1
|
Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| |
Collapse
|
2
|
Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
|
3
|
Synthesis and characterization of a fluorescent adenosine derivative for detection of intermolecular RNA G-quadruplexes. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
4
|
Minero AS, Lukashevich OV, Cherepanova NA, Kolbanovskiy A, Geacintov NE, Gromova ES. Probing murine methyltransfease Dnmt3a interactions with benzo[a]pyrene-modified DNA by fluorescence methods. FEBS J 2012; 279:3965-80. [PMID: 22913541 DOI: 10.1111/j.1742-4658.2012.08756.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 11/29/2022]
Abstract
The impact of bulky carcinogen-DNA adducts positioned at or near recognition sites (CpG) of eukaryotic DNA methyltransferases on their catalytic activities is poorly understood. In the present study, we employed site-specifically modified 30-mer oligodeoxyribonucleotides containing stereoisomeric benzo[a]pyrene diol epoxide (B[a]PDE)-derived guanine (B[a]PDE-N(2)-dG) or adenine (B[a]PDE-N(6)-dA) adducts of different conformations as substrates of the catalytic domain of murine Dnmt3a (Dnmt3a-CD). The fluorescence of these lesions was used to examine interactions between Dnmt3a-CD and DNA. In B[a]PDE-DNA•Dnmt3a-CD complexes, the intensity of fluorescence of the covalently bound B[a]PDE residues is enhanced relative to the protein-free value when the B[a]PDE is positioned in the minor groove [(+)- and (-)-trans-B[a]PDE-N(2)-dG adducts in the CpG site] and when it is intercalated on the 5'-side of the CpG site [(+)-trans-B[a]PDE-N(6)-dA adduct]. The fluorescence of B[a]PDE-modified DNA•Dnmt3a-CD complexes exhibits only small changes when the B[a]PDE is intercalated with base displacement in (+)- and (-)-cis-B[a]PDE-N(2)-dG adducts and without base displacement in the (-)-trans-B[a]PDE-N(6)-dA adduct. The initial rates of methylation were significantly reduced by the minor groove trans-B[a]PDE-N(2)-dG adducts, regardless of their position in the substrate and by the intercalated cis-B[a]PDE-N(2)-dG adducts within the CpG site. The observed changes in fluorescence and methylation rates are consistent with the flipping of the target cytosine and a catalytic loop motion within the DNA•Dnmt3a-CD complexes. In the presence of the regulatory factor Dnmt3L, an enhancement of both methylation rates and fluorescence was observed, which is consistent with a Dnmt3L-mediated displacement of the catalytic loop towards the CpG site.
Collapse
Affiliation(s)
- Antonio S Minero
- Department of Chemistry, Moscow State University, Moscow, Russia
| | | | | | | | | | | |
Collapse
|
5
|
Lee IJ, Park M, Joo T, Kim BH. Using fluorescence changes of F1U units at terminal and mid-loop positions to probe i-motif structures. ACTA ACUST UNITED AC 2012; 8:486-90. [DOI: 10.1039/c1mb05343d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
6
|
Yun BH, Dedon PC, Geacintov NE, Shafirovich V. One-electron oxidation of a pyrenyl photosensitizer covalently attached to DNA and competition between its further oxidation and DNA hole injection. Photochem Photobiol 2010; 86:563-70. [PMID: 20408978 DOI: 10.1111/j.1751-1097.2010.00719.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The photosensitized hole injection and guanine base damage phenomena have been investigated in the DNA sequence, 5'-d(CATG(1)(Py)CG(2)TCCTAC) with a site-specifically positioned pyrene-like (Py) benzo[a]pyrene 7,8-diol 9,10-epoxide-derived N(2)-guanine adduct (G(1)(Py)). Generation of the Py radical cation and subsequent hole injection into the DNA strand by a 355 nm nanosecond laser pulses (approximately 4 mJ cm(-2)) results in the transformation of G(1)(Py) to the imidazolone derivative Iz(1)(Py) and a novel G(1)(Py*) photoproduct that has a mass larger by 16 Da (M+16) than the mass (M) of G(1)(Py). In addition, hole transfer and the irreversible oxidation of G(2), followed by the formation of Iz(2) was observed (Yun et al. [2007], J. Am. Chem. Soc., 129, 9321). Oxygen-18 and deuterium isotope labeling methods, in combination with an extensive analysis of the MS/MS fragmentation patterns of the individual dG(Py*) nucleoside adduct and other data show that dG(Py*) has an unusual structure with a ruptured cyclohexenyl ring with a carbonyl group at the rupture site and intact guanine and pyrenyl residues. The formation of this product competes with hole injection and thus diminishes the efficiency of oxidation of guanines within the oligonucleotide strand by at least 15% in comparison with that in the dG(Py) nucleoside adduct.
