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Choi S, Meyer MO, Bevilacqua PC, Keating CD. Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles. Nat Chem 2022; 14:1110-1117. [PMID: 35773489 DOI: 10.1038/s41557-022-00980-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/20/2022] [Indexed: 12/20/2022]
Abstract
Liquid-liquid phase separation has emerged as an important means of intracellular RNA compartmentalization. Some membraneless organelles host two or more compartments serving different putative biochemical roles. The mechanisms for, and functional consequences of, this subcompartmentalization are not yet well understood. Here we show that adjacent phases of decapeptide-based multiphase model membraneless organelles differ markedly in their interactions with RNA. Single- and double-stranded RNAs preferentially accumulate in different phases within the same droplet, and one phase is more destabilizing for RNA duplexes than the other. Single-phase peptide droplets did not capture this behaviour. Phase coexistence introduces new thermodynamic equilibria that alter RNA duplex stability and RNA sorting by hybridization state. These effects require neither biospecific RNA-binding sites nor full-length proteins. As such, they are more general and point to primitive versions of mechanisms operating in extant biology that could aid understanding and enable the design of functional artificial membraneless organelles.
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Affiliation(s)
- Saehyun Choi
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - McCauley O Meyer
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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2
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Bansal A, Phogat P, Kukreti S. A novel G·G·T non-conventional intramolecular triplex formed by the double repeat sequence of Chlamydomonas telomeric DNA. RSC Adv 2022; 12:15918-15924. [PMID: 35733691 PMCID: PMC9134377 DOI: 10.1039/d2ra00861k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
The competition among the DNA non-canonical structures has been widely studied in repetitive DNA sequences. The Chlamydomonas reinhardtii telomere (TTTTAGGG)n is found an exception to the general idea of forming folded G-quadruplex by few repeats of any telomeric sequence.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
- Department of Chemistry, Hansraj College, University of Delhi, (North Campus), Delhi, 110007, India
| | - Priyanka Phogat
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
| | - Shrikant Kukreti
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India
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Bianco PR. Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays. Methods 2021; 204:348-360. [PMID: 34896247 PMCID: PMC9534331 DOI: 10.1016/j.ymeth.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
There are multiple assays available that can provide insight into the biochemical mechanism of DNA helicases. For the first 22 years since their discovery, bulk-phase assays were used. These include gel-based, spectrophotometric, and spectrofluorometric assays that revealed many facets of these enzymes. From 2001, single-molecule studies have contributed additional insight into these DNA nanomachines to reveal details on energy coupling, step size, processivity as well as unique aspects of individual enzyme behavior that were masked in the averaging inherent in ensemble studies. In this review, important aspects of the study of helicases are discussed including beginning with active, nuclease-free enzyme, followed by several bulk-phase approaches that have been developed and still find widespread use today. Finally, two single-molecule approaches are discussed, and the resulting findings are related to the results obtained in bulk-phase studies.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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4
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Affiliation(s)
- Xiao-yan Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Hai-yan Fan
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiao-dong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Shi-lin Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Guang-zhao Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
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5
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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6
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Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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7
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Rao AN, Rodesch CK, Grainger DW. Real-time fluorescent image analysis of DNA spot hybridization kinetics to assess microarray spot heterogeneity. Anal Chem 2012; 84:9379-87. [PMID: 23043216 DOI: 10.1021/ac302165h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current microarray assay technology predominately uses fluorescence as a detectable signal end point. This study assessed real-time in situ surface hybridization capture kinetics for single printed DNA microspots on solid array surfaces using fluorescence. The influence of the DNA target and probe cyanine dye position on oligo-DNA duplex formation behavior was compared in solution versus surface-hybridized single DNA printed spots using fluorescence resonance energy transfer (FRET) analysis. Fluorophore Cy3/Cy5 fluorescence intensities were analyzed both through the printed hybridized DNA spot thickness and radially across single-spot surfaces. Confocal single-spot imaging shows that real-time in situ hybridization kinetics with constant target concentrations changes as a function of the printed probe density. Target-specific imaging in single spots exhibits a heterogeneous printed probe radial density that influences hybridization spatially and temporally via radial hemispherical diffusion of dye-labeled target from the outside edge of the spot to the interior. FRET of the surface-captured target occurs irrespective of the probe/target fluorophore position, resulting from excess printed probe density and spot thickness. Both heterogeneous probe density distributions in printed spots and the fluorophore position on short DNA oligomers influence duplex formation kinetics, hybridization efficiencies, and overall fluorescence intensity end points in surface-capture formats. This analysis is important to understanding, controlling, and quantifying the array assay signal essential to reliable application of the surface-capture format.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, School of Medicine, University of Utah, Salt Lake City, Utah 84112, United States
