PEGs + ionic liquid/water solutions: Role of solute-solvent or solvent-solvent interactions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Desai AM, Pandey SP, Singh PK. Effect of counter-anions on the aggregation of Thioflavin-T. Phys Chem Chem Phys 2021; 23:9948-9961. [PMID: 33861224 DOI: 10.1039/d1cp00193k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aggregation of small molecules in aqueous solution is known to be influenced by the ionic strength of the medium; however, the role played by the identity of salt in the phenomenon of small molecule aggregation is rarely investigated. In the present contribution, we have investigated the effect of counter-anions on the aggregation of a popular cationic amyloid sensing probe, Thioflavin-T (ThT), by taking six different anions, viz. chloride, bromide, acetate, iodide, tetrafluoroborate, and perchlorate. Our results clearly indicate that it is not the ionic strength of the medium which solely controls aggregation of small molecules but distinct ions behave distinctly with regard to the organization. In fact, distinct ion effects play a major role in the salt induced organization of fluorophores. Using detailed steady-state emission, time-resolved emission, and ground-state absorption measurements, the optical properties of salt induced aggregates of ThT have been characterized. We have rationalized our observations on the basis of the theory of matching water affinity, which suggests that the matching free hydration energy is a critical aspect for the formation of contact ion pairs, which eventually results in aggregation. In brief, a larger sized anion, perchlorate, has a lower free energy of hydration and forms a suitable contact ion pair, with a larger organic cation, ThT, having weaker hydration. This contact ion-pair formation subsequently leads to the formation of an aggregate assembly which is found to be emissive in nature. Therefore, it is possible to induce aggregation of ThT by selecting the right counterion with the appropriate size, which may help us to evaluate the false positive signals when high ionic strength and specific counterions are present in the sensing matrix.
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Affiliation(s)
- Akshat M Desai
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
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5
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Mudliar NH, Pettiwala AM, Awasthi AA, Singh PK. On the Molecular Form of Amyloid Marker, Auramine O, in Human Insulin Fibrils. J Phys Chem B 2016; 120:12474-12485. [PMID: 27973839 DOI: 10.1021/acs.jpcb.6b10078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Designing extrinsic fluorescence sensors for amyloid fibrils is a very active and important area of research. Recently, an ultrafast molecule rotor dye, Auramine O (AuO), has been projected as a fluorescent amyloid marker. It has been claimed that AuO scores better than the most extensively utilized gold-standard amyloid probe, Thioflavin-T (ThT). This advantage arises from the fact that AuO, in addition to its usual emission band (∼500 nm), also displays a large red-shifted emission band (∼560 nm), exclusively in the presence of human insulin fibril medium and not in the native protein or buffer media. On the contrary, for ThT, the emission maximum (∼490 nm) largely remains unchanged while going from protein to fibril. This otherwise unknown large red-shifted emission band of AuO, observed in the presence of human insulin fibrils, was tentatively attributed to a species formed upon fast proton dissociation from excited AuO. It was proposed that because of the long excited-state lifetime (∼1.8 ns) of AuO upon association with human insulin fibrils, this fast proton dissociation from excited AuO could be observed, which is otherwise not observed in buffer or native protein media, owing to its very short excited-state lifetime (∼1 ps). Herein, we show that despite the long excited-state lifetime of AuO in other fibrillar media (human serum albumin and lysozyme), the new red-shifted emission band at 560 nm is not observed, thus possibly suggesting a different origin of the red-shifted emission band of AuO in human insulin fibril medium. We convincingly show that this red-shifted band of AuO (∼560 nm) could be observed under conditions that promote dye aggregation, such as a premicellar concentration of surfactants and polyelectrolytes. These AuO aggregates display strong emission wavelength dependence of transient decay traces, similar to that for AuO in human insulin fibril medium. Detailed time-resolved emission spectral (TRES) measurements suggest that the AuO/premicellar surfactant and AuO/human insulin fibril system share similar features, such as a dynamic red-shift in TRES and an isoemissive point in the time-resolved area-normalized emission spectra, suggesting that the characteristic red-shifted emission band of AuO in human insulin fibril medium may arise from AuO aggregates.
