1
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Le HN, Kuchlyan J, Baladi T, Albinsson B, Dahlén A, Wilhelmsson LM. Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue. Chemistry 2024:e202303539. [PMID: 38230625 DOI: 10.1002/chem.202303539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
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Affiliation(s)
- Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Tom Baladi
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Anders Dahlén
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
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2
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Sundar Rajan V, Wypijewska Del Nogal A, Levin S, Wilhelmsson LM, Westerlund F. Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues. Nanoscale 2024; 16:752-764. [PMID: 38087988 PMCID: PMC10763987 DOI: 10.1039/d3nr04110g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/06/2023] [Indexed: 01/04/2024]
Abstract
The parasitic nature of the SARS-CoV-2 virus demands selective packaging of its RNA genome (gRNA) from the abundance of other nucleic acids present in infected cells. Despite increasing evidence that stem-loop 4 (SL4) of the gRNA 5' UTR is involved in the initiation of this process by binding the nucleocapsid (N) protein, little is known about its conformational dynamics. Here, we unravel the stability, dynamics and (un)folding pathways of SL4 using optical tweezers and a base analogue, tCO, that provides a local and subtle increase in base stacking without perturbing hydrogen bonding. We find that SL4 (un)folds mainly in a single step or through an intermediate, encompassing nucleotides from the central U bulge to the hairpin loop. Due to an upper-stem CU mismatch, SL4 is prone to misfold, the extent of which can be tuned by incorporating tCO at different positions. Our study contributes to a better understanding of SARS-CoV-2 packaging and the design of drugs targeting SL4. We also highlight the generalizability of using base analogues in optical tweezers experiments for probing intramolecular states and conformational transitions of various nucleic acids at the level of single molecules and with base-pair resolution.
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Affiliation(s)
- Vinoth Sundar Rajan
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
- Division of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Anna Wypijewska Del Nogal
- Division of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Sune Levin
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - L Marcus Wilhelmsson
- Division of Chemistry and Biochemistry, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
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3
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Nilsson JR, Benitez-Martin C, Sansom HG, Pfeiffer P, Baladi T, Le HN, Dahlén A, Magennis SW, Wilhelmsson LM. Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA. Phys Chem Chem Phys 2023. [PMID: 37475592 DOI: 10.1039/d3cp01147j] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, however, is that they typically require excitation in the UV region, which for imaging in biological samples may have disadvantages related to phototoxicity, tissue penetration, and out-of-focus photobleaching. Multiphoton excitation has the potential to alleviate these issues and therefore, in this work, we characterize the multiphoton absorption properties and detectability of the highly fluorescent quadracyclic adenine analogue 2CNqA as a ribonucleotide monomer as well as incorporated, at one or two positions, into a 16mer antisense oligonucleotide (ASO). We found that 2CNqA has a two-photon absorption cross section that, among FBAs, is exceptionally high, with values of σ2PA(700 nm) = 5.8 GM, 6.8 GM, and 13 GM for the monomer, single-, and double-labelled oligonucleotide, respectively. Using fluorescence correlation spectroscopy, we show that the 2CNqA has a high 2P brightness as the monomer and when incorporated into the ASO, comparing favorably to other FBAs. We furthermore demonstrate the usefulness of the 2P imaging mode for improving detectability of 2CNqA-labelled ASOs in live cells.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Carlos Benitez-Martin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Henry G Sansom
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Tom Baladi
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hoang-Ngoan Le
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
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4
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Mahale S, Setia M, Prajapati B, Subhash S, Yadav MP, Thankaswamy Kosalai S, Deshpande A, Kuchlyan J, Di Marco M, Westerlund F, Wilhelmsson LM, Kanduri C, Kanduri M. HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells. Nat Commun 2022; 13:4865. [PMID: 36038571 PMCID: PMC9424213 DOI: 10.1038/s41467-022-32537-0] [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: 05/13/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
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Affiliation(s)
- Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Meenakshi Setia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bharat Prajapati
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Ananya Deshpande
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
| | - Meena Kanduri
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
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5
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Sundar Rajan V, Viader-Godoy X, Lin YL, Dutta U, Ritort F, Westerlund F, Wilhelmsson LM. Mechanical characterization of base analogue modified nucleic acids by force spectroscopy. Phys Chem Chem Phys 2021; 23:14151-14155. [PMID: 34180930 PMCID: PMC8261857 DOI: 10.1039/d1cp01985f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We use mechanical unfolding of single DNA hairpins with modified bases to accurately assess intra- and intermolecular forces in nucleic acids. As expected, the modification stabilizes the hybridized hairpin, but we also observe intriguing stacking interactions in the unfolded hairpin. Our study highlights the benefit of using base-modified nucleic acids in force-spectroscopy.
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Affiliation(s)
- Vinoth Sundar Rajan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden.
| | - Xavier Viader-Godoy
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/Marti i Franques 1, Barcelona 08028, Spain
| | - Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden.
| | - Uttama Dutta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden.
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/Marti i Franques 1, Barcelona 08028, Spain
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Sweden.
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden.
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6
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Nilsson JR, Baladi T, Gallud A, Baždarević D, Lemurell M, Esbjörner EK, Wilhelmsson LM, Dahlén A. Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics. Sci Rep 2021; 11:11365. [PMID: 34059711 PMCID: PMC8166847 DOI: 10.1038/s41598-021-90629-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dženita Baždarević
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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7
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Bood M, Del Nogal AW, Nilsson JR, Edfeldt F, Dahlén A, Lemurell M, Wilhelmsson LM, Grøtli M. Interbase-FRET binding assay for pre-microRNAs. Sci Rep 2021; 11:9396. [PMID: 33931703 PMCID: PMC8087795 DOI: 10.1038/s41598-021-88922-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
The aberrant expression of microRNAs (miRs) has been linked to several human diseases. A promising approach for targeting these anomalies is the use of small-molecule inhibitors of miR biogenesis. These inhibitors have the potential to (i) dissect miR mechanisms of action, (ii) discover new drug targets, and (iii) function as new therapeutic agents. Here, we designed Förster resonance energy transfer (FRET)-labeled oligoribonucleotides of the precursor of the oncogenic miR-21 (pre-miR-21) and used them together with a set of aminoglycosides to develop an interbase-FRET assay to detect ligand binding to pre-miRs. Our interbase-FRET assay accurately reports structural changes of the RNA oligonucleotide induced by ligand binding. We demonstrate its application in a rapid, qualitative drug candidate screen by assessing the relative binding affinity between 12 aminoglycoside antibiotics and pre-miR-21. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were used to validate our new FRET method, and the accuracy of our FRET assay was shown to be similar to the established techniques. With its advantages over SPR and ITC owing to its high sensitivity, small sample size, straightforward technique and the possibility for high-throughput expansion, we envision that our solution-based method can be applied in pre-miRNA–target binding studies.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Anna Wypijewska Del Nogal
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Fredrik Edfeldt
- Structure & Biophysics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, 412 96, Gothenburg, Sweden.