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Affiliation(s)
- Yuichi Ohya
- a Department of Applied Chemistry, Faculty of Engineering and High Technology Research Center , Kansai University , Suita, 564-8680, Osaka, Japan
| | - Kentaro Yabuki
- a Department of Applied Chemistry, Faculty of Engineering and High Technology Research Center , Kansai University , Suita, 564-8680, Osaka, Japan
| | - Motonari Tokuyama
- a Department of Applied Chemistry, Faculty of Engineering and High Technology Research Center , Kansai University , Suita, 564-8680, Osaka, Japan
| | - Tatsuro Ouchi
- a Department of Applied Chemistry, Faculty of Engineering and High Technology Research Center , Kansai University , Suita, 564-8680, Osaka, Japan
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9
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Gbaj A, Bichenkova E, Walsh L, Savage H, Sardarian A, Etchells L, Gulati A, Hawisa S, Douglas K. New concepts of fluorescent probes for specific detection of DNA sequences: bis-modified oligonucleotides in excimer and exciplex detection. Libyan J Med 2009; 4:152-9. [PMID: 21483539 PMCID: PMC3066750 DOI: 10.4176/090801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The detection of single base mismatches in DNA is important for diagnostics, treatment of genetic diseases, and identification of single nucleotide polymorphisms. Highly sensitive, specific assays are needed to investigate genetic samples from patients. The use of a simple fluorescent nucleoside analogue in detection of DNA sequence and point mutations by hybridisation in solution is described in this study. The 5′-bispyrene and 3′-naphthalene oligonucleotide probes form an exciplex on hybridisation to target in water and the 5′-bispyrene oligonucleotide alone is an adequate probe to determine concentration of target present. It was also indicated that this system has a potential to identify mismatches and insertions. The aim of this work was to investigate experimental structures and conditions that permit strong exciplex emission for nucleic acid detectors, and show how such exciplexes can register the presence of mismatches as required in SNP analysis. This study revealed that the hybridisation of 5′-bispyrenyl fluorophore to a DNA target results in formation of a fluorescent probe with high signal intensity change and specificity for detecting a complementary target in a homogeneous system. Detection of SNP mutations using this split-probe system is a highly specific, simple, and accessible method to meet the rigorous requirements of pharmacogenomic studies. Thus, it is possible for the system to act as SNP detectors and it shows promise for future applications in genetic testing.
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Affiliation(s)
- A Gbaj
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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10
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Abstract
We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays.
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Affiliation(s)
- Arjang Hassibi
- Institute for Cellular and Molecular Biology, University of Texas at Austin, TX 78712, USA.
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11
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Li F, Hou B, Chen L, Yao Z, Hong G. In vitroobservation of the molecular interaction between NodD and its inducer naringenin as monitored by fluorescence resonance energy transfer. Acta Biochim Biophys Sin (Shanghai) 2008. [DOI: 10.1111/j.1745-7270.2008.00462.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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Gbaj A, Bichenkova E, Walsh L, Savage H, Sardarian A, Etchells L, Gulati A, Hawisa S, Douglas K. New Concepts of Fluorescent Probes for Specific Detection of DNA Sequences: Bis-Modified Oligonucleotides in Excimer and Exciplex Detection. Libyan J Med 2008. [DOI: 10.3402/ljm.v4i4.4841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Gbaj
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
- National Centre for Medical Research, Zawia-Libya
| | - E.V. Bichenkova
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - L. Walsh
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - H.E. Savage
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - A.R. Sardarian
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
- Present address; Department of Chemistry, Shiraz University, Shiraz, Iran and
| | - L.L. Etchells
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - A. Gulati
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
| | - S. Hawisa
- National Centre for Medical Research, Zawia-Libya
| | - K.T. Douglas
- Wolfson Centre for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, UK
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Barken KB, Haagensen JAJ, Tolker-Nielsen T. Advances in nucleic acid-based diagnostics of bacterial infections. Clin Chim Acta 2007; 384:1-11. [PMID: 17689512 DOI: 10.1016/j.cca.2007.07.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 05/23/2007] [Accepted: 07/02/2007] [Indexed: 11/25/2022]
Abstract
Methods for rapid detection of infectious bacteria and antimicrobial-resistant pathogens have evolved significantly over the last decade. Many of the new procedures are nucleic acid-based and replace conventional diagnostic methods like culturing which is time consuming especially with fastidious and slow growing microorganisms. The widespread use of antibiotics has resulted in an increased number of cases with resistant microorganisms such as methicillin-resistant Staphylococcus aureus, vancomycin resistant enterococci, and multidrug-resistant Mycobacterium tuberculosis. Rapid detection of these pathogens is important to isolate patients and prevent further spreading of the diseases. Newly developed diagnostic procedures are superior with respect to turnaround time, sensitivity and specificity. Methods like multiplex real time PCR and different array-based technologies offer the possibility of multiparameter assays where several pathogens and antibiotic resistance genes can be detected simultaneously.
