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Article ; Online: Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues.

Sundar Rajan, Vinoth / Wypijewska Del Nogal, Anna / Levin, Sune / Wilhelmsson, L Marcus / Westerlund, Fredrik

2024 Volume 16, Issue 2, Page(s) 752–764

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 ... ...

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, tC
MeSH term(s)	Humans ; SARS-CoV-2 ; RNA, Viral/chemistry ; Base Sequence ; Nucleic Acid Conformation ; Optical Tweezers ; COVID-19 ; RNA, Guide, CRISPR-Cas Systems
Chemical Substances	RNA, Viral ; RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d3nr04110g
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Article ; Online: Synthesis and Photophysical Characterization of a pH-Sensitive Quadracyclic Uridine (qU) Analogue.

Le, Hoang-Ngoan / Kuchlyan, Jagannath / Baladi, Tom / Albinsson, Bo / Dahlén, Anders / Wilhelmsson, L Marcus

Chemistry (Weinheim an der Bergstrasse, Germany)

2024 Volume 30, Issue 18, Page(s) e202303539

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/ ... ...

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.
MeSH term(s)	Uridine/chemistry ; Fluorescent Dyes/chemistry ; Nucleic Acids ; Hydrogen-Ion Concentration ; Uracil
Chemical Substances	Uridine (WHI7HQ7H85) ; Fluorescent Dyes ; Nucleic Acids ; Uracil (56HH86ZVCT)
Language	English
Publishing date	2024-02-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202303539
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Article ; Online: Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers.

Wypijewska Del Nogal, Anna / Sundar Rajan, Vinoth / Westerlund, Fredrik / Wilhelmsson, L Marcus

International journal of molecular sciences

2021 Volume 22, Issue 16

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.
MeSH term(s)	Heart Failure/genetics ; Humans ; MicroRNAs/genetics ; MicroRNAs/ultrastructure ; Nanotechnology ; Nucleic Acid Conformation ; Optical Tweezers ; RNA/chemistry ; RNA Folding/genetics ; RNA Folding/physiology ; RNA Processing, Post-Transcriptional/genetics ; RNA Processing, Post-Transcriptional/physiology ; Single Molecule Imaging/methods
Chemical Substances	MicroRNAs ; RNA (63231-63-0)
Language	English
Publishing date	2021-08-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22169008
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Article ; Online: Fluorescent nucleic acid base analogues.

Wilhelmsson, L Marcus

Quarterly reviews of biophysics

2010 Volume 43, Issue 2, Page(s) 159–183

Abstract: The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent ...

Abstract	The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
MeSH term(s)	Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Humans ; Nucleic Acids/chemistry ; Staining and Labeling
Chemical Substances	Fluorescent Dyes ; Nucleic Acids
Language	English
Publishing date	2010-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	209912-3
ISSN	1469-8994 ; 0033-5835
ISSN (online)	1469-8994
ISSN	0033-5835
DOI	10.1017/S0033583510000090
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Article ; Online: Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition.

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

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 9

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
MeSH term(s)	Circular Dichroism ; DNA/chemistry ; Fluorescence ; Fluorescent Dyes/chemistry ; Hydrogen Bonding ; Nucleic Acid Conformation ; Poly A/chemistry ; Poly C/chemistry ; Poly G/chemistry ; Poly U/chemistry ; Pyrenes/chemical synthesis ; Pyrenes/chemistry ; RNA/chemistry ; RNA, Double-Stranded/chemistry ; Solvents/chemistry ; Spectrometry, Fluorescence ; Water/chemistry
Chemical Substances	Fluorescent Dyes ; Pyrenes ; RNA, Double-Stranded ; Solvents ; Water (059QF0KO0R) ; Poly A (24937-83-5) ; Poly G (25191-14-4) ; Poly U (27416-86-0) ; Poly C (30811-80-4) ; RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2020-05-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25092188
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Article ; Online: Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA.

Nilsson, Jesper R / Benitez-Martin, Carlos / Sansom, Henry G / Pfeiffer, Pauline / Baladi, Tom / Le, Hoang-Ngoan / Dahlén, Anders / Magennis, Steven W / Wilhelmsson, L Marcus

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 30, Page(s) 20218–20224

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, ... ...

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
MeSH term(s)	Fluorescent Dyes/chemistry ; Oligonucleotides ; Spectrometry, Fluorescence/methods ; Purine Nucleosides ; Adenine/chemistry
Chemical Substances	Fluorescent Dyes ; Oligonucleotides ; Purine Nucleosides ; Adenine (JAC85A2161)
Language	English
Publishing date	2023-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp01147j
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Article ; Online: Mechanical characterization of base analogue modified nucleic acids by force spectroscopy.

Sundar Rajan, Vinoth / Viader-Godoy, Xavier / Lin, Yii-Lih / Dutta, Uttama / Ritort, Felix / Westerlund, Fredrik / Wilhelmsson, L Marcus

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 26, Page(s) 14151–14155

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 ... ...

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.
MeSH term(s)	DNA/chemistry ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes/chemistry ; Mechanical Phenomena ; Models, Molecular ; Nucleic Acid Conformation ; Single Molecule Imaging ; Thermodynamics ; Transition Temperature
Chemical Substances	Fluorescent Dyes ; DNA (9007-49-2)
Language	English
Publishing date	2021-06-28
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d1cp01985f
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Article ; Online: Interbase-FRET binding assay for pre-microRNAs.

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

Scientific reports

2021 Volume 11, Issue 1, Page(s) 9396

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 ... ...

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.
MeSH term(s)	Aminoglycosides/metabolism ; Fluorescence Resonance Energy Transfer/methods ; Humans ; Kinetics ; MicroRNAs/analysis ; MicroRNAs/chemistry ; MicroRNAs/metabolism ; Protein Binding ; Surface Plasmon Resonance/methods
Chemical Substances	Aminoglycosides ; MicroRNAs
Language	English
Publishing date	2021-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-88922-0
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Article ; Online: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics.

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

Scientific reports

2021 Volume 11, Issue 1, Page(s) 11365

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 ... ...

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, tC
MeSH term(s)	Cell Survival/drug effects ; Flow Cytometry ; Fluorescent Dyes/chemistry ; HEK293 Cells ; Humans ; Microscopy, Fluorescence ; Nucleic Acid Conformation ; Oligonucleotides, Antisense/chemistry ; Oligonucleotides, Antisense/pharmacology ; Real-Time Polymerase Chain Reaction ; Reverse Transcription ; Spectrophotometry, Ultraviolet
Chemical Substances	Fluorescent Dyes ; Oligonucleotides, Antisense
Language	English
Publishing date	2021-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-90629-1
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Article ; Online: Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair.

Dumat, Blaise / Larsen, Anders Foller / Wilhelmsson, L Marcus

Nucleic acids research

2016 Volume 44, Issue 11, Page(s) e101

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 ... ...

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.
MeSH term(s)	Algorithms ; Base Pairing ; Circular Dichroism ; Cytosine/chemistry ; DNA/chemistry ; DNA, Z-Form/chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Models, Molecular ; Models, Theoretical ; Nucleic Acid Conformation ; Oligonucleotides/chemistry
Chemical Substances	DNA, Z-Form ; Oligonucleotides ; Cytosine (8J337D1HZY) ; DNA (9007-49-2)
Language	English
Publishing date	2016-06-20
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkw114
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