Collapse
Affiliation(s)
- Byeong Hwa Yun
- Chemistry Department and Radiation and Solid State Laboratory, New York University, New York City, NY, USA
| | | | | | | |
Collapse
|
7
|
Bueno C, Pavez P, Salazar R, Encinas MV. Photophysics and photochemical studies of the vitamin B6 group and related derivatives. Photochem Photobiol 2009; 86:39-46. [PMID: 19930123 DOI: 10.1111/j.1751-1097.2009.00643.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The photophysics and photochemical properties of vitamin B6 constituents and analogs were studied as function of pH and solvent. The pK of the phenolic oxygen and the pyridine ring nitrogen depends on the electron donor-acceptor ability of the 4-substituent, and agrees with the calculated proton affinity. For all studied compounds, the fluorescence properties showed that the phenolic oxygen is 8 units more acidic in the lowest singlet excited state than in the ground state. The pyridine N-atom is slightly more basic in the excited state. At pH of biological significance, pH 6-8, pyridoxamine and 4-pyridoxic acid are the more efficient chromophores with higher fluorescence yield and longer lifetime. Spectroscopic studies showed that the tautomeric equilibrium depends on the nature of the 4-substituent. The quenching of the singlet excited state of pyridoxamine and 4-pyridoxic acid by amino acids, free or in a peptide, and DNA bases at pH 7 was studied by time-resolved fluorescence techniques. The quenching rate constants are well correlated with the redox properties of the pyridoxinic compound and amino acids, and are related to the free energy change in the electron transfer process. Guanosine and pyrimidine bases also are efficient quenchers, involving an electron transfer reaction.
Collapse
Affiliation(s)
- Claudia Bueno
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | | | | | | |
Collapse
|
8
|
Lee IJ, Yi JW, Kim BH. Probe for i-motif structure and G-rich strands using end-stacking ability. Chem Commun (Camb) 2009:5383-5. [PMID: 19724792 DOI: 10.1039/b908624b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We suggest a novel method for probing human i-motif structure based on a pi-stacking interaction between a base pair of two cytosines and a non-polar aromatic fluorophore, PyA, at the end position.
Collapse
Affiliation(s)
- Il Joon Lee
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | |
Collapse
|
9
|
Cuomo F, Palazzo G, Ceglie A, Lopez F. Quenching efficiency of pyrene fluorescence by nucleotide monophosphates in cationic micelles. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2008.10.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
10
|
Jeong HS, Kang S, Lee JY, Kim BH. Probing specific RNA bulge conformations by modified fluorescent nucleosides. Org Biomol Chem 2009; 7:921-5. [DOI: 10.1039/b816768k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Seo YJ, Lee IJ, Kim BH. Detection of structure-switching in G-quadruplexes using end-stacking ability. Bioorg Med Chem Lett 2008; 18:3910-3. [PMID: 18585032 DOI: 10.1016/j.bmcl.2008.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/04/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
Abstract
G-quadruplex-forming ODNs containing nonpolar aromatic fluorophore moiety, A(PY) at the dangling ends undergo pi-stacking on surface of G-quadruplex, and the fluorescence change can be used to distinguish the structure-switching between the mixed parallel/antiparallel structure and antiparallel structure.
