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- Umek, Tea
(författare)
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Anti-gene oligonucleotides : DNA binding and therapeutic application
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The field of nucleic acid therapeutics has in the last decade experienced substantial growth. This is evident from a multitude of new publications, an increasing number of clinical trials and several approved therapeutics on the market. Therapeutic oligonucleotides (ONs) are designed to treat mostly genetic disorders, caused by the expression of non-functional or toxic ribonucleic acids (RNA) or proteins. They can be divided into protein-, RNA- and DNA targeting ONs. While the first two have already had approved therapies, the last is still in its infancy. This thesis focuses on the improvement and assessment of DNA targeting ONs, also termed anti-gene ONs. Paper I evaluates a strand-invading anti-gene ON (AGO) for the treatment of Huntington’s disease (HD) and its mRNA down-regulating effect during in vitro differentiation from induced pluripotent stem cells to neurons. It shows that the locked nucleic acid (LNA)/DNA mixmer ON with a phosphorothioate (PS) backbone directed against the repeat region of the huntingtin (HTT) gene downregulates HTT mRNA and protein without affecting the process of differentiation. In Paper II, anti-gene LNA/DNA mixmer clamp-type ONs, which hybridize to the target by forming both Watson-Crick (WC) and Hoogsteen hydrogen bonds, are optimized to achieve improved invasion into double stranded DNA. By positioning an intercalating moiety between or on the WC and Triplex Forming ON (TFO) arms, the AGOs achieve efficient invasion at nanomolar concentrationsin vitro. Furthermore, the corresponding PS modified ONs are tested in HD cell model for their effect on mRNA expression, where they cause significant downregulation of HTT mRNA. In Paper III, a non-B-DNA structure formed by a sequence in the MYC gene promoter is analyzed in vitro. Furthermore, the effect of this structure, more specifically an H-DNA, on the strand-invasion efficiency of LNA/DNA mixmer tail-clamp AGOs was evaluated. The results show that the invasion of the ON can be positively influenced by an H-DNA if the ON does not have an intercalating moiety.
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| 2. |
- Umek, Tea, et al.
(författare)
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Oligonucleotide Binding to Non-B-DNA in MYC
- 2019
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Ingår i: Molecules. - : MDPI AG. - 1431-5157 .- 1420-3049. ; 24:5
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Tidskriftsartikel (refereegranskat)abstract
- MYC, originally named c-myc, is an oncogene deregulated in many different forms of cancer. Translocation of the MYC gene to an immunoglobulin gene leads to