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  1. AU="L. Marcus Wilhelmsson"
  2. AU=Filocamo Giovanni
  3. AU="Andrea Terán-Valdez"
  4. AU=Cleverley Joanne AU=Cleverley Joanne
  5. AU="Feng, Shiguang"
  6. AU="De Falco, Antonio"
  7. AU="Plenter, R J"
  8. AU="Malarz, Janusz"

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  1. Artikel ; Online: Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers

    Anna Wypijewska del Nogal / Vinoth Sundar Rajan / Fredrik Westerlund / L. Marcus Wilhelmsson

    International Journal of Molecular Sciences, Vol 22, Iss 9008, p

    2021  Band 9008

    Abstract: Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and ... ...

    Abstract Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sodium and magnesium, while type 1 and 2 take place in all buffers, with type 1 being the most prevalent. By reducing the size of the native hairpin loop from fourteen to four nucleotides, we demonstrate that the folding heterogeneity originates from the large size of the hairpin loop. Further, while efficient pre-miRNA-377 binders are lacking, we demonstrate that the recently developed C2 ligand displays bimodal activity: it enhances the mechanical stability of the pre-miRNA-377 hairpin and perturbs its folding. The knowledge regarding pre-miRNA stability and dynamics that we provide is important in understanding its regulatory function and how it can be modulated to achieve a therapeutic effect, e.g., in heart failure treatment.
    Schlagwörter single-molecule force spectroscopy ; optical tweezers ; RNA dynamics ; RNA folding heterogeneity ; miRNA ; pre-miRNA ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-08-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition

    Željka Ban / Josipa Matić / Biserka Žinić / Anders Foller Füchtbauer / L. Marcus Wilhelmsson / Ivo Piantanida

    Molecules, Vol 25, Iss 2188, p

    2020  Band 2188

    Abstract: We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into ... ...

    Abstract We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λ max = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λ max = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.
    Schlagwörter DNA/RNA recognition ; hydrogen bonding ; fluorescent nucleobase ; pyrene ; intramolecular pre-organization ; Organic chemistry ; QD241-441
    Thema/Rubrik (Code) 540
    Sprache Englisch
    Erscheinungsdatum 2020-05-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

    Jesper R. Nilsson / Tom Baladi / Audrey Gallud / Dženita Baždarević / Malin Lemurell / Elin K. Esbjörner / L. Marcus Wilhelmsson / Anders Dahlén

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 13

    Abstract: 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 ... ...

    Abstract 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.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Interbase-FRET binding assay for pre-microRNAs

    Mattias Bood / Anna Wypijewska del Nogal / Jesper R. Nilsson / Fredrik Edfeldt / Anders Dahlén / Malin Lemurell / L. Marcus Wilhelmsson / Morten Grøtli

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 9

    Abstract: 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) ... ...

    Abstract 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.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 500
    Sprache Englisch
    Erscheinungsdatum 2021-04-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells

    Sagar Mahale / Meenakshi Setia / Bharat Prajapati / Santhilal Subhash / Mukesh Pratap Yadav / Subazini Thankaswamy Kosalai / Ananya Deshpande / Jagannath Kuchlyan / Mirco Di Marco / Fredrik Westerlund / L. Marcus Wilhelmsson / Chandrasekhar Kanduri / Meena Kanduri

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Band 20

    Abstract: Using fibroblast growth factor 2 (FGF-2) induced sense and antisense transcripts IER3 and IER3-AS1 as a model system, authors highlight the role of HnRNPK in regulating double strand RNA formation in the loci with overlapping transcripts. ...

    Abstract Using fibroblast growth factor 2 (FGF-2) induced sense and antisense transcripts IER3 and IER3-AS1 as a model system, authors highlight the role of HnRNPK in regulating double strand RNA formation in the loci with overlapping transcripts.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2022-08-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Fluorescent nucleobase analogues for base–base FRET in nucleic acids

    Mattias Bood / Sangamesh Sarangamath / Moa S. Wranne / Morten Grøtli / L. Marcus Wilhelmsson

    Beilstein Journal of Organic Chemistry, Vol 14, Iss 1, Pp 114-

    synthesis, photophysics and applications

    2018  Band 129

    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 ... ...