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8
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Baladi T, Nilsson JR, Gallud A, Celauro E, Gasse C, Levi-Acobas F, Sarac I, Hollenstein MR, Dahlén A, Esbjörner EK, Wilhelmsson LM. Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery. J Am Chem Soc 2021; 143:5413-5424. [PMID: 33797236 PMCID: PMC8154517 DOI: 10.1021/jacs.1c00014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Indexed: 12/15/2022]
Abstract
![]()
Methods for tracking
RNA inside living cells without perturbing
their natural interactions and functions are critical within biology
and, in particular, to facilitate studies of therapeutic RNA delivery.
We present a stealth labeling approach that can efficiently, and with
high fidelity, generate RNA transcripts, through enzymatic incorporation
of the triphosphate of tCO, a fluorescent tricyclic cytosine
analogue. We demonstrate this by incorporation of tCO in
up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding
for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization
of this mRNA shows that the incorporation rate of tCO is
similar to cytosine, which allows for efficient labeling and controlled
tuning of labeling ratios for different applications. Using live cell
confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently translated into H2B:GFP inside human
cells. Hence, we not only develop the use of fluorescent base analogue
labeling of nucleic acids in live-cell microscopy but also, importantly,
show that the resulting transcript is translated into the correct
protein. Moreover, the spectral properties of our transcripts and
their translation product allow for their straightforward, simultaneous
visualization in live cells. Finally, we find that chemically transfected
tCO-labeled RNA, unlike a state-of-the-art fluorescently
labeled RNA, gives rise to expression of a similar amount of protein
as its natural counterpart, hence representing a methodology for studying
natural, unperturbed processing of mRNA used in RNA therapeutics and
in vaccines, like the ones developed against SARS-CoV-2.
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Affiliation(s)
- Tom Baladi
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Emanuele Celauro
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Cécile Gasse
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Fabienne Levi-Acobas
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Ivo Sarac
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Marcel R Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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9
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Füchtbauer AF, Wranne MS, Sarangamath S, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4. Chempluschem 2021; 85:319-326. [PMID: 32045137 DOI: 10.1002/cplu.201900712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/06/2019] [Revised: 01/24/2020] [Indexed: 12/20/2022]
Abstract
The fluorescent adenine analogue qAN4 was recently shown to possess promising photophysical properties, including a high brightness as a monomer. Here we report the synthesis of the phosphoramidite of qAN4 and its successful incorporation into DNA oligonucleotides using standard solid-phase synthesis. Circular dichroism and thermal melting studies indicate that the qAN4-modification has a stabilizing effect on the B-form of DNA. Moreover, qAN4 base-pairs selectively with thymine with mismatch penalties similar to those of mismatches of adenine. The low energy absorption band of qAN4 inside DNA has its peak around 358 nm and the emission in duplex DNA is partly quenched and blue-shifted (ca. 410 nm), compared to the monomeric form. The spectral properties of the fluorophore also show sensitivity to pH; a property that may find biological applications. Quantum yields in single-stranded DNA range from 1-29 % and in duplex DNA from 1-7 %. In combination with the absorptive properties, this gives an average brightness inside duplex DNA of 275 M-1 cm-1 , more than five times higher than the most used environment-sensitive fluorescent base analogue, 2-aminopurine. Finally, we show that qAN4 can be used to advantage as a donor for interbase FRET applications in combination with adenine analogue qAnitro as an acceptor.
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Affiliation(s)
- Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.,Cardiovascular Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.,Chemistry Branch Department of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Henrik Gradén
- Cardiovascular Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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10
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Wypijewska Del Nogal A, Füchtbauer AF, Bood M, Nilsson JR, Wranne MS, Sarangamath S, Pfeiffer P, Rajan VS, El-Sagheer AH, Dahlén A, Brown T, Grøtli M, Wilhelmsson LM. Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor. Nucleic Acids Res 2020; 48:7640-7652. [PMID: 32558908 PMCID: PMC7641321 DOI: 10.1093/nar/gkaa525] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/15/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.
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Affiliation(s)
- Anna Wypijewska Del Nogal
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and EarlyDevelopment, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Vinoth Sundar Rajan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Anders Dahlén
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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11
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Füchtbauer AF, Wranne MS, Bood M, Weis E, Pfeiffer P, Nilsson JR, Dahlén A, Grøtli M, Wilhelmsson LM. Interbase FRET in RNA: from A to Z. Nucleic Acids Res 2019; 47:9990-9997. [PMID: 31544922 PMCID: PMC6821158 DOI: 10.1093/nar/gkz812] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/12/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 01/22/2023] Open
Abstract
Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tCO and the non-emissive acceptor tCnitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.