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Affiliation(s)
- Kim B Barken
- Centre for BioScience and Technology, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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14
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Korshun VA, Balakin KV, Proskurina TS, Mikhalev II, Malakhov AD, Berlin YA. A Pyrene Seco-Pseudonucleoside in Constructing Interaction-Sensitive Fluorescent DNA Probes. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044632] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Vladimir A. Korshun
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
| | - Konstantin V. Balakin
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
| | - Tatyana S. Proskurina
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
| | - Ilya I. Mikhalev
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
| | - Andrei D. Malakhov
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
| | - Yuri A. Berlin
- a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , ul. Miklukho-Maklaya 16/10, GSP-7 Moscow , 117871 , Russia Fax: E-mail:
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Vijayanathan V, Thomas TJ, Nair SK, Shirahata A, Gallo MA, Thomas T. Bending of the estrogen response element by polyamines and estrogen receptors alpha and beta: a fluorescence resonance energy transfer study. Int J Biochem Cell Biol 2006; 38:1191-1206. [PMID: 16767802 DOI: 10.1016/j.biocel.2005.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Estrogenic regulation of gene expression is mediated by the binding of the hormone to its receptors (ERalpha and ERbeta) followed by their binding to estrogen response element (ERE). Previous studies showed that natural polyamines -- putrescine, spermidine, and spermine -- facilitated ERalpha.ERE recognition. We determined the effects of natural and synthetic polyamines on the bending of a 27-mer oligonucleotide (ODN) harboring the ERE (ERE-ODN), using fluorescence resonance energy transfer (FRET) technique. Complementary strands of the ERE-ODN were labeled with fluorescein and tetramethylrhodamine, as donor and acceptor, respectively. The ERE-ODN was intrinsically bent with an end-to-end distance of 76 +/- 2 Angstrom, compared to a theoretical value of 98 Angstrom. The end-to-end distance of the ERE-ODN was reduced to 64 Angstrom in the presence of 250 microM spermine. A control ODN with scrambled sequence did not show intrinsic bending or spermine-induced bending. Alkyl substitution at the pendant amino groups reduced the ability of spermine to bend the ERE-ODN. Both ERalpha and ERbeta decreased the end-to-end distance of the ERE-ODN, although ERalpha was more efficient than ERbeta in inducing ERE bending. Spermine-induced bending of the ERE-ODN was significantly increased by ERalpha. Fluorescence anisotropy measurement showed that the equilibrium association constant of ERalpha-ERE binding increased by 12-fold in the presence of 250 microM spermine compared to control. The free energy change (Delta G) of ERalpha.ERE complex formation was -13.1 kcal/mol at 22 degrees C in the presence of spermine. Our results suggest that polyamine-induced bending of the ERE might be a mechanism for enhancing ERalpha-ERE binding affinity and thereby fine-tuning the transcriptional response of estrogen-responsive genes.