Collapse
Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | | | | |
Collapse
|
12
|
Walsh L, Gbaj A, Etchells LL, Douglas KT, Bichenkova EV. SNP detection for cytochrome P450 alleles by target-assembled tandem oligonucleotide systems based on exciplexes. J Biomol Struct Dyn 2008; 25:629-40. [PMID: 18399696 DOI: 10.1080/07391102.2008.10507209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We report the first use of exciplex-based split-probes for detection of the wild type and *3 mutant alleles of human cytochrome P450 2C9. A tandem 8-mer split DNA oligonucleotide probe system was designed that allows detection of the complementary target DNA sequence. This exciplex-based fluorescence detector system operates by means of a contiguous hybridization of two oligonucleotide exciplex split-probes to a complementary target nucleic acid target. Each probe oligonucleotide is chemically modified at one of its termini by a potential exciplex-forming partner, each of which is fluorescently silent at the wavelength of detection. Under conditions that ensure correct three-dimensional assembly, the chemical moieties on suitable photoexcitation form an exciplex that fluoresces with a large Stokes shift (in this case 130 nm). Preliminary proof-of-concept studies used two 8-mer probe oligonucleotides, but in order to give better specificity for genomic applications, probe length was extended to give coverage of 24 bases. Eight pairs of tandem 12-mer oligonucleotide probes spanning the 2C9*3 region were designed and tested to find the best set of probes. Target sequences tested were in the form of (i) synthetic oligonucleotides, (ii) embedded in short PCR products (150 bp), or (iii) inserted into plasmid DNA (approximately 3 Kbp). The exciplex system was able to differentiate wild type and human cytochrome P450 2C9 *3 SNP (1075 A-->C) alleles, based on fluorescence emission spectra and DNA melting curves, indicating promise for future applications in genetic testing and molecular diagnostics.
Collapse
Affiliation(s)
- Lindsey Walsh
- Wolfson Center for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, M13 9PL, U.K
| | | | | | | | | |
Collapse
|
13
|
Abstract
Scorpion probes, specific DNA probe sequences maintained in a hairpin–loop, can be modified to carry the components of an exciplex for use as a novel fluorescence-based method for specific detection of DNA. The exciplex partners (5′-pyrenyl and 3′-naphthalenyl) were attached to oligonucleotides via phosphoramidate links to terminal phosphate groups. Hybridization of the probe to a complementary target in a buffer containing trifluoroethanol produced an obvious fluorescence change from blue (pyrene locally excited state emission) to green (exciplex emission).
Collapse
|
14
|
Lee YA, Durandin A, Dedon PC, Geacintov NE, Shafirovich V. Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions. J Phys Chem B 2008; 112:1834-44. [PMID: 18211057 DOI: 10.1021/jp076777x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotides with noncontiguous guanines G and grouped as contiguous GG and GGG sequences were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd:YAG laser pulses, the DNA-bound BPT molecules were photoionized to BPT*+ radicals by a consecutive two-photon ionization mechanism. The BPT*+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron-transfer reactions, and the rate constants of these reactions follow the trend 5'-..GGG.. > 5'-..GG.. > 5'-..G... In the case of CO3*- radicals, the oxidation of guanine occurs by intermolecular collision pathways, and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO3*- radicals, as well as by BPT*+, are base sequence context-dependent and are greater than those in isolated guanines at the 5'-G in 5'-...GG... sequences, and the first two 5'- guanines in the 5'-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkali-labile guanine products. In the case of the intermolecular one-electron oxidant CO3*-, the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA-bound oxidant BPT*+, the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.
Collapse
Affiliation(s)
- Young Ae Lee
- Chemistry Department, New York University, New York, NY 10003-5180, USA
| | | | | | | | | |
Collapse
|
15
|
Krishnamurthy NV, Reddy AR, Bhudevi B. Wavelength dependant quenching of 2,5-diphenyloxazole fluorescence by nucleotides. J Fluoresc 2007; 18:29-34. [PMID: 17768610 DOI: 10.1007/s10895-007-0231-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 07/23/2007] [Indexed: 11/29/2022]
Abstract
The quenching of 2,5-diphenyloxazole (PPO) fluorescence by nucleotides has been investigated by electronic absorption and steady state fluorescence spectra. Five purine nucleotides AMP, ADP, ATP, GMP and dGMP, one pyrimidine nucleotide UMP and one dinucleotide NAD have been employed in the present study. Electronic absorption studies indicate that there is no ground state complexation between the nucleotides and PPO. The quenching of PPO fluorescence was investigated at two different wavelengths. When excited at 304 nm, the lambda(max) of PPO, the fluorescence spectra of PPO is quenched following Stern-Volmer kinetics. The quenching ability of nucleotides are in the order NAD>AMP>ADP>GMP>dGMP>UMP. The K(SV) and k(q) values obtained indicate that AMP is a better quencher of PPO fluorescence than GMP, which is contrary to commonly observed pattern. The quenching is found to be dynamic in nature. However, when excited at 260 nm, the absorption maximum of the nucleotides, the fluorescence intensity of PPO is reduced with increase in the concentration of the nucleotide. This is attributed to the primary inner filter effect arising due to the absorption of the incident radiation by the nucleotides. Thus the inner filter effect phenomenon can be employed to assay the non-fluorescent molecules by fluorimetry.