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Affiliation(s)
- Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Erik Weis
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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12
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Fisher RS, Nobis D, Füchtbauer AF, Bood M, Grøtli M, Wilhelmsson LM, Jones AC, Magennis SW. Pulse-shaped two-photon excitation of a fluorescent base analogue approaches single-molecule sensitivity. Phys Chem Chem Phys 2018; 20:28487-28498. [PMID: 30412214 DOI: 10.1039/c8cp05496g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorescent nucleobase analogues (FBAs) have many desirable features in comparison to extrinsic fluorescent labels, but they are yet to find application in ultrasensitive detection. Many of the disadvantages of FBAs arise from their short excitation wavelengths (often in the ultraviolet), making two-photon excitation a potentially attractive approach. Pentacyclic adenine (pA) is a recently developed FBA that has an exceptionally high two-photon brightness. We have studied the two-photon-excited fluorescence properties of pA and how they are affected by incorporation in DNA. We find that pA is more photostable under two-photon excitation than via resonant absorption. When incorporated in an oligonucleotide, pA has a high two-photon cross section and emission quantum yield, varying with sequence context, resulting in the highest reported brightness for such a probe. The use of a two-photon microscope with ultrafast excitation and pulse shaping has allowed the detection of pA-containing oligonucleotides in solution with a limit of detection of ∼5 molecules, demonstrating that practical single-molecule detection of FBAs is now within reach.
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Affiliation(s)
- Rachel S Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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13
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Lawson CP, Füchtbauer AF, Wranne MS, Giraud T, Floyd T, Dumat B, Andersen NK, H El-Sagheer A, Brown T, Gradén H, Wilhelmsson LM, Grøtli M. Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue. Sci Rep 2018; 8:13970. [PMID: 30228309 PMCID: PMC6143597 DOI: 10.1038/s41598-018-31897-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022] Open
Abstract
Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1 in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Tristan Giraud
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Thomas Floyd
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Nicolai K Andersen
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Henrik Gradén
- Cardiovascular, Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, Molndal, SE-431 83, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden.
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14
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Bood M, Füchtbauer AF, Wranne MS, Ro JJ, Sarangamath S, El-Sagheer AH, Rupert DLM, Fisher RS, Magennis SW, Jones AC, Höök F, Brown T, Kim BH, Dahlén A, Wilhelmsson LM, Grøtli M. Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue. Chem Sci 2018; 9:3494-3502. [PMID: 29780479 PMCID: PMC5934695 DOI: 10.1039/c7sc05448c] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 12/23/2017] [Accepted: 03/01/2018] [Indexed: 12/16/2022] Open
Abstract
A highly fluorescent, non-perturbing, pentacyclic adenine analog was designed, synthesized, incorporated into DNA and photophysical evaluated.
Emissive base analogs are powerful tools for probing nucleic acids at the molecular level. Herein we describe the development and thorough characterization of pentacyclic adenine (pA), a versatile base analog with exceptional fluorescence properties. When incorporated into DNA, pA pairs selectively with thymine without perturbing the B-form structure and is among the brightest nucleobase analogs reported so far. Together with the recently established base analog acceptor qAnitro, pA allows accurate distance and orientation determination via Förster resonance energy transfer (FRET) measurements. The high brightness at emission wavelengths above 400 nm also makes it suitable for fluorescence microscopy, as demonstrated by imaging of single liposomal constructs coated with cholesterol-anchored pA–dsDNA, using total internal reflection fluorescence microscopy. Finally, pA is also highly promising for two-photon excitation at 780 nm, with a brightness (5.3 GM) that is unprecedented for a base analog.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Jong Jin Ro
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Afaf H El-Sagheer
- Chemistry Branch , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Déborah L M Rupert
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Rachel S Fisher
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Steven W Magennis
- WestCHEM , School of Chemistry , University of Glasgow , Glasgow , G12 8QQ , UK
| | - Anita C Jones
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Fredrik Höök
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Tom Brown
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK
| | - Byeang Hyean Kim
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Anders Dahlén
- AstraZeneca R&D , Innovative Medicines , Cardiovascular & Metabolic Diseases (CVMD) , Pepparedsleden 1, SE-431 83 Mölndal , Gothenburg , Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
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15
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Bood M, Sarangamath S, Wranne MS, Grøtli M, Wilhelmsson LM. Fluorescent nucleobase analogues for base-base FRET in nucleic acids: synthesis, photophysics and applications. Beilstein J Org Chem 2018; 14:114-129. [PMID: 29441135 PMCID: PMC5789401 DOI: 10.3762/bjoc.14.7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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] [Received: 11/08/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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16
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Ro JJ, Go GH, Wilhelmsson LM, Kim BH. Fluorescence properties of 6-aryl-2'-deoxy-furanouridine and -pyrrolocytidine and their derivatives. Methods Appl Fluoresc 2017; 6:015004. [PMID: 28933349 DOI: 10.1088/2050-6120/aa8e19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
2'-deoxyfuranouridine derivatives presenting various aryl groups have been synthesized through Cu(I)-catalyzed intramolecular cyclizations. Moreover, corresponding pyrrolo-dC derivatives have been synthesized and both families of compounds thoroughly characterized using UV/vis and fluorescence spectroscopy as well as time-dependent density functional theory calculations. The photophysical characterization, show that our newly synthesized derivatives of the important pyrrolo-dC family have high fluorescence quantum yields (QYs) and brightness values. Pyrrolo-dC derivative, 3a, shows an environment sensitive QY of up to >60% and brightness of almost 3000, in low polarity solvents and excitation and emission maxima between 365-381 nm and 479-510 nm, respectively, in solvents of different polarities. Two other derivatives, 3b and 3c, show high QYs and brightness values of up to 3300 that are fairly insensitive to their microenvironment. These promising photophysical features suggest future applicability as fluorescent nucleobase analogs.