    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.
    Schlagwörter B-to-Z-DNA transition ; fluorescent base analogues ; FRET ; netropsin ; nucleic acid structure and dynamics ; quadracyclic adenines ; tricyclic cytosines ; Z-DNA ; Science ; Q ; Organic chemistry ; QD241-441
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2018-01-01T00:00:00Z
    Verlag Beilstein-Institut
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Fluorescent RNA cytosine analogue – an internal probe for detailed structure and dynamics investigations

    Anders Foller Füchtbauer / Søren Preus / Karl Börjesson / Scott A. McPhee / David M. J. Lilley / L. Marcus Wilhelmsson

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Band 8

    Abstract: 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 ... ...

    Abstract 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.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2017-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel: Antibody mediated fluorescence enhancement of nucleoside analogue 1,3-diaza-2-oxophenoxazine (tC°)

    Sellrie, Frank / Anika Andersson / Christine Lenz / Jörg A. Schenk / L. Marcus Wilhelmsson

    Talanta. 2014 June 15, v. 124

    2014  

    Abstract: We report on the generation and analytical application of the monoclonal antibody G93-ED2 raised against the tricyclic fluorescent nucleoside analogue 1,3-diaza-2-oxophenoxazine (tC°). G93-ED2 is specifically binding this deoxycytidine analogue and was ... ...

    Abstract We report on the generation and analytical application of the monoclonal antibody G93-ED2 raised against the tricyclic fluorescent nucleoside analogue 1,3-diaza-2-oxophenoxazine (tC°). G93-ED2 is specifically binding this deoxycytidine analogue and was found to raise its fluorescence intensity by a factor of 5. This unique feature makes it a valuable tool in fluorescence dependent immunoassays. G93-ED2 was successfully applied in a homogeneous fluorescence quenching immunoassay (DNA-Q) for the sequence specific determination of DNA.
    Schlagwörter deoxycytidine ; DNA ; fluorescence ; immunoassays ; monoclonal antibodies
    Sprache Englisch
    Erscheinungsverlauf 2014-0615
    Umfang p. 67-70.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 1500969-5
    ISSN 1873-3573 ; 0039-9140
    ISSN (online) 1873-3573
    ISSN 0039-9140
    DOI 10.1016/j.talanta.2014.02.046
    Datenquelle NAL Katalog (AGRICOLA)

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  9. Artikel ; Online: Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue

    Christopher P. Lawson / Anders F. Füchtbauer / Moa S. Wranne / Tristan Giraud / Thomas Floyd / Blaise Dumat / Nicolai K. Andersen / Afaf H. El-Sagheer / Tom Brown / Henrik Gradén / L. Marcus Wilhelmsson / Morten Grøtli

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Band 9

    Abstract: 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 ...

    Abstract 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.
    Schlagwörter Thymine Analogue ; Oligonucleotide Incorporation ; Fluorescent Base Analogues (FBAs) ; Natural Nucleobases ; MeCN Water ; Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2018-09-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel: 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein

    Tokugawa, Munefumi / Yoshiaki Masaki / Jan Christian Canggadibrata / Kazuhei Kaneko / Takashi Shiozawa / Takashi Kanamori / Morten Grøtli / L. Marcus Wilhelmsson / Mitsuo Sekine / Kohji Seio

    Chemical communications. 2016 Feb. 25, v. 52, no. 19

    2016  

    Abstract: 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (ᴮFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN). The single-stranded ODN containing ᴮFdG shows 91-fold fluorescence enhancement upon binding of single-strand DNA binding protein. ...

    Abstract 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (ᴮFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN). The single-stranded ODN containing ᴮFdG shows 91-fold fluorescence enhancement upon binding of single-strand DNA binding protein.
    Schlagwörter DNA-binding proteins ; chemical compounds ; chemical reactions ; fluorescence ; oligodeoxyribonucleotides
    Sprache Englisch
    Erscheinungsverlauf 2016-0225
    Umfang p. 3809-3812.
    Erscheinungsort The Royal Society of Chemistry
    Dokumenttyp Artikel
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c5cc09700b
    Datenquelle NAL Katalog (AGRICOLA)

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