Collapse
Affiliation(s)
- N V Krishnamurthy
- Jonaki, Labeled Biomolecules Laboratory, Regional Centre, Board of Radiation and Isotope Technology, Hyberabad, India
| | | | | |
Collapse
|
16
|
Seo YJ, Lee IJ, Yi JW, Kim BH. Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene-adenosine. Chem Commun (Camb) 2007:2817-9. [PMID: 17609786 DOI: 10.1039/b707278c] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pyrene-modified adenosines in the dangling positions of G-rich oligodeoxynucleotides undergo pi-stacking in their G-quadruplex formation, but not in their single strands, which can be characterized by fluorescence lambda(max) changes that occur on stacking.
Collapse
Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
| | | | | | | |
Collapse
|
17
|
|
18
|
Seo YJ, Kim BH. Probing the B-to-Z-DNA duplex transition using terminally stacking ethynyl pyrene-modified adenosine and uridine bases. Chem Commun (Camb) 2005:150-2. [PMID: 16372088 DOI: 10.1039/b514079j] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrene-modified adenosine and uridine bases located in the dangling positions of G,C-alternating oligodeoxynucleotides undergo pi-stacking in their B-DNA duplexes, but not in their Z-DNA duplexes; fluorescence quenching in the former, through photoinduced electron transfer, but not in the latter, allows the state of the B-to-Z-DNA transition to be characterized visually.
Collapse
Affiliation(s)
- Young Jun Seo
- National Research Laboratory, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | | |
Collapse
|
19
|
Seo YJ, Ryu JH, Kim BH. Quencher-Free, End-Stacking Oligonucleotides for Probing Single-Base Mismatches in DNA. Org Lett 2005; 7:4931-3. [PMID: 16235925 DOI: 10.1021/ol0518582] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
[reaction: see text] Fluorescence can be quenched through PET from the fluorophore to neighboring C, T, and G bases, but not to the A moiety. The hairpin stem stability arising from pi-stacking and the PET between the pyrene-labeled 2'-deoxynucleotide units and their neighboring bases are the two main factors that affect the operation of these novel fluorescent oligonucleotides.
Collapse
Affiliation(s)
- Young Jun Seo
- National Research Laboratory, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Korea
| | | | | |
Collapse
|
20
|
Kawai K, Yoshida H, Sugimoto A, Fujitsuka M, Majima T. Kinetics of Transient End-to-End Contact of Single-Stranded DNAs. J Am Chem Soc 2005; 127:13232-7. [PMID: 16173752 DOI: 10.1021/ja0524999] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of the pyrene (Py) dimer radical cation (Py(2)(*+)) was used to measure the kinetics of the intrastrand end-to-end contact rates of single-stranded DNAs (ssDNAs) in the 10 nanoseconds to the tens of microseconds time range. ssDNAs labeled with Py at both ends with the lengths of 3, 6, and 9 mer were synthesized, and the two-photon ionization method was employed to generate a Py(*+), which enables the measurements of the end-to-end contact rates from 10 ns. The formation rate of Py(2)(*+) depended on the length and the sequence of the ssDNAs, and about 1 order of magnitude faster rates were observed for the T-rich ssDNAs compared to those for the corresponding length of A-rich ssDNAs, showing that ssDNA made from adenines is much more rigid than that composed of thymidines. As for the T-rich ssDNAs, the formation of Py(2)(*+) attributed to the misfolded structures was also observed, which is consistent with the configurational diffusion model suggested by Ansari and co-workers.
Collapse
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Ibaraki, Osaka 567-0047, Japan.