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Affiliation(s)
- Jong Jin Ro
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
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17
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Wranne MS, Füchtbauer AF, Dumat B, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Toward Complete Sequence Flexibility of Nucleic Acid Base Analogue FRET. J Am Chem Soc 2017; 139:9271-9280. [PMID: 28613885 DOI: 10.1021/jacs.7b04517] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Förster resonance energy transfer (FRET) using fluorescent base analogues is a powerful means of obtaining high-resolution nucleic acid structure and dynamics information that favorably complements techniques such as NMR and X-ray crystallography. Here, we expand the base-base FRET repertoire with an adenine analogue FRET-pair. Phosphoramidite-protected quadracyclic 2'-deoxyadenosine analogues qAN1 (donor) and qAnitro (acceptor) were synthesized and incorporated into DNA by a generic, reliable, and high-yielding route, and both constitute excellent adenine analogues. The donor, qAN1, has quantum yields reaching 21% and 11% in single- and double-strands, respectively. To the best of our knowledge, this results in the highest average brightness of an adenine analogue inside DNA. Its potent emissive features overlap well with the absorption of qAnitro and thus enable accurate FRET-measurements over more than one turn of B-DNA. As we have shown previously for our cytosine analogue FRET-pair, FRET between qAN1 and qAnitro positioned at different base separations inside DNA results in efficiencies that are highly dependent on both distance and orientation. This facilitates significantly enhanced resolution in FRET structure determinations, demonstrated here in a study of conformational changes of DNA upon binding of the minor groove binder netropsin. Finally, we note that the donor and acceptor of our cytosine FRET-pair, tCO and tCnitro, can be conveniently combined with the acceptor and donor of our current adenine pair, respectively. Consequently, our base analogues can now measure base-base FRET between 3 of the 10 possible base combinations and, through base-complementarity, between all sequence positions in a duplex.
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Affiliation(s)
- Moa S Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Anders Foller Füchtbauer
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden.,Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom.,Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom
| | - Henrik Gradén
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
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18
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Füchtbauer AF, Preus S, Börjesson K, McPhee SA, Lilley DMJ, Wilhelmsson LM. Fluorescent RNA cytosine analogue - an internal probe for detailed structure and dynamics investigations. Sci Rep 2017; 7:2393. [PMID: 28539582 PMCID: PMC5443824 DOI: 10.1038/s41598-017-02453-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
The bright fluorescent cytosine analogue tCO stands out among fluorescent bases due to its virtually unquenched fluorescence emission in duplex DNA. However, like most reported base analogues, it has not been thoroughly characterized in RNA. We here report on the first synthesis and RNA-incorporation of tCO, and characterize its base-mimicking and fluorescence properties in RNA. As in DNA, we find a high quantum yield inside RNA duplexes (<ΦF> = 0.22) that is virtually unaffected by the neighbouring bases (ΦF = 0.20-0.25), resulting in an average brightness of 1900 M-1 cm-1. The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are required to fit the exponential decays. Fluorescence properties in ssRNA are defined by a small increase in average quantum yield (<ΦF > = 0.24) compared to dsRNA, with a broader distribution (ΦF = 0.17-0.34) and slightly shorter average lifetimes. Using circular dichroism, we find that the tCO-modified RNA duplexes form regular A-form helices and in UV-melting experiments the stability of the duplexes is only slightly higher than that of the corresponding natural RNA (<ΔT m> = + 2.3 °C). These properties make tCO a highly interesting fluorescent RNA base analogue for detailed FRET-based structural measurements, as a bright internal label in microscopy, and for fluorescence anisotropy measurements of RNA dynamics.
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Affiliation(s)
- Anders Foller Füchtbauer
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden
| | - Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Karl Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, SE-41296, Sweden
| | - Scott A McPhee
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - L Marcus Wilhelmsson
- Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-41296, Sweden.
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19
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Aissaoui N, Moth-Poulsen K, Käll M, Johansson P, Wilhelmsson LM, Albinsson B. FRET enhancement close to gold nanoparticles positioned in DNA origami constructs. Nanoscale 2017; 9:673-683. [PMID: 27942672 DOI: 10.1039/c6nr04852h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Here we investigate the energy transfer rates of a Förster resonance energy transfer (FRET) pair positioned in close proximity to a 5 nm gold nanoparticle (AuNP) on a DNA origami construct. We study the distance dependence of the FRET rate by varying the location of the donor molecule, D, relative to the AuNP while maintaining a fixed location of the acceptor molecule, A. The presence of the AuNP induces an alteration in the spontaneous emission of the donor (including radiative and non-radiative rates) which is strongly dependent on the distance between the donor and AuNP surface. Simultaneously, the energy transfer rates are enhanced at shorter D-A (and D-AuNP) distances. Overall, in addition to the direct influence of the acceptor and AuNP on the donor decay there is also a significant increase in decay rate not explained by the sum of the two interactions. This leads to enhanced energy transfer between donor and acceptor in the presence of a 5 nm AuNP. We also demonstrate that the transfer rate in the three "particle" geometry (D + A + AuNP) depends approximately linearly on the transfer rate in the donor-AuNP system, suggesting the possibility to control FRET process with electric field induced by 5 nm AuNPs close to the donor fluorophore. It is concluded that DNA origami is a very versatile platform for studying interactions between molecules and plasmonic nanoparticles in general and FRET enhancement in particular.
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Affiliation(s)
- Nesrine Aissaoui
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Kasper Moth-Poulsen
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Mikael Käll
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Peter Johansson
- School of Science and Technology, Örebro University, Örebro, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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20
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Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
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21
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Dumat B, Larsen AF, Wilhelmsson LM. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair. Nucleic Acids Res 2016; 44:e101. [PMID: 26896804 PMCID: PMC4914084 DOI: 10.1093/nar/gkw114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/16/2016] [Indexed: 11/28/2022] Open
Abstract
Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins.
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Affiliation(s)
- Blaise Dumat
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
| | - Anders Foller Larsen
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
| | - L Marcus Wilhelmsson
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
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22
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Tokugawa M, Masaki Y, Canggadibrata JC, Kaneko K, Shiozawa T, Kanamori T, Grøtli M, Wilhelmsson LM, Sekine M, Seio K. 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein. Chem Commun (Camb) 2016; 52:3809-12. [DOI: 10.1039/c5cc09700b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (BFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN).
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Affiliation(s)
- Munefumi Tokugawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | | | - Kazuhei Kaneko
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Shiozawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- S-41296 Gothenburg
- Sweden
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry
- Chalmers University of Technology
- S-41296 Gothenburg
- Sweden
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
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23
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Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Marcus Wilhelmsson L, Grøtli M. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design. Sci Rep 2015; 5:12653. [PMID: 26227585 PMCID: PMC4530663 DOI: 10.1038/srep12653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023] Open
Abstract
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.