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Affiliation(s)
- Veena Vijayanathan
- Department of Medicine, University of Medicine and Dentistry of New Jersey--Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
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Mahara A, Iwase R, Sakamoto T, Yamaoka T, Yamana K, Murakami A. Detection of acceptor sites for antisense oligonucleotides on native folded RNA by fluorescence spectroscopy. Bioorg Med Chem 2003; 11:2783-90. [PMID: 12788352 DOI: 10.1016/s0968-0896(03)00227-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Antisense strategy has high potential for curing diseases and studying gene functions by suppressing the translation step. For the strategy, it is essential to detect acceptor sites of antisense molecules on mRNA under physiological conditions. We propose a new analytical method for the detection of acceptor sites of antisense molecules with high sensitivity. 2'-O-Methyloligoribonucleotide containing 2'-O-(1-pyrenylmethyl)uridine (OMUpy) was chosen as the fluorescence probe. The fluorescence intensity due to the pyrene in single-stranded OMUpy was scarcely observed. When OMUpy was hybridized with the complementary oligoRNA, the fluorescence intensity at 375 nm was remarkably increased. It was found that the increase was derived from the localization of the pyrene by the measurements of time-resolved fluorescence spectroscopy, CD and UV absorption spectra. These results suggest that the change of the fluorescence intensity of OMUpy can be a useful index to monitor hybridization. In this study, we chose Escherichia coli. 16S-rRNA as the model RNA and chose seven regions for probing by OMUpy based on the reported secondary structure of 16S-rRNA. The fluorescence intensity of an equimolar mixture of OMUpy with 16S-rRNA varied depending on the sequence. In particular, the increment in the system of OMUpy-8, which can hybridize with region 887-896 nt of 16S-rRNA, was most significant among the systems. These results indicated that the site targeted by OMUpy-8 was exposed to regulatory molecules, and suggest that the method presented here is useful to design antisense molecules.
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Affiliation(s)
- Atsushi Mahara
- Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
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17
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Onuki R, Nagasaki A, Kawasaki H, Baba T, Uyeda TQP, Taira K. Confirmation by FRET in individual living cells of the absence of significant amyloid beta -mediated caspase 8 activation. Proc Natl Acad Sci U S A 2002; 99:14716-21. [PMID: 12409609 PMCID: PMC137485 DOI: 10.1073/pnas.232177599] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
When cells are exposed to death-inducing molecules such as tumor necrosis factor-alpha or Fas, caspase 8 is activated and cleaves an apoptotic facilitator, Bid, that is a member of the Bcl-2 family. After additional modification, the C-terminal moiety of Bid is translocated to the mitochondria and induces the release of cytochrome c into the cytoplasm. In an attempt to directly observe the cleavage of Bid and the following events in living cells, we constructed a vector that encoded Bid fused with yellow fluorescent protein (YFP) and cyan fluorescent protein (CFP) (YFP-Bid-CFP). On expression of YFP-Bid-CFP in mammalian cells, we were able to observe the efficient transfer of energy from excited CFP to YFP within the YFP-Bid-CFP molecule and, importantly, the fusion protein YFP-Bid-CFP was fully functional in cells. When YFP-Bid-CFP was cleaved by caspase 8, on activation by anti-Fas Abs but not by Abeta or tunicamycin, no such transfer of energy was detected. To our knowledge, this is the first report of (i) visualization of the activation of Bid by proteolytic cleavage, with direct observation of the cleavage of YFP-Bid-CFP in the cytoplasm and subsequent translocation of the cleaved Bid to mitochondria and (ii) the absence of Abeta- or tunicamycin-mediated significant activation of caspase 8 in individual living cells.
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Affiliation(s)
- Reiko Onuki
- Gene Function Research Laboratory, National Institute of Advanced Industrial Science and Technology, Central 4, 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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Yamana K, Iwai T, Ohtani Y, Sato S, Nakamura M, Nakano H. Bis-pyrene-labeled oligonucleotides: sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA. Bioconjug Chem 2002; 13:1266-73. [PMID: 12440862 DOI: 10.1021/bc025530u] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and properties of a new pyrene excimer-forming probe of DNA have been described. 2,2-(Aminomethyl)propanediol was converted by the reaction with 1-pyrenebutylic acid to bis-pyrene-modified propanediol as a fluorescent non-nucleosidic linker. The bis-pyrene-modified linker can be incorporated via phosphoramidite chemistry into the 5'-terminal or internal positions of oligonucleotides (ODNs). The terminally modified ODNs showed almost similar affinity for complementary DNA when compared with the corresponding unmodified ODNs. The duplexes containing the bis-pyrene in the main chain exhibited higher melting temperatures relative to the corresponding duplexes containing propanediol linker at the same position. The UV and CD spectral studies indicate that the stacking interactions between the pyrene and DNA bases occur in the internally modified duplex and do not in the terminally modified duplex. The bis-pyrene modified linker itself displays excimer (E at 480 nm) and monomer (M at 380 nm) emission in a quantum yield (QY) of 0.17 and the E/M intensity ratio of 15. Incorporation of this linker into the terminal or internal positions of ODNs reduced the QY (0.003-0.009) and the E/M ratio (0.3-0.8). While small changes in the QY and E/M ratio was obtained in binding of the internally labeled ODNs to DNA, up to 27-fold increase in the QY and 17-fold increase in the E/M ratio was observed upon hybridization of the terminally labeled ODNs with DNA. The excimer and monomer fluorescence changes were found to be sensitive to a mismatch base present in the target DNA. The bis-pyrene-modified ODNs thus provide a sequence-sepcific fluorescent probe of DNA.