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Affiliation(s)
- Niyati H Mudliar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
| | - Aafrin M Pettiwala
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
| | - Ankur A Awasthi
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
| | - Prabhat K Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Mumbai 400 085, India
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6
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Samanta S, Raghunathan D, Mukherjee S. Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study. J Mol Graph Model 2016; 66:9-19. [PMID: 27017424 DOI: 10.1016/j.jmgm.2016.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/25/2023]
Abstract
DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.
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Affiliation(s)
- Sudipta Samanta
- BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, 117543, Republic of Singapore; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Devanathan Raghunathan
- Prochem Solutions Pte. Ltd., 89C Science Park Drive, The Rutherford, # 04-13, Singapore Science Park 1, 118261, Singapore
| | - Sanchita Mukherjee
- Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India
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7
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Abstract
The fluorescent intensity of Cy3 and Cy5 dyes is strongly dependent on the nucleobase sequence of the labeled oligonucleotides. Sequence-dependent fluorescence may significantly influence the data obtained from many common experimental methods based on fluorescence detection of nucleic acids, such as sequencing, PCR, FRET, and FISH. To quantify sequence dependent fluorescence, we have measured the fluorescence intensity of Cy3 and Cy5 bound to the 5' end of all 1024 possible double-stranded DNA 5mers. The fluorescence intensity was also determined for these dyes bound to the 5' end of fixed-sequence double-stranded DNA with a variable sequence 3' overhang adjacent to the dye. The labeled DNA oligonucleotides were made using light-directed, in situ microarray synthesis. The results indicate that the fluorescence intensity of both dyes is sensitive to all five bases or base pairs, that the sequence dependence is stronger for double- (vs single-) stranded DNA, and that the dyes are sensitive to both the adjacent dsDNA sequence and the 3'-ssDNA overhang. Purine-rich sequences result in higher fluorescence. The results can be used to estimate measurement error in experiments with fluorescent-labeled DNA, as well as to optimize the fluorescent signal by considering the nucleobase environment of the labeling cyanine dye.
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Affiliation(s)
- Nicole Kretschy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna , Althanstraße 14 (UZA II), A-1090 Vienna, Austria
| | - Matej Sack
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna , Althanstraße 14 (UZA II), A-1090 Vienna, Austria
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna , Althanstraße 14 (UZA II), A-1090 Vienna, Austria
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8
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Mazur AK, Shepelyansky DL. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule. PHYSICAL REVIEW LETTERS 2015; 115:188104. [PMID: 26565502 DOI: 10.1103/physrevlett.115.188104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Indexed: 06/05/2023]
Abstract
The statistics of Poincaré recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in a realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the decay of recurrences is described by an algebraic law with the Poincaré exponent close to β=1.2. This value is directly related to the correlation decay exponent ν=β-1, which is close to ν≈0.15 observed in the time resolved Stokes shift experiments. By applying the virial theorem we analyze the chaotic dynamics in polynomial potentials and demonstrate analytically that an exponent β=1.2 is obtained assuming the dominance of dipole-dipole interactions in the relevant DNA dynamics. Molecular dynamics simulations also reveal the presence of strong low frequency noise with the exponent η=1.6. We trace parallels with the chaotic dynamics of symplectic maps with a few degrees of freedom characterized by the Poincaré exponent β~1.5.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, 75005, France
| | - D L Shepelyansky
- Laboratoire de Physique Théorique du CNRS (IRSAMC), Université de Toulouse, UPS, F-31062 Toulouse, France
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9
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Muntean CM, Bratu I, Leopold N, Morari C, Buimaga-Iarinca L, Purcaru MAP. Subpicosecond surface dynamics in genomic DNA from in vitro-grown plant species: a SERS assessment. Phys Chem Chem Phys 2015; 17:21323-30. [PMID: 25687823 DOI: 10.1039/c4cp05425c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.
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Affiliation(s)
- Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, 67-103 Donat Str., 400293 Cluj-Napoca, Romania.