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Affiliation(s)
- Anders Foller Larsen
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Moa S. Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Christopher P. Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | - Søren Preus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | | | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
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24
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Lawson CP, Dierckx A, Miannay FA, Wellner E, Wilhelmsson LM, Grøtli M. Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues. Org Biomol Chem 2015; 12:5158-67. [PMID: 24912077 DOI: 10.1039/c4ob00904e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent nucleic acid base analogues are powerful probes of DNA structure. Here we describe the synthesis and photo-physical characterisation of a series of 2-(4-amino-5-(1H-1,2,3-triazol-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl) and 2-(4-amino-3-(1H-1,2,3-triazol-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl) analogues via Sonogashira cross-coupling and [3 + 2]-cycloaddition reactions as the key steps in the synthesis. Compounds with a nitrogen atom in position 8 showed an approximately ten-fold increase in quantum yield and decreased Stokes shift compared to analogues with a carbon atom in position 8. Furthermore, the analogues containing nitrogen in the 8-position showed a more red-shifted and structured absorption as opposed to those which have a carbon incorporated in the same position. Compared to the previously characterised C8-triazole modified adenine, the emissive potential was significantly lower (tenfold or more) for this new family of triazoles-adenine compounds. However, three of the compounds have photophysical properties which will make them interesting to monitor inside DNA.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry, Medicinal Chemistry, University of Gothenburg, S-41296 Gothenburg, Sweden.
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25
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Dumat B, Bood M, Wranne MS, Lawson CP, Larsen AF, Preus S, Streling J, Gradén H, Wellner E, Grøtli M, Wilhelmsson LM. Second-generation fluorescent quadracyclic adenine analogues: environment-responsive probes with enhanced brightness. Chemistry 2015; 21:4039-48. [PMID: 25641628 DOI: 10.1002/chem.201405759] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 10/21/2014] [Indexed: 01/10/2023]
Abstract
Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds.
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Affiliation(s)
- Blaise Dumat
- Department of Chemical and Chemical Engineering/, Chemistry and Biochemistry, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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26
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Posse V, Hoberg E, Dierckx A, Shahzad S, Koolmeister C, Larsson NG, Wilhelmsson LM, Hällberg BM, Gustafsson CM. The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation. Nucleic Acids Res 2014; 42:3638-47. [PMID: 24445803 PMCID: PMC3973307 DOI: 10.1093/nar/gkt1397] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [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] [Indexed: 11/13/2022] Open
Abstract
Mammalian mitochondrial transcription is executed by a single subunit mitochondrial RNA polymerase (Polrmt) and its two accessory factors, mitochondrial transcription factors A and B2 (Tfam and Tfb2m). Polrmt is structurally related to single-subunit phage RNA polymerases, but it also contains a unique N-terminal extension (NTE) of unknown function. We here demonstrate that the NTE functions together with Tfam to ensure promoter-specific transcription. When the NTE is deleted, Polrmt can initiate transcription in the absence of Tfam, both from promoters and non-specific DNA sequences. Additionally, when in presence of Tfam and a mitochondrial promoter, the NTE-deleted mutant has an even higher transcription activity than wild-type polymerase, indicating that the NTE functions as an inhibitory domain. Our studies lead to a model according to which Tfam specifically recruits wild-type Polrmt to promoter sequences, relieving the inhibitory effect of the NTE, as a first step in transcription initiation. In the second step, Tfb2m is recruited into the complex and transcription is initiated.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg, Sweden, Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden, Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden, Department of Laboratory Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden, Max Planck Institute for Biology of Ageing, Gleueler Str. 50 a D-50931 Cologne, Germany, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany and European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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27
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Preus S, Jønck S, Pittelkow M, Dierckx A, Karpkird T, Albinsson B, Wilhelmsson LM. The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting. Photochem Photobiol Sci 2013; 12:1416-22. [PMID: 23689311 DOI: 10.1039/c3pp50057h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
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28
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Preus S, Kilså K, Miannay FA, Albinsson B, Wilhelmsson LM. FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids. Nucleic Acids Res 2012; 41:e18. [PMID: 22977181 PMCID: PMC3592456 DOI: 10.1093/nar/gks856] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [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] [Indexed: 01/25/2023] Open
Abstract
Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base–base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
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29
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Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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30
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Dierckx A, Miannay FA, Ben Gaied N, Preus S, Björck M, Brown T, Wilhelmsson LM. Quadracyclic adenine: a non-perturbing fluorescent adenine analogue. Chemistry 2012; 18:5987-97. [PMID: 22437923 DOI: 10.1002/chem.201103419] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Indexed: 12/26/2022]
Abstract
Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Gothenburg, Sweden
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31
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Lundberg EP, Plesa C, Wilhelmsson LM, Lincoln P, Brown T, Nordén B. Nanofabrication yields. Hybridization and click-fixation of polycyclic DNA nanoassemblies. ACS Nano 2011; 5:7565-7575. [PMID: 21827213 DOI: 10.1021/nn202568q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We demonstrate the stepwise assembly of a fully addressable polycyclic DNA hexagon nanonetwork for the preparation of a four-ring system, one of the biggest networks yet constructed from tripodal building blocks. We find that the yield exhibits a distinct upper level <100%, a fundamental problem of thermodynamic DNA assembly that appears to have been overlooked in the DNA nanotechnology literature. A simplistic model based on a single step-yield parameter y can quantitatively describe the total yield of DNA assemblies in one-pot reactions as Y = y(duplex)(n), with n the number of hybridization steps. Experimental errors introducing deviations from perfect stoichiometry and the thermodynamics of hybridization equilibria contribute to decreasing the value of y(duplex) (on average y = 0.96 for our 10 base pair hybridization). For the four-ring system (n = 31), the total yield is thus less than 30%, which is clearly unsatisfactory if bigger nanoconstructs of this class are to be designed. Therefore, we introduced site-specific click chemistry for making and purifying robust building blocks for future modular constructs of larger assemblies. Although the present yield of this robust module was only about 10%, it demonstrates a first step toward a general fabrication approach. Interestingly, we find that the click yields follow quantitatively a binomial distribution, the predictability of which indicates the usefulness of preparing pools of pure and robust building blocks in this way. The binomial behavior indicates that there is no interference between the six simultaneous click reactions but that step-yield limiting factors such as topological constraints and Cu(I) catalyst concentration are local and independent.