| | | | | | | | | |
Collapse
|
21
|
Raunkjær M, Haselmann K, Wengel J. Oligodeoxynucleotides Containing Diastereomeric O2′,C3′‐linked Bicyclic Nucleotide Units for Functionalization of the Major Groove of Nucleic Acid Duplexes: A Summary and Novel Derivatives*. J Carbohydr Chem 2005. [DOI: 10.1081/car-200067044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
22
|
Lyles MB, Cameron IL, Rawls HR. Structural basis for the binding affinity of xanthines with the DNA intercalator acridine orange. J Med Chem 2001; 44:4650-60. [PMID: 11741482 DOI: 10.1021/jm9904708] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Caffeine (CAF), a methyl-substituted xanthine, interacts with polyaromatic DNA intercalators and has been hypothesized to interfere with their intercalation into DNA. Optical absorption spectroscopy was used to determine the binding affinities (K(assoc)) and structural effects of a series of methyl-substituted xanthines and a series of methyl-substituted uric acids (8-oxoxanthine) with the known DNA intercalator acridine orange (AO). There is evidence that complexation occurred (K(assoc) > or = 150 M(-1); binding curve saturation approximately > or =50%) between AO and 1,7-dimethylxanthine (155 M(-1)), 1,3-dimethylxanthine (theophylline, 157 M(-1)), 1,3,7-trimethylxanthine (CAF, 256 M(-1)), 1,3-dimethyl-8-chloroxanthine (413 M(-1)), 1,3,7,9-tetramethyl-8-oxyxanthine (tetramethyl uric acid or TMU, 552 M(-1)), and theophylline ethylenediamine (aminophylline, 596 M(-1)). No definitive evidence of complexation occurred between AO and 16 other substituted xanthines or purines, although there was some evidence of weak complexation (K(assoc) < 150 M(-1)) between AO and eight of the sixteen. Three common structural similarities were identified among those compounds found to form significant bonding with AO: (i) the N(1) or N(3) on the xanthine structure must be substituted with a methyl group; (ii) oxygen or chlorine substitution at C(8) increases binding affinity to AO when resonate states remain unchanged; and (iii) K(assoc) increases with an increase in number of methyl group substitutions on the 1- or 3-methylxanthine core structure. These results are explained on the basis of complex stabilization due predominately to hydrophobic attraction, with a contribution from charge transfer between donor and acceptor components. This information can be used in the manipulation of the physical or chemical characteristics of biologically active polyaromatic molecules.
Collapse
Affiliation(s)
- M B Lyles
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA
| | | | | |
Collapse
|
23
|
French DJ, Archard CL, Brown T, McDowell DG. HyBeacon probes: a new tool for DNA sequence detection and allele discrimination. Mol Cell Probes 2001; 15:363-74. [PMID: 11851380 DOI: 10.1006/mcpr.2001.0384] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Technologies that permit rapid investigation of DNA sequences, such as those containing single nucleotide polymorphisms (SNPs), are of great consequence to many sectors that perform molecular diagnostic analyses. We have developed a novel fluorescent oligonucleotide probe technology, termed HyBeacons, which provides a new homogeneous method for fluorescence-based sequence detection, allele discrimination and DNA quantification. Hybridization of HyBeacons to complementary DNA target sequences results in a measurable elevation of probe fluorescence emission. HyBeacon probes may be incorporated into real-time polymerase chain reaction (PCR) assays to detect the presence and monitor the accumulation of specific DNA sequences. Furthermore, closely related sequences differing by as little as a single nucleotide may be discriminated by measuring the melting temperatures (T(m)) of various probe/target duplexes and exploiting the differences in T(m) that exist between different duplexes. We demonstrate here that HyBeacon probes are efficient tools for rapid sequence analysis and that a single probe may be employed to reliably identify homozygous and heterozygous samples. Additional benefits exhibited by the HyBeacon technology derive from their simple mode of action, ease of design, relatively inexpensive synthesis and potential for multiplex analysis.
Collapse
Affiliation(s)
- D J French
- BioAnalytical Innovations, LGC (Teddington) Ltd, Queens Road, Teddington, TW11 0LY, UK.
| | | | | | | |
Collapse
|
24
|
Torimura M, Kurata S, Yamada K, Yokomaku T, Kamagata Y, Kanagawa T, Kurane R. Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base. ANAL SCI 2001; 17:155-60. [PMID: 11993654 DOI: 10.2116/analsci.17.155] [Citation(s) in RCA: 299] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Fluorescently labeled oligonucleotide probes have been widely used in biotechnology, and fluorescence quenching by the interaction between the dyes and a nucleobase has been pointed out. This quenching causes big problem in analytical methods, but is useful in some other cases. Therefore, it is necessary to estimate the fluorescence quenching intensity under various conditions. We focused on the redox properties of some commercially available fluorescent dyes, and investigated dye-nucleotide interactions between a free dye and a nucleotide in aqueous solution by electrochemical and spectroscopic techniques. Our results suggested that the quenching was accompanied by photoinduced electron transfer between a thermodynamically quenchable excited dye and a specific base. Several kinds of fluorescent dyes labeled to the 5'-end of oligonucleotide C10T6 were prepared, and their quenching ratios compared upon hybridization with the complementary oligonucleotide A6G10. The quenching was completely reversible and their efficiencies depended on the attached fluorophore types. The fluorescence of 5-FAM, BODIPY FL or TAMRA-modified probe was strongly quenched by hybridization.