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Affiliation(s)
- Kazushige Yamana
- Department of Applied Chemistry, Himeji Institute of Technology, 2167 Shosha, Himeji, Hyogo 671-2201, Japan.
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Malicka J, Gryczynski I, Kusba J, Shen Y, Lakowicz JR. Effects of metallic silver particles on resonance energy transfer in labeled bovine serum albumin. Biochem Biophys Res Commun 2002; 294:886-92. [PMID: 12061790 PMCID: PMC2737421 DOI: 10.1016/s0006-291x(02)00555-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Resonance energy transfer (RET) is widely used to detect proximity between biomolecules. In transparent solution the maximum donor-to-acceptor distance for RET is about 70 A. We measured the effects of metallic silver island films on RET from the intrinsic tryptophan of a protein to a bound probe as the acceptor. These preliminary experiments revealed a dramatic increase in the apparent Förster distance increasing from 28.6 to 63 A. These results suggest the use of silver island films for detecting long range proximity between biomolecules and for biotechnology applications based on RET.
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Kang JS, Piszczek G, Lakowicz JR. Enhanced Emission Induced by FRET from a Long-Lifetime, Low Quantum Yield Donor to a Long-Wavelength, High Quantum Yield Acceptor. J Fluoresc 2002; 12:97-103. [PMID: 32148386 DOI: 10.1023/a:1015375622992] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report observation of high quantum yield, long-lifetime fluorescence from a red dye BO-PRO-3 excited by resonance energy transfer (RET). The acceptor fluorescence was highly enhanced upon binding to the donor-labeled DNA. A ruthenium complex (Ru) was chosen as a donor in this system because of its long fluorescence lifetime. Both donor and acceptor were non-covalently bound to DNA. Emission from the donor-acceptor system (DA) at wavelengths exceeding 600 nm still preserves the long-lifetime component of the Ru donor, retaining average fluorescence lifetimes in the range of 30-50 ns. Despite the low quantum yield of the Ru donor in the absence of acceptor, its overall quantum yield of the DA pair was increased by energy transfer to the higher quantum yield acceptor BO-PRO-3. The wavelength-integrated intensity of donor and acceptor bound to DNA was many-fold greater than the intensity of the donor and acceptor separately bound to DNA. The origin of this effect is due to an efficient energy transfer from the donor, competing with non-radiative depopulation of the donor excited state. The distinctive features of DA complexes can be used in the development of a new class of engineered luminophores that display both long lifetime and long-wavelength emission. Similar DA complexes can be applied as proximity indicators, exhibiting strong fluorescence of adjacently located donors and acceptors over the relatively weak fluorescence of separated donors and acceptors.
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Affiliation(s)
- Jung Sook Kang
- Department of Oral Biochemistry and Molecular Biology, College of Dentistry, Pusan National University, Pusan 602-739, Korea
| | - Grzegorz Piszczek
- Institute of Experimental Physics, University of Gdańsk, ul. Wita Stwosza 57, 80-952, Gdańsk, Poland
| | - Joseph R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, 725 West Lombard Street, Baltimore, MD 21201.,To whom correspondence should be addressed
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21
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Abstract
Fluorescence resonance energy transfer studies allow to determine global shape properties of nucleic acids and nucleoprotein complexes. In many DNA-protein complexes, the DNA is more or less bent and the degree of bending can be obtained by FRET. For example, the DNA in complex with the integration host factor (IHF) is kinked by approximately 160 degrees building a U-shaped structure. The two DNA helix ends come close to one another in space in a distance range easily measurable by FRET. The global DNA structure of this complex can be mimicked by introducing two regions with unpaired bases ('bulges') into the DNA each producing a sharp kink of approximately 80 degrees. These U-shaped DNA constructs were used to measure the electrostatic interaction of the two nearly parallel negatively charged DNA helix arms. The electrostatic repulsion between the helix arms, and as a consequence their distance, decreases with growing salt concentration of mono- or divalent cations. This experimental approach also allows the sensitive study of the local structure of DNA sequences positioned between the two bulges.
