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- Bergquist, Helen, 1979-
(författare)
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Development of benzoquinoquinoxaline derivatives as triplex-specific probes : Recognition of DNA structures at repeats sequences
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Repeat sequences are associated with several human diseases, such as Friedreich’s ataxia, polycystic kidney disease and cancer. These sequences can form non-B-DNA structures, including triplex (H-DNA) DNA, and are associated with genomic instability and altered gene expression. The occurrence of triplex structures in vivo and identification of their links to biological processes have been challenging. The lack of effective probes has restrained the study of triplex structures in living cells. Here, the triplex binding small molecule benzoquinoquinoxaline (BQQ) and its derivatives were developed as tools to study triplex formation at genomic repeat sequences. The triplex binding efficiency towards both purine and pyrimidine triplex motifs was determined for BQQ, the DNA cleaving BQQ-1,10-(ortho)-phenanthroline (BQQ-OP) and the fluorescent BQQ-Bodipy compounds. BQQ was shown to have the most stabilising effect on both triplex motifs. Moreover, H-DNA structure formation at a pkd1 derived sequence was demonstrated for the first time by BQQ-OP at physiologically relevant conditions. H-DNA formation was also shown at (GAA)n repeats associated with Friedreich’s ataxia and the structure was further analysed on one nucleotide resolution, confirming that (GAA)n repeats form a pyrimidine H-DNA. However, a mixture of different isomers formed at longer (GAA)n repeats. To this end, the interaction between the peptide nucleic acids (PNA) and BQQ was investigated. PNA is a DNA mimic that binds sequence-specifically to dsDNA and can form several PNA-DNA complexes. The results of PNA binding to frataxin (GAA)n expansion in plasmid were evaluated, and in the presence of GAA-PNA no triplex structure could be detected by BQQ-OP cleavage. When the structure formed in the presence of either GAA-PNA or CTT-PNA was further analysed, it was found that GAA-PNA formed a duplex invasion complex preventing H-DNA formation, whereas CTT-PNA formed a triplex invasion complex.
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| 2. |
- Bergquist, Helen, et al.
(författare)
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Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)(n) Repeats by PNA or LNA Targeting
- 2016
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Ingår i: PLOS ONE. - : PLOS. - 1932-6203. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Expansion of (GAA)(n) repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich's ataxia. (GAA)(n) expansions form non-canonical structures, including intramolecular triplex (H-DNA), and Rloops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)(n) expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)(n) repeats of different lengths (short: n= 9, medium: n= 75 or long: n= 115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA) 4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT) 5-PNA did not. We present evidence that (GAA) 4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT) 5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression.
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| 6. |
- Bergquist, Helen, et al.
(författare)
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Structural Insights into Human Adenovirus Type 4 Virus-Associated RNA I
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 23:6
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Tidskriftsartikel (refereegranskat)abstract
- RNA molecules can adopt specific RNA triplex structures to execute critical biological functions. Human adenoviruses (HAdVs) are abundant pathogens encoding the essential, noncoding virus-associated RNA I (VA RNAI). Here, we employ a triplex-specific probing assay, based on the intercalating and cleaving agent benzoquinoquinoxaline 1, 10-phenanthroline (BQQ-OP), to unravel a potential RNA triplex formation in VA RNAI. The BQQ-OP cleavage of the pathogenic HAdV type 4 (HAdV-4) VA RNAI indicates that a potential triplex is formed involving the highly conserved stem 4 of the central domain and side stem 7. Further, the integrity of the HAdV-4 VA RNAI side stem 7 contributes to a potential triplex formation in vitro and virus growth in vivo. Collectively, we propose that the HAdV-4 VA RNAI can potentially form a biologically relevant triplex structure.
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| 8. |
- Bergquist, Helen, 1979-, et al.
(författare)
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Structure-Specific Recognition of Friedreich’s Ataxia (GAA)n Repeats by Benzoquinoquinoxaline Derivatives
- 2009
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Ingår i: ChemBioChem (Print). - : Wiley. - 1439-4227 .- 1439-7633. ; 10:16, s. 2629-2637
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Tidskriftsartikel (refereegranskat)abstract
- Expansion of GAA triplet repeats in intron 1 of the FXN gene reduces frataxin expression and causes Friedreich's ataxia. (GAA)nrepeats form non-B-DNA structures, including triple helix H-DNA and higher-order structures (sticky DNA). In the proposed mechanisms of frataxin gene silencing, central unanswered questions involve the characterization of non-B-DNA structure(s) that are strongly suggested to play a role in frataxin expression. Here we examined (GAA)nbinding by triplex-stabilizing benzoquinoquinoxaline (BQQ) and the corresponding triplex-DNA-cleaving BQQ-1,10-phenanthroline (BQQ-OP) compounds. We also examined the ability of these compounds to act as structural probes for H-DNA formation within higher-order structures at pathological frataxin sequences in plasmids. DNA-complex-formation analyses with a gel-mobility-shift assay and sequence-specific probing of H-DNA-forming (GAA)nsequences by single-strand oligonucleotides and triplex-directed cleavage demonstrated that a parallel pyrimidine (rather than purine) triplex is the more stable motif formed at (GAA)nrepeats under physiologically relevant conditions.
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| 9. |
- Geny, Sylvain, et al.
(författare)
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Next-generation bis-locked nucleic acids with stacking linker and 2 '-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes
- 2016
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 44:5, s. 2007-2019
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Tidskriftsartikel (refereegranskat)abstract
- Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson-Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2'-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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| 10. |
- Ghidini, Alice, et al.
(författare)
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Clamping of RNA with PNA enables targeting of microRNA
- 2016
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Ingår i: Organic and biomolecular chemistry. - : Royal Society of Chemistry (RSC). - 1477-0520 .- 1477-0539. ; 14:23, s. 5210-5213
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Tidskriftsartikel (refereegranskat)abstract
- To be able to target microRNAs also at stages where these are in a double stranded or hairpin form we have studied BisPNA designed to clamp the target and give sufficient affinity to allow for strand invasion. We show that BisPNA complexes are more stable with RNA than with DNA. In addition, 24-mer BisPNA (AntimiR) constructs form complexes with a hairpin RNA that is a model of the microRNA miR-376b, suggesting that PNA-clamping may be an effective way of targeting microRNAs.
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