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10
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Hessz D, Hégely B, Kállay M, Vidóczy T, Kubinyi M. Solvation and protonation of coumarin 102 in aqueous media: a fluorescence spectroscopic and theoretical study. J Phys Chem A 2014; 118:5238-47. [PMID: 24945906 DOI: 10.1021/jp504496k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ground- and excited-state protonation of Coumarin 102 (C102), a fluorescent probe applied frequently in heterogeneous systems with an aqueous phase, has been studied in aqueous solutions by spectroscopic experiments and theoretical calculations. For the dissociation constant of the protonated form in the ground state, pKa = 1.61 was obtained from the absorption spectra; for the excited-state dissociation constant, pKa* = 2.19 was obtained from the fluorescence spectra. These values were closely reproduced by theoretical calculations via a thermodynamic cycle (the value of pKa* also by calculations via the Förster cycle) using an implicit–explicit solvation model (polarized continuum model + addition of a solvent molecule). The theoretical calculations indicated that (i) in the ground state, C102 occurs primarily as a hydrogen-bonded water complex, with the oxo group as the binding site, (ii) this hydrogen bond becomes stronger upon excitation, and (iii) in the ground state, the amino nitrogen atom is the protonation site, and in the excited state, the carboxy oxygen atom is the protonation site. A comprehensive analysis of fluorescence decay data yielded the values kpr = 3.27 × 10(10) M(–1) s(–1) for the rate constant of the excited-state protonation and kdpr = 2.78 × 10(8) s(–1) for the rate constant of the reverse process (kpr and kdpr were treated as independent parameters). This, considering the relatively long fluorescence lifetimes of neutral C102 (6.02 ns) and its protonated form (3.06 ns) in aqueous media, means that a quasi-equilibrium state of excited-state proton transfer is reached in strongly acidic solutions.
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Affiliation(s)
- Dóra Hessz
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , P.O. Box 286, 1519 Budapest, Hungary
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11
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Hövelmann F, Bethge L, Seitz O. Single labeled DNA FIT probes for avoiding false-positive signaling in the detection of DNA/RNA in qPCR or cell media. Chembiochem 2012; 13:2072-81. [PMID: 22936610 DOI: 10.1002/cbic.201200397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 12/13/2022]
Abstract
Oligonucleotide hybridization probes that fluoresce upon binding to complementary nucleic acid targets allow the real-time detection of DNA or RNA in homogeneous solution. The most commonly used probes rely on the distance-dependent interaction between a fluorophore and another label. Such dual-labeled oligonucleotides signal the change of the global conformation that accompanies duplex formation. However, undesired nonspecific binding events and/or probe degradation also lead to changes in the label-label distance and, thus, to ambiguities in fluorescence signaling. Herein, we introduce singly labeled DNA probes, "DNA FIT probes", that are designed to avoid false-positive signals. A thiazole orange (TO) intercalator dye serves as an artificial base in the DNA probe. The probes show little background because the attachment mode hinders 1) interactions of the "TO base" in cis with the disordered nucleobases of the single strand, and 2) intercalation of the "TO nucleotide" with double strands in trans. However, formation of the probe-target duplex enforces stacking and increases the fluorescence of the TO base. We explored open-chain and carbocyclic nucleotides. We show that the incorporation of the TO nucleotides has no effect on the thermal stability of the probe-target complexes. DNA and RNA targets provided up to 12-fold enhancements of the TO emission upon hybridization of DNA FIT probes. Experiments in cell media demonstrated that false-positive signaling was prevented when DNA FIT probes were used. Of note, DNA FIT probes tolerate a wide range of hybridization temperature; this enabled their application in quantitative polymerase chain reactions.
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Affiliation(s)
- Felix Hövelmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany
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12
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Berndt F, Ioffe I, Granovsky AA, Mahrwald R, Tannert S, Kovalenko SA, Ernsting NP. 7-Amino-dibenzofuran-3-carboxylate: A new probe for femtosecond dynamic microsolvation studies of biomolecules. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Holzberger B, Strohmeier J, Siegmund V, Diederichsen U, Marx A. Enzymatic synthesis of 8-vinyl- and 8-styryl-2'-deoxyguanosine modified DNA--novel fluorescent molecular probes. Bioorg Med Chem Lett 2012; 22:3136-9. [PMID: 22483394 DOI: 10.1016/j.bmcl.2012.03.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 12/19/2022]
Abstract
Fluorescent analogs of the natural nucleobases are widely used as molecular probes for investigating DNA hybridization and topology. In this study the guanosine analogs 8-vinyl- and 8-styryl-2'-deoxyguanosine were synthesized and converted into the corresponding 5'-triphosphates. These C8 modified nucleotides were processed by various DNA polymerases to create fluorescent DNA. Whereas the 8-styryl modified nucleotide somewhat hampers DNA synthesis 8-vinyl-2'-deoxyguanosine is processed by DNA polymerases emphasizing the broad applicability as a molecular probe for fluorescence spectroscopy.