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Affiliation(s)
- Erik P Lundberg
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
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32
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Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS Nano 2011; 5:3405-18. [PMID: 21604810 PMCID: PMC3102291 DOI: 10.1021/nn200989r] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23-25, 2010) ( http://www.eng.uc.edu/nanomedicine/RNA2010/ ), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries.
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Affiliation(s)
- Girish C. Shukla
- Center for Gene Regulation in Health and Disease, Department of Biological Sciences, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Farzin Haque
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jean-Jacques Toulmé
- Université Bordeaux Segalen, INSERM U869, Bâtiment 3A 1er étage, 33076 Bordeaux Cedex, France
| | - Hervé Isambert
- Institut Curie, Research Division, CNRS UMR 168, 11 rue P. & M. Curie, 75005 Paris, France
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Scott A. Tenenbaum
- College of Nanoscale Science & Engineering, University at Albany-SUNY, Albany, New York 12203, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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33
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Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM. Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA. Nucleic Acids Res 2011; 39:4513-24. [PMID: 21278417 PMCID: PMC3105426 DOI: 10.1093/nar/gkr010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [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] [Indexed: 12/29/2022] Open
Abstract
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (AT) and its photophysical characterization inside DNA. AT shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, AT shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that AT only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that AT shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, AT shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden
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34
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Börjesson K, Tumpane J, Ljungdahl T, Wilhelmsson LM, Nordén B, Brown T, Mårtensson J, Albinsson B. A membrane anchored DNA-based energy/electron transfer assembly. ACTA ACUST UNITED AC 2010:691. [PMID: 18776568 DOI: 10.1093/nass/nrn349] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In this work the trapping and conversion of visible light energy into chemical energy is examined using a supramolecular assembly. This consists of a light absorbing antenna and a porphyrin redox centre both covalently attached to a DNA strand, which in turn is bound to a lipid membrane. The excitation energy is finally trapped as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions.
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Affiliation(s)
- Karl Börjesson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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35
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Börjesson K, Tumpane J, Ljungdahl T, Wilhelmsson LM, Nordén B, Brown T, Mårtensson J, Albinsson B. Membrane-anchored DNA assembly for energy and electron transfer. J Am Chem Soc 2010; 131:2831-9. [PMID: 19199439 DOI: 10.1021/ja8038294] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [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
In this work we examine the trapping and conversion of visible light energy into chemical energy using a supramolecular assembly. The assembly consists of a light-absorbing antenna and a porphyrin redox center, which are covalently attached to two complementary 14-mer DNA strands, hybridized to form a double helix and anchored to a lipid membrane. The excitation energy is finally trapped in the lipid phase of the membrane as a benzoquinone radical anion that could potentially be used in subsequent chemical reactions. In addition, in this model complex, the hydrophobic porphyrin moiety acts as an anchor into the liposome positioning the DNA construct on the lipid membrane surface. The results show the suitability of our system as a prototype for DNA-based light-harvesting devices, in which energy transfer from the aqueous phase to the interior of the lipid membrane is followed by charge separation.
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Affiliation(s)
- Karl Börjesson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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36
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Preus S, Kilså K, Wilhelmsson LM, Albinsson B. Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family. Phys Chem Chem Phys 2010; 12:8881-92. [PMID: 20532361 DOI: 10.1039/c000625d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tC(O) and tC(nitro); all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tC(nitro) is an internal conversion of a different origin than the decay pathways of tC and tC(O). tC(nitro) is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S(0) potential energy surfaces of tC and tC(nitro) possess two global minima corresponding to geometries folded along the middle sulfur-nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311+G(2d,p) level. The ground-state potential energy surface of tC(O) is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tC(O) in various confined (biological) environments. The S(1) equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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37
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Lundberg EP, El-Sagheer AH, Kocalka P, Wilhelmsson LM, Brown T, Nordén B. A new fixation strategy for addressable nano-network building blocks. Chem Commun (Camb) 2010; 46:3714-6. [PMID: 20386862 DOI: 10.1039/c001513j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Rapid controlled self-assembly makes DNA ideal for building nanostructures. A problem using hybridized intermediates in hierarchic assembly is their thermodynamic lability. We demonstrate a click-fixation technology by which robust hexagonal DNA modules can be made. This principle is applicable to a wide variety of DNA nanoconstructs.
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Affiliation(s)
- Erik P Lundberg
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
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38
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Abstract
The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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39
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Preus S, Börjesson K, Kilså K, El-Sagheer AH, Brown T, Albinsson B, Wilhelmsson LM. The First All-Nucleobase Analog FRET Pair. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.3164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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40
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Stengel G, Purse BW, Wilhelmsson LM, Urban M, Kuchta RD. Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment. Biochemistry 2009; 48:7547-55. [PMID: 19580325 DOI: 10.1021/bi9006995] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We studied the incorporation of the fluorescent cytidine analogues 1,3-diaza-2-oxophenothiazine (tC) and 1,3-diaza-2-oxophenoxazine (tCo) by human DNA polymerase alpha and Klenow fragment of DNA polymerase I (Escherichia coli). These tricyclic nucleobases possess the regular hydrogen bonding interface of cytosine but are significantly expanded in size toward the major groove. Despite the size alteration, both DNA polymerases insert dtCTP and dtCoTP with remarkable catalytic efficiency. Polymerization opposite guanine is comparable to the insertion of dCTP, while the insertion opposite adenine is only approximately 4-11 times less efficient than the formation of a T-A base pair. Both enzymes readily extend the formed tC(o)-G and tC(o)-A base pairs and can incorporate at least four consecutive nucleotide analogues. Consistent with these results, both DNA polymerases efficiently polymerize dGTP and dATP when tC and tCo are in the template strand. Klenow fragment inserts dGTP with a 4-9-fold higher probability than dATP, while polymerase alpha favors dGTP over dATP by a factor of 30-65. Overall, the properties of tC(o) as a templating base and as an incoming nucleotide are surprisingly symmetrical and may be universal for A and B family DNA polymerases. This finding suggests that the aptitude for ambivalent base pairing is a consequence of the electronic properties of tC(o).