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Affiliation(s)
- Mike Lorenz
- Institut für Molekulare Biotechnologie, Jena, Germany
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22
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Ota N, Sato T, Taira K, Ohkawa J. Molecular tryst peeping: detection of interactions between nonlabeled nucleic acids by fluorescence resonance energy transfer. Biochem Biophys Res Commun 2001; 289:1067-74. [PMID: 11741300 DOI: 10.1006/bbrc.2001.6098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed a new method for monitoring the interactions between nonlabeled RNAs that involves detection of fluorescence resonance energy transfer (FRET) between two DNA probes with different fluorescent label. The sequences of the probes are complementary to those of the RNAs. In this study, we examined the interaction between a portion of the LTR RNA of HIV-1 and the corresponding antisense RNA. The antisense RNA was designed not to bind to the fluorescent DNA without prior hybridization to the target RNA. A mixture of RNAs and DNA probes with fluorescent labels was fractionated by electrophoresis on a nondenaturing polyacrylamide gel and then the gel was analyzed with a fluorescence imaging analyzer. FRET was observed only in the presence of target RNA, antisense RNA, and both of the fluorescent DNA probes. This strategy should be useful for the detection of interactions between nucleic acids that cannot be subjected to chemical modification, such as RNA transcripts inside cells.
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Affiliation(s)
- N Ota
- Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku, Yokohama, 223-8522, Japan
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23
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Abstract
In polyacrylamide gels, we have quantitatively determined Forster transfer (fluorescense resonance energy transfer, FRET) between two fluorescent dyes attached to DNA in protein-DNA complexes. The donor-dye fluorescein labeled to DNA retains its free mobility in the polyacrylamide gel, however, its fluorescence properties change. The different quantum yield of fluorescein in the gel is found to be independent of the gel concentration and can thus be quantitatively taken into account by a reduced Forster distance R0 of 46 A compared to 50 A in solution. We have determined global structural properties of two proteins binding to double-labeled DNA using a novel gel-based fluorescence resonance energy transfer assay. In polyacrylamide gels we have analyzed the binding of integration host factor (IHF) and the high mobility group protein NHP6a to their substrate DNA. The measured Forster transfer efficiency allows us to deduce information on the overall shape and the DNA bending angle in the complex.
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Affiliation(s)
- M Lorenz
- Department of Molecular Biology, Institute for Molecular Biotechnology, Jena, Germany
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24
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Affiliation(s)
- S Hashimoto
- Departments of Chemistry and Biology University of Virginia, Charlottesville, Virginia 22901, USA
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25
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Abstract
Fluorescence resonance energy transfer (FRET) provides information on the distance between a donor and an acceptor dye in the range 10 to 100 A. Knowledge of the exact positions of some dyes with respect to nucleic acids now enables us to translate these data into precise structural information using molecular modeling. Advances in the preparation of dye-labeled nucleic acid molecules and in new techniques, such as the measurement of FRET in polyacrylamide gels or in vivo, will lead to an increasingly important role of FRET in structural and molecular biology.
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Affiliation(s)
- A Hillisch
- EnTec GmbH, Adolf-Reichwein-Strasse 20, D-07745 Jena, Germany.
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26
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Matsuo H, Okamura T, Chen J, Takanaga H, Ohtani H, Kaneda Y, Naito M, Tsuruo T, Sawada Y. Efficient introduction of macromolecules and oligonucleotides into brain capillary endothelial cells using HVJ-liposomes. J Drug Target 2001; 8:207-16. [PMID: 11144231 DOI: 10.3109/10611860008997899] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we examined the feasibility of introducing macromolecules into cultured mouse brain capillary endothelial cells (MBEC4 cells) by utilizing the hemagglutating virus of Japan (HVJ)-liposomes with fusogenic activity. We used fluorescein isothiocyanate dextran (FITC-Dextran) and FITC-labeled oligodeoxynucleotide (FITC-ODN) as models of a macromolecule and an ODN, respectively. Intracellular fluorescence appeared rapidly after the exposure of MBEC4 cells to FITC-Dextran-containing HVJ-liposomes, and remained detectable for at least 3 days. Only a control level of intracellular fluorescence was seen after treatment with FITC-Dextran alone, FITC-Dextran with empty HVJ-liposomes or FITC-Dextran-containing liposomes without fusogenic activity. In the early phase after administration (0-30 min), the introduction of FITC-Dextran into MBEC4 cells by the HVJ-liposome method resulted in a rapid and time-dependent increase of intracellular fluorescence intensity. Moreover, FITC-ODN was also introduced into MBEC4 cells by the HVJ-liposome method, although FITC-ODN alone was not introduced. These results indicate that the HVJ-liposome method is useful for the efficient introduction of macromolecules, including ODN, into brain capillary endothelial cells.