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Affiliation(s)
- Bastian Holzberger
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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14
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Xu S, Shao Y, Ma K, Cui Q, Liu G, Wu F, Li M. Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe. Analyst 2011; 136:4480-5. [PMID: 21946800 DOI: 10.1039/c1an15652g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.
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Affiliation(s)
- Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
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15
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Agbavwe C, Somoza MM. Sequence-dependent fluorescence of cyanine dyes on microarrays. PLoS One 2011; 6:e22177. [PMID: 21799789 PMCID: PMC3143128 DOI: 10.1371/journal.pone.0022177] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/17/2011] [Indexed: 11/19/2022] Open
Abstract
Cy3 and Cy5 are among the most commonly used oligonucleotide labeling molecules. Studies of nucleic acid structure and dynamics use these dyes, and they are ubiquitous in microarray experiments. They are sensitive to their environment and have higher quantum yield when bound to DNA. The fluorescent intensity of terminal cyanine dyes is also known to be significantly dependent on the base sequence of the oligonucleotide. We have developed a very precise and high-throughput method to evaluate the sequence dependence of oligonucleotide labeling dyes using microarrays and have applied the method to Cy3 and Cy5. We used light-directed in-situ synthesis of terminally-labeled microarrays to determine the fluorescence intensity of each dye on all 1024 possible 5′-labeled 5-mers. Their intensity is sensitive to all five bases. Their fluorescence is higher with 5′ guanines, and adenines in subsequent positions. Cytosine suppresses fluorescence. Intensity falls by half over the range of all 5-mers for Cy3, and two-thirds for Cy5. Labeling with 5′-biotin-streptavidin-Cy3/-Cy5 gives a completely different sequence dependence and greatly reduces fluorescence compared with direct terminal labeling.
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Affiliation(s)
- Christy Agbavwe
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
- * E-mail:
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16
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Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2'-deoxyguanosine as a fluorescent 2'-deoxyguanosine mimic for investigating DNA hybridization and topology. Angew Chem Int Ed Engl 2011; 50:5392-6. [PMID: 21542071 DOI: 10.1002/anie.201100078] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/10/2022]
Affiliation(s)
- André Nadler
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
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17
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Nadler A, Strohmeier J, Diederichsen U. 8-Vinyl-2′-desoxyguanosin als fluoreszierendes 2′-Desoxyguanosin- Analogon zur Untersuchung von DNA-Hybridisierung und Topologie. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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18
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Furse KE, Corcelli SA. Effects of an unnatural base pair replacement on the structure and dynamics of DNA and neighboring water and ions. J Phys Chem B 2011; 114:9934-45. [PMID: 20614919 DOI: 10.1021/jp105761b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating small molecule probes into biomolecular systems to report on local structure and dynamics is a powerful strategy that underlies a wide variety of experimental techniques, including fluorescence, electron paramagnetic resonance (EPR), and Forster resonance energy transfer (FRET) measurements. When an unnatural probe is inserted into a protein or DNA, the degree to which the presence of the probe has perturbed the local structure and dynamics it was intended to study is always an important concern. Here, molecular dynamics (MD) simulations are used to systematically study the effect of replacing a DNA base pair with a fluorescent probe, coumarin 102 deoxyriboside, at six unique sites along an A-tract DNA dodecamer. While the overall structure of the DNA oligonucleotide remains intact, replacement of A*T base pairs leads to widespread structural and dynamic perturbations up to four base pairs away from the probe site, including widening of the minor groove and increased DNA flexibility. New DNA conformations, not observed in the native sequence, are sometimes found in the vicinity of the probe and its partner abasic site analog. Strong correlations are demonstrated between DNA surface topology and water mobility.