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Affiliation(s)
- Gudrun Stengel
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 30309-0215, USA
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41
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Dyrager C, Friberg A, Dahlén K, Fridén-Saxin M, Börjesson K, Wilhelmsson LM, Smedh M, Grøtli M, Luthman K. 2,6,8-Trisubstituted 3-Hydroxychromone Derivatives as Fluorophores for Live-Cell Imaging. Chemistry 2009; 15:9417-23. [PMID: 19670192 DOI: 10.1002/chem.200900279] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Christine Dyrager
- Department of Chemistry-Medicinal Chemistry, University of Gothenburg, 412 96 Göteborg, Sweden
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42
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Börjesson K, Preus S, El-Sagheer AH, Brown T, Albinsson B, Wilhelmsson LM. Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems. J Am Chem Soc 2009; 131:4288-93. [PMID: 19317504 DOI: 10.1021/ja806944w] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tC(O), 1,3-diaza-2-oxophenoxazine, as an energy donor and the newly developed tC(nitro), 7-nitro-1,3-diaza-2-oxophenothiazine, as an energy acceptor. The FRET-pair successfully monitors distances covering up to more than one turn of the DNA duplex. Importantly, we show that the rigid stacking of the two base analogs, and consequently excellent control of their exact positions and orientations, results in a high control of the orientation factor and hence very distinct FRET changes as the number of bases separating tC(O) and tC(nitro) is varied. A set of DNA strands containing the FRET-pair at wisely chosen locations will, thus, make it possible to accurately distinguish distance- from orientation-changes using FRET. In combination with the good nucleobase analog properties, this points toward detailed studies of the inherent dynamics of nucleic acid structures. Moreover, the placement of FRET-pair chromophores inside the base stack will be a great advantage in studies where other (biomacro)molecules interact with the nucleic acid. Lastly, our study gives possibly the first truly solid experimental support to the dependence of energy transfer efficiency on orientation of involved transition dipoles as predicted by the Forster theory.
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Affiliation(s)
- Karl Börjesson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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43
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Sandin P, Stengel G, Ljungdahl T, Börjesson K, Macao B, Wilhelmsson LM. Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment. Nucleic Acids Res 2009; 37:3924-33. [PMID: 19401439 PMCID: PMC2709563 DOI: 10.1093/nar/gkp266] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [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] [Indexed: 11/15/2022] Open
Abstract
Studies of the mechanisms by which DNA polymerases select the correct nucleotide frequently employ fluorescently labeled DNA to monitor conformational rearrangements of the polymerase-DNA complex in response to incoming nucleotides. For this purpose, fluorescent base analogs play an increasingly important role because they interfere less with the DNA-protein interaction than do tethered fluorophores. Here we report the incorporation of the 5'-triphosphates of two exceptionally bright cytosine analogs, 1,3-diaza-2-oxo-phenothiazine (tC) and its oxo-homolog, 1,3-diaza-2-oxo-phenoxazine (tC(O)), into DNA by the Klenow fragment. Both nucleotide analogs are polymerized with slightly higher efficiency opposite guanine than cytosine triphosphate and are shown to bind with nanomolar affinity to the DNA polymerase active site, according to fluorescence anisotropy measurements. Using this method, we perform competitive binding experiments and show that they can be used to determine the dissociation constant of any given natural or unnatural nucleotide. The results demonstrate that the active site of the Klenow fragment is flexible enough to tolerate base pairs that are size-expanded in the major groove. In addition, the possibility to enzymatically polymerize a fluorescent nucleotide with high efficiency complements the tool box of biophysical probes available to study DNA replication.
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Affiliation(s)
- Peter Sandin
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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44
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Olsson M, Tang KW, Persson C, Wilhelmsson LM, Billeter M, Elias P. Stepwise evolution of the herpes simplex virus origin binding protein and origin of replication. J Biol Chem 2009; 284:16246-16255. [PMID: 19351883 DOI: 10.1074/jbc.m807551200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The herpes simplex virus replicon consists of cis-acting sequences, oriS and oriL, and the origin binding protein (OBP) encoded by the UL9 gene. Here we identify essential structural features in the initiator protein OBP and the replicator sequence oriS, and we relate the appearance of these motifs to the evolutionary history of the alphaherpesvirus replicon. Our results reveal two conserved sequence elements in herpes simplex virus type 1, OBP; the RVKNL motif, common to and specific for all alphaherpesviruses, is required for DNA binding, and the WP XXXGAXXFXX L motif, found in a subset of alphaherpesviruses, is required for specific binding to the single strand DNA-binding protein ICP8. A 121-amino acid minimal DNA binding domain containing conserved residues is not soluble and does not bind DNA. Additional sequences present 220 amino acids upstream from the RVKNL motif are needed for solubility and function. We also examine the binding sites for OBP in origins of DNA replication and how they are arranged. NMR and DNA melting experiments demonstrate that origin sequences derived from many, but not all, alphaherpesviruses can adopt stable boxI/boxIII hairpin conformations. Our results reveal a stepwise evolutionary history of the herpes simplex virus replicon and suggest that replicon divergence contributed to the formation of major branches of the herpesvirus family.
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Affiliation(s)
- Monica Olsson
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg
| | - Ka-Wei Tang
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg
| | - Cecilia Persson
- The Swedish NMR Centre at University of Gothenburg, Box 465, S-405 30 Gothenburg
| | - L Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg
| | - Martin Billeter
- Biophysics Group, Department of Chemistry, University of Gothenburg, Box 462, S-405 30 Gothenburg, Sweden
| | - Per Elias
- From the Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, S-405 30 Gothenburg.