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Affiliation(s)
- H Matsuo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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27
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Abstract
Fluorescence resonance energy transfer (FRET) results from nonradiative coupling of two fluorophores and reports on distances in the range 10-100 A. It is therefore a suitable probe to determine distances in RNA molecules and define their global structure, to follow kinetics of RNA conformational changes during folding in real time, to monitor ion binding, or to analyze conformational equilibria and assess the thermodynamic stability of tertiary structure conformers. Along with the basic principles of steady-state and time-resolved fluorescence resonance energy transfer measurements, approaches to investigate RNA conformational transitions and folding are described and illustrated with selected examples. The versatility of FRET-based techniques has recently been demonstrated by implementations of FRET in high-throughput screening of potential drugs as well as studies of energy transfer that monitor RNA conformational changes on the single-molecule level.
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Affiliation(s)
- D Klostermeier
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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28
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Abstract
We describe an approach to creating a new class of luminophores which display both long wavelength emissions exceeding 600 nm and long lifetimes. These luminophores are based on resonance energy transfer (RET) from a long lifetime donor to a short lifetime but long wavelength acceptor. We demonstrated the possibility of obtaining these desirable spectral properties using donors and acceptors noncovalently bound to DNA. The donor was a ruthenium (Ru) metal-ligand complex in which one of the diimine ligands intercalated into double-helix DNA. The acceptors were either nile blue, TOTO-3, or TO-PRO-3. Upon binding of the acceptor to donor-labeled DNA, we found that the acceptor quantum yield was remarkably enhanced so that the wavelength-integrated intensities of the donor and acceptor bound to DNA were many-fold greater than the intensity of the donor and acceptor alone when separately bound to DNA. The origin of this effect is efficient energy transfer from the donor. Under these conditions the effective overall quantum yield approaches that of the acceptor. Importantly, the increased quantum yield can be obtained while maintaining usefully long apparent acceptor lifetimes of 30 to 80 ns. The effect of an increased quantum yield from a low quantum yield donor may find use in assays to detect macromolecular binding interactions. These results suggest the synthesis of covalently linked donor-acceptor pairs with the desirable spectral properties of long wavelength emission, high quantum yield, and moderately long lifetimes for gated detection.
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Affiliation(s)
- J R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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29
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Okamura Y, Kondo S, Sase I, Suga T, Mise K, Furusawa I, Kawakami S, Watanabe Y. Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res 2000; 28:E107. [PMID: 11121494 PMCID: PMC115251 DOI: 10.1093/nar/28.24.e107] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A set of fluorescently-labeled DNA probes that hybridize with the target RNA and produce fluorescence resonance energy transfer (FRET) signals can be utilized for the detection of specific RNA. We have developed probe sets to detect and discriminate single-strand RNA molecules of plant viral genome, and sought a method to improve the FRET signals to handle in vivo applications. Consequently, we found that a double-labeled donor probe labeled with Bodipy dye yielded a remarkable increase in fluorescence intensity compared to a single-labeled donor probe used in an ordinary FRET. This double-labeled donor system can be easily applied to improve various FRET probes since the dependence upon sequence and label position in enhancement is not as strict. Furthermore this method could be applied to other nucleic acid substances, such as oligo RNA and phosphorothioate oligonucleotides (S-oligos) to enhance FRET signal. Although the double-labeled donor probes labeled with a variety of fluorophores had unexpected properties (strange UV-visible absorption spectra, decrease of intensity and decay of donor fluorescence) compared with single-labeled ones, they had no relation to FRET enhancement. This signal amplification mechanism cannot be explained simply based on our current results and knowledge of FRET. Yet it is possible to utilize this double-labeled donor system in various applications of FRET as a simple signal-enhancement method.