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Affiliation(s)
- K E Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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19
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 665] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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20
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Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Hainke S, Seitz O. Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed Engl 2010; 48:8250-3. [PMID: 19790219 DOI: 10.1002/anie.200903194] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Hainke
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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22
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Hainke S, Seitz O. Binaphthyl-DNA: Stapelung und Fluoreszenz eines nichtplanaren aromatischen Basensurrogates in DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Furse KE, Corcelli SA. Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations. J Chem Theory Comput 2009; 5:1959-67. [DOI: 10.1021/ct9001416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristina E. Furse
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
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24
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Otosu T, Nishimoto E, Yamashita S. Fluorescence Decay Characteristics of Indole Compounds Revealed by Time-Resolved Area-Normalized Emission Spectroscopy. J Phys Chem A 2009; 113:2847-53. [DOI: 10.1021/jp8078937] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuhiro Otosu
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Etsuko Nishimoto
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
| | - Shoji Yamashita
- Institute of Biophysics, Faculty of Agriculture, Graduate School of Kyushu University, Hakozaki, Fukuoka 812-8581, Japan
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25
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Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 2009; 131:1724-35. [PMID: 19191698 PMCID: PMC2750815 DOI: 10.1021/ja805405a] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.
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Affiliation(s)
- Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India
| | - Daniele Andreatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | | | | | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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26
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Singh PK, Kumbhakar M, Pal H, Nath S. Modulation in the Solute Location in Block Copolymer−Surfactant Supramolecular Assembly: A Time-resolved Fluorescence Study. J Phys Chem B 2009; 113:1353-9. [DOI: 10.1021/jp808123m] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Prabhat K. Singh
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Manoj Kumbhakar
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Haridas Pal
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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27
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Sankaran NB, Sato Y, Sato F, Rajendar B, Morita K, Seino T, Nishizawa S, Teramae N. Small-Molecule Binding at an Abasic Site of DNA: Strong Binding of Lumiflavin for Improved Recognition of Thymine-Related Single Nucleotide Polymorphisms. J Phys Chem B 2009; 113:1522-9. [DOI: 10.1021/jp808576t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. B. Sankaran
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Fuyuki Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Burki Rajendar
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Kotaro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Takehiro Seino
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan, and CREST, Japan Science and Technology Agency (JST), Sendai 980-8578, Japan
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28
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Mondal SK, Sahu K, Bhattacharyya K. Study of Biological Assemblies by Ultrafast Fluorescence Spectroscopy. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Klymchenko AS, Shvadchak VV, Yushchenko DA, Jain N, Mély Y. Excited-State Intramolecular Proton Transfer Distinguishes Microenvironments in Single- And Double-Stranded DNA. J Phys Chem B 2008; 112:12050-5. [DOI: 10.1021/jp8058068] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrey S. Klymchenko
- Photophysique des Interactions Biomoléculaires, UMR 7175 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 67401, Illkirch, France
| | - Volodymyr V. Shvadchak
- Photophysique des Interactions Biomoléculaires, UMR 7175 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 67401, Illkirch, France
| | - Dmytro A. Yushchenko
- Photophysique des Interactions Biomoléculaires, UMR 7175 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 67401, Illkirch, France
| | - Namrata Jain
- Photophysique des Interactions Biomoléculaires, UMR 7175 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 67401, Illkirch, France
| | - Yves Mély
- Photophysique des Interactions Biomoléculaires, UMR 7175 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 67401, Illkirch, France
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30
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Singh PK, Kumbhakar M, Pal H, Nath S. Effect of Electrostatic Interaction on the Location of Molecular Probe in Polymer−Surfactant Supramolecular Assembly: A Solvent Relaxation Study. J Phys Chem B 2008; 112:7771-7. [DOI: 10.1021/jp800701v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prabhat K. Singh
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Manoj Kumbhakar
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Haridas Pal
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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31
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Choudhury SD, Nath S, Pal H. Excited-State Proton Transfer Behavior of 7-Hydroxy-4-methylcoumarin in AOT Reverse Micelles. J Phys Chem B 2008; 112:7748-53. [DOI: 10.1021/jp8004019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Haridas Pal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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32
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Singh PK, Nath S, Kumbhakar M, Bhasikuttan AC, Pal H. Quantitative Distinction between Competing Intramolecular Bond Twisting and Solvent Relaxation Dynamics: An Ultrafast Study. J Phys Chem A 2008; 112:5598-603. [DOI: 10.1021/jp801862j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | | | - Haridas Pal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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33
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Sinkeldam RW, Greco NJ, Tor Y. Polarity of major grooves explored by using an isosteric emissive nucleoside. Chembiochem 2008; 9:706-9. [PMID: 18286575 DOI: 10.1002/cbic.200700714] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Renatus W Sinkeldam
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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34
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Menacher F, Rubner M, Berndl S, Wagenknecht HA. Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer. J Org Chem 2008; 73:4263-6. [PMID: 18442293 DOI: 10.1021/jo8004793] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.