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45
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Dyrager C, Börjesson K, Dinér P, Elf A, Albinsson B, Wilhelmsson LM, Grøtli M. Synthesis and Photophysical Characterisation of Fluorescent 8-(1H-1,2,3-Triazol-4-yl)adenosine Derivatives. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900018] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Affiliation(s)
- L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Ngarita Kingi
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
| | - Jan Bergman
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, Unit for Organic Chemistry, Department of Biosciences and Nutrition, Karolinska Institute, SE-14157, Huddinge, Sweden, and Drug Development, Vironova AB, Smedjegatan 6, SE-13134 Nacka, Sweden
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47
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Banchelli M, Betti F, Berti D, Caminati G, Bombelli FB, Brown T, Wilhelmsson LM, Nordén B, Baglioni P. Phospholipid membranes decorated by cholesterol-based oligonucleotides as soft hybrid nanostructures. J Phys Chem B 2008; 112:10942-52. [PMID: 18693696 DOI: 10.1021/jp802415t] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA monomers and oligomers are currently showing great promise as building blocks for supramolecular arrays that can self-assemble in a fashion preprogrammed by the base pairing code. The design and build-up of hybrid DNA/amphiphilic self-assemblies can expand the range of possible architectures and enhance the selectivity toward a well-specified geometry. We report on the self-assembly properties in aqueous solution of a cholesteryl-tetraethylenglycol single stranded 18-mer oligonucleotide (ON 1TEG-Chol) and on its spontaneous insertion in fluid phospholipid membranes. Up to 500 units of these lipophilic ss-oligonucleotides can be incorporated in the outer leaflet of 350 A radius POPC vesicle. The insertion and hybridization with the complementary oligonucleotide are monitored through light scattering as an increase of hydrodynamic thickness, which is interpreted in terms of average distance between anchoring sites. The conformation of the ss-oligonucleotidic portion is strongly dependent on surface coverage, passing from a quasi-random coil to a more rigid configuration, as concentration increases. Interestingly, conformational details affect in a straightforward fashion the hybridization kinetics. Liposomes with single- and double-strand decorations remain stable within the experimental time window (about one week). The structure represents an example of successful and stable amphiphile/DNA supramolecular hybrid, where a DNA guest is held in a membrane by hydrophobic interactions. The lipophilic oligonucleotide under investigation is therefore a suitable building block that can effectively serve as a hydrophobic anchor in the fluid bilayer to assemble supramolecular constructs based on the DNA digital code.
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Affiliation(s)
- Martina Banchelli
- Department of Chemistry and CSGI, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
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48
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Lundberg E, Tumpane J, Kumar R, Sandin P, Gale N, Nandhakumar IS, Albinsson B, Lincoln P, Wilhelmsson LM, Brown T, Nordén B. Addressable molecular node assembly--high information density DNA nanostructures. Nucleic Acids Symp Ser (Oxf) 2008; 52:683-684. [PMID: 18776564 DOI: 10.1093/nass/nrn345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The inherent self-assembly properties of DNA make it ideal in nanotechnology. We present a fully addressable DNA nanostructure with the smallest possible unit cell, a hexagon with a side-length of only 3.4 nm.(2,3) Using novel three-way oligonucleotides, where each side has a unique double-stranded DNA sequence that can be assigned a specific address, we will build a non-repetitive two-dimensional grid.
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Affiliation(s)
- Erik Lundberg
- Department of Chemical & Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
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49
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Tumpane J, Lundberg EP, Wilhelmsson LM, Brown T, Nordén B. Addressable molecular node assembly--functional DNA nanostructures. Nucleic Acids Symp Ser (Oxf) 2008; 52:97-98. [PMID: 18776271 DOI: 10.1093/nass/nrn050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The use of nucleic acids as a nanomaterial is becoming increasingly widespread due to the suitability of the hydrogen-bonding patterns and sequence specificity inherent to the double-helix. As minimisation of size becomes ever more important it is imperative to employ nucleic acids in the most efficient and functional manner possible. To this end we have constructed DNA nanostructures on what may be the smallest possible scale (basic components of just 10 bp) that not only reliably self-assemble but also where each unit of a 2-dimensional DNA network can be uniquely identified and selectively functionalized.(1,2.3) On this length scale and using full addressability of the network to engrave specific pathways on the scaffold, energy and electron transfer become efficient for potential information storage applications.(4).
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Affiliation(s)
- John Tumpane
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg 412 96, Sweden.
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50
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Tumpane J, Kumar R, Lundberg EP, Sandin P, Gale N, Nandhakumar IS, Albinsson B, Lincoln P, Wilhelmsson LM, Brown T, Nordén B. Triplex addressability as a basis for functional DNA nanostructures. Nano Lett 2007; 7:3832-3839. [PMID: 17983251 DOI: 10.1021/nl072512i] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Here, we present the formation of a fully addressable DNA nanostructure that shows the potential to be exploited as, for example, an information storage device based on pH-driven triplex strand formation or nanoscale circuits based on electron transfer. The nanostructure is composed of two adjacent hexagonal unit cells (analogous to naphthalene) in which each of the eleven edges has a unique double-stranded DNA sequence, constructed using novel three-way oligonucleotides. This allows each ten base-pair side, just 3.4 nm in length, to be assigned a specific address according to its sequence. Such constructs are therefore an ideal precursor to a nonrepetitive two-dimensional grid on which the "addresses" are located at a precise and known position. Triplex recognition of these addresses could function as a simple yet efficient means of information storage and retrieval. Future applications that may be envisaged include nanoscale circuits as well as subnanometer precision in nanoparticle templating. Characterization of these precursor nanostructures and their reversible targeting by triplex strand formation is shown here using gel electrophoresis, atomic force microscopy, and fluorescence resonance energy transfer (FRET) measurements. The durability of the system to repeated cycling of pH switching is also confirmed by the FRET studies.
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Affiliation(s)
- John Tumpane
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
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