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Affiliation(s)
- Y Okamura
- Laboratory of Molecular Biophotonics, 5000 Hirakuchi, Hamakita, Shizuoka 434-8555, Japan
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30
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Abstract
Fluorescence resonance energy transfer is a spectroscopic method that provides distance information on macromolecules in solution in the range 20-80 A. It is particularly suited to the analysis of the global structure of nucleic acids because the long-range distance information provides constraints when modelling these important structures. The application of fluorescence resonance energy transfer to nucleic acid structure has seen a resurgence of interest in the past decade, which continues to increase. An especially exciting development is the recent extension to single-molecule studies.
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Affiliation(s)
- D M Lilley
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 4HN, UK.
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31
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Ishida K, Zhu BL, Maeda H. Novel approach to quantitative reverse transcription PCR assay of mRNA component in autopsy material using the TaqMan fluorogenic detection system: dynamics of pulmonary surfactant apoprotein A. Forensic Sci Int 2000; 113:127-31. [PMID: 10978613 DOI: 10.1016/s0379-0738(00)00252-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel approach to quantitative reverse transcription (RT)-PCR assay of mRNA component using fluorescent TaqMan methodology and a new instrument (ABI Prism 7700 sequence detection system) was developed for autopsy materials. Pulmonary surfactant apoprotein A (SP-A) mRNA from a cadaveric lung was quantitated in real-time. The target SP-A gene and the endogenous reference of glyceraldehyde-3-phosphate (GAPDH) were amplified in the same tube, and an amount of the target was normalized to the reference. This assay had a high reproducibility and discrimination even in forensic autopsy materials up to 96 h postmortem. Elevated SP-A expressions were determined in some cases. This system without post-PCR sample handling would be a very useful tool in pathological diagnosis and DNA analysis.
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Affiliation(s)
- K Ishida
- Department of Legal Medicine, Osaka City University Medical School Asahi-machi 1-4-3, Abeno, 545-8585, Osaka, Japan.
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32
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Ying L, Wallace MI, Balasubramanian S, Klenerman D. Ratiometric Analysis of Single-Molecule Fluorescence Resonance Energy Transfer Using Logical Combinations of Threshold Criteria: A Study of 12-mer DNA. J Phys Chem B 2000. [DOI: 10.1021/jp993914k] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liming Ying
- The Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Mark I. Wallace
- The Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - Shankar Balasubramanian
- The Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
| | - David Klenerman
- The Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW United Kingdom
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33
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34
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Abstract
BACKGROUND Chronic myelogenous leukemia (CML) results from chromosome 22 translocations (the Philadelphia chromosome) that creates BCR-ABL fusion genes, which encode two abnormal mRNAs (b3a2 and b2a2). Various attempts to design antisense oligonucleotides that specifically cleave abnormal L6 BCR-ABL fusion mRNA have not been successful. Because b2a2 mRNA cannot be effectively cleaved by hammerhead ribozymes near the BCR-ABL junction, it has proved very difficult to engineer specific cleavage of this chimeric mRNA. Nonspecific effects associated with using antisense molecules make the use of such antisense molecules questionable. RESULTS The usefulness of DNA enzymes in specifically suppressing expression of L6 BCR-ABL mRNA in mammalian cells is demonstrated. Although the efficacy of DNA enzymes with natural linkages decreased 12 hours after transfection, partially modified DNA enzymes, with either phosphorothioate or 2'-O-methyl groups at both their 5' and 3' ends, remained active for much longer times in mammalian cells. Moreover, the DNA enzyme with only 2'-O-methyl modifications was also highly specific for abnormal mRNA. CONCLUSIONS DNA enzymes with 2'-O-methyl modifications are potentially useful as gene-inactivating agents in the treatment of diseases such as CML. In contrast to conventional antisense DNAs, some of the DNA enzymes used in this study were highly specific and cleaved only abnormal BCR-ABL mRNA.
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MESH Headings
- Cells, Cultured
- Enzyme Stability
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Genes, Reporter
- HeLa Cells
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Oligodeoxyribonucleotides/chemical synthesis
- Oligodeoxyribonucleotides/metabolism
- Philadelphia Chromosome
- RNA, Messenger/metabolism
- Substrate Specificity
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Affiliation(s)
- M Warashina
- National Institute for Advanced Interdisciplinary Research, AIST, Tsukuba Science City 305-8562, Japan
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