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Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, Universitätsstrasse 31, Regensburg, Germany
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35
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Khurmi C, Berg MA. Analyzing Nonexponential Kinetics with Multiple Population-Period Transient Spectroscopy (MUPPETS). J Phys Chem A 2008; 112:3364-75. [DOI: 10.1021/jp710711w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Champak Khurmi
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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36
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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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37
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Kumbhakar M. Aggregation of Ionic Surfactants to Block Copolymer Assemblies: A Simple Fluorescence Spectral Study. J Phys Chem B 2007; 111:14250-5. [DOI: 10.1021/jp077220k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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38
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Choudhury SD, Kumbhakar M, Nath S, Pal H. Photoinduced bimolecular electron transfer kinetics in small unilamellar vesicles. J Chem Phys 2007; 127:194901. [DOI: 10.1063/1.2794765] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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39
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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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40
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Toptygin D, Gronenborn AM, Brand L. Nanosecond relaxation dynamics of protein GB1 identified by the time-dependent red shift in the fluorescence of tryptophan and 5-fluorotryptophan. J Phys Chem B 2007; 110:26292-302. [PMID: 17181288 DOI: 10.1021/jp064528n] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The B1 domain of Streptococcal protein G (GB1) is a small, thermostable protein containing a single tryptophan residue. We recorded time-resolved fluorescence of the wild-type GB1 and its 5-fluorotryptophan (5FTrp) variant at more than 30 emission wavelengths between 300 and 470 nm. The time-resolved emission spectra reveal no signs of heterogeneity, but show a time-dependent red shift characteristic of microscopic dielectric relaxation. This is true for both 5FTrp and unmodified Trp in GB1. The time-dependent red shifts in the fluorescence of 5FTrp and unmodified Trp are essentially identical, confirming that the shift is caused by the relaxation of the protein matrix rather than by the fluorophore itself. The total amplitude (but not the rate) of the time-dependent red shift depends on the fluorophore, specifically, on the magnitude of the vector difference between its excited state and ground state electric dipole moments; for 5FTrp this is estimated to be about 88% of that for the unmodified Trp. The decay of the excited state fluorophore population is not monoexponential for either fluorophore; however, the deviation from the monoexponential decay law is larger in the case of unmodified Trp. The relaxation dynamics of GB1 was found to be considerably faster than that of other proteins studied previously, consistent with the small size, tightly packed core, and high thermodynamic stability of GB1.
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Affiliation(s)
- Dmitri Toptygin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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41
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Pal S, Maiti PK, Bagchi B, Hynes JT. Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations. J Phys Chem B 2007; 110:26396-402. [PMID: 17181299 DOI: 10.1021/jp065690t] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.
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Affiliation(s)
- Subrata Pal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India
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42
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Sen S, Gearheart LA, Rivers E, Liu H, Coleman RS, Murphy CJ, Berg MA. Role of Monovalent Counterions in the Ultrafast Dynamics of DNA. J Phys Chem B 2006; 110:13248-55. [PMID: 16805639 DOI: 10.1021/jp056327+] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.
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Affiliation(s)
- Sobhan Sen
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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43
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Andreatta D, Sen S, Lustres JLP, Kovalenko SA, Ernsting NP, Murphy CJ, Coleman RS, Berg MA. Ultrafast dynamics in DNA: "fraying" at the end of the helix. J Am Chem Soc 2006; 128:6885-92. [PMID: 16719468 PMCID: PMC2528932 DOI: 10.1021/ja0582105] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics of the electric fields in the interior of DNA are measured by using oligonucleotides in which a native base pair is replaced by a dye molecule (coumarin 102) whose emission spectrum is sensitive to the local electric field. Time-resolved measurements of the emission spectrum have been extended to a six decade time range (40 fs to 40 ns) by combining results from time-correlated photon counting, fluorescence up-conversion, and transient absorption. Recent results showed that when the reporter is placed in the center of the oligonucleotide, the dynamics are very broadly distributed over this entire time range and do not show specific time constants associated with individual processes (Andreatta, D.; et al. J. Am. Chem. Soc. 2005, 127, 7270). This paper examines an oligonucleotide with the reporter near its end. The broadly distributed relaxation seen before remains with little attenuation. In addition, a new relaxation with a well-defined relaxation time of 5 ps appears. This process is assigned to the rapid component of "fraying" at the end of the helix.