Collapse
Affiliation(s)
- M Torimura
- National Institute of Bioscience and Human Technology, Agency of Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
| | | | | | | | | | | | | |
Collapse
|
25
|
|
26
|
Zou Y, Bassett H, Walker R, Bishop A, Amin S, Geacintov NE, Van Houten B. Hydrophobic forces dominate the thermodynamic characteristics of UvrA-DNA damage interactions. J Mol Biol 1998; 281:107-19. [PMID: 9680479 DOI: 10.1006/jmbi.1998.1903] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli DNA repair proteins UvrA, UvrB and UvrC work together to recognize and incise DNA damage during the process of nucleotide excision repair (NER). To gain an understanding of the damage recognition properties of UvrA, we have used fluorescence spectroscopy to study the thermodynamics of its interaction with a defined DNA substrate containing a benzo[a]pyrene diol epoxide (BPDE) adduct. Oligonucleotides containing a single site-specifically modified N2-guanine (+)-trans-, (-)-trans-, (+)-cis-, or (-)-cis-BPDE adducts were ligated into 50-base-pair DNA fragments. All four stereoisomers of DNA-BPDE adducts show an excitation maximum at 350 nm and an emission maximum around 380 to 385 nm. Binding of UvrA to the BPDE-DNA adducts results in a five to sevenfold fluorescence enhancement. Titration of the BPDE-adducted DNA with UvrA was used to generate binding isotherms. The equilibrium dissociation constants for UvrA binding to (+)-trans-, (-)-trans-, (+)-cis-, and (-)-cis- BPDE adduct were: 7.4+/-1.9, 15. 8+/-5.4, 11.3+/-2.7 and 22.4+/-2.0 nM, respectively. There was a large negative change in heat capacity DeltaCpo,obs, (-3.3 kcal mol-1 K-1) accompanied by a relatively unchanged DeltaGoobs with temperature. Furthermore, varying the concentration of KCl showed that the number of ions released upon formation of UvrA-DNA complex is about 3.4, a relatively small value compared to the contact size of UvrA with the substrate. These data suggest that hydrophobic interactions are an important driving force for UvrA binding to BPDE-damaged DNA.
Collapse
Affiliation(s)
- Y Zou
- Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | | | | | | | | | | | | |
Collapse
|
27
|
Geacintov NE, Solntsev K, Johnson LW, Chen J, Kolbanovskiy AD, Liu T, Shafirovich VY. Photoinduced electron transfer and strand cleavage in pyrenyl-DNA complexes and adducts. J PHYS ORG CHEM 1998. [DOI: 10.1002/(sici)1099-1395(199808/09)11:8/9<561::aid-poc61>3.0.co;2-a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
28
|
Abstract
The interaction of methylene violet (MV) and 4-bromomethylene violet (BrMV) with calf thymus and supercoiled phi X174 phage RF I DNA is reported. Measurements employing UV-visible absorption spectroscopy and equilibrium dialysis give evidence for the formation of complexes by each dye with DNA in the dark. They covalently bind to DNA, and MV nicks DNA, when the nucleic acid/dye mixtures are irradiated with visible light in a deoxygenated environment. Quantum efficiencies for singlet oxygen formation are 0.27 and 0.25 for MV and BrMV, respectively. A higher value (0.49) is observed for 4-iodomethylene violet (IMV).
Collapse
Affiliation(s)
- H Morrison
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-1393, USA
| | | | | |
Collapse
|
29
|
Lewis FD, Zhang Y, Letsinger RL. Bispyrenyl Excimer Fluorescence: A Sensitive Oligonucleotide Probe. J Am Chem Soc 1997. [DOI: 10.1021/ja9641214] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frederick D. Lewis
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208
| | - Yifan Zhang
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208
| | - Robert L. Letsinger
- Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston, Illinois 60208
| |
Collapse
|
30
|
Widengren J, Dapprich J, Rigler R. Fast interactions between Rh6G and dGTP in water studied by fluorescence correlation spectroscopy. Chem Phys 1997. [DOI: 10.1016/s0301-0104(97)00014-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
31
|
Magnetic field effect on triplet formation as a probe of intersystem crossing mechanisms in benzo [a] pyrene diol epoxide derivative-guanosine complexes and covalent adducts. Chem Phys Lett 1994. [DOI: 10.1016/0009-2614(94)00302-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|