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44
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Liu LT, Yaron D, Sluch MI, Berg MA. Modeling the Effects of Torsional Disorder on the Spectra of Poly- and Oligo-(p-phenyleneethynylenes). J Phys Chem B 2006; 110:18844-52. [PMID: 16986875 DOI: 10.1021/jp056284x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The absorption spectra of phenyleneethynylene oligomers show an unusual change in shape with oligomer length. The unusual aspects of the spectra arise from rotation of the phenylene rings about the long axis of the oligomer. In the ground electronic state, the barrier to this rotation is low and the spectra in room temperature come from an ensemble of different structures. In the excited electronic state, the barrier to rotation is substantially higher, giving rise to strong nonlinear electron-phonon coupling. A multidimensional semiempirical model that includes these effects is developed for the photophysics of phenyleneethynylene oligomers. The ground-state energy is modeled with a molecular mechanics expression, and the excitation energy is modeled with an exciton model. Intermediate Neglect of Differential Overlap/Singles Configuration Interaction (INDO/SCI) calculations verify the exciton model and provide initial estimates of the model parameters. These parameters generate the qualitative features seen in experimental spectra. Inclusion of entropy effects from the multiple torsional coordinates is essential. Refinement of the parameters yields quantitative agreement with experiment. This agreement shows that coupling to torsional motion is a major factor in the spectroscopy and photophysics of these conjugated polymers.
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Affiliation(s)
- Lu Tian Liu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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45
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Sen S, Paraggio NA, Gearheart LA, Connor EE, Issa A, Coleman RS, Wilson DM, Wyatt MD, Berg MA. Effect of protein binding on ultrafast DNA dynamics: characterization of a DNA:APE1 complex. Biophys J 2005; 89:4129-38. [PMID: 16199493 PMCID: PMC1366978 DOI: 10.1529/biophysj.105.062695] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthetic oligonucleotides with a fluorescent coumarin group replacing a basepair have been used in recent time-resolved Stokes-shift experiments to measure DNA dynamics on the femtosecond to nanosecond timescales. Here, we show that the APE1 endonuclease cleaves such a modified oligonucleotide at the abasic site opposite the coumarin with only a fourfold reduction in rate. In addition, a noncatalytic mutant (D210N) binds tightly to the same oligonucleotide, albeit with an 85-fold reduction in binding constant relative to a native oligonucleotide containing a guanine opposite the abasic site. Thus, the modified oligonucleotide retains substantial biological activity and serves as a useful model of native DNA. In the complex of the coumarin-containing oligonucleotide and the noncatalytic APE1, the dye's absorption spectrum is shifted relative to its spectrum in either water or within the unbound oligonucleotide. Thus the dye occupies a site within the DNA:protein complex. This result is consistent with modeling, which shows that the complex accommodates coumarin at the site of the orphaned base with little distortion of the native structure. Stokes-shift measurements of the complex show surprisingly little change in the dynamics within the 40 ps-40 ns time range.
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Affiliation(s)
- Sobhan Sen
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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Andreatta D, Pérez Lustres JL, Kovalenko SA, Ernsting NP, Murphy CJ, Coleman RS, Berg MA. Power-Law Solvation Dynamics in DNA over Six Decades in Time. J Am Chem Soc 2005; 127:7270-1. [PMID: 15898749 DOI: 10.1021/ja044177v] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-resolved Stokes shifts in a dye-containing oligonucleotide have been observed over the entire time range from 40 fs to 40 ns. The dynamics fit to a power law with a small exponent of 0.15. Similar relaxation has been seen in proteins but has not been anticipated in DNA. Distinct relaxation components due to specific subcomponents of the system, bulk water, bound water, counterions, backbone, bases, and so on, are not found. The various subcomponents may be so strongly coupled that their motions cannot be treated separately.
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Affiliation(s)
- Daniele Andreatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, 29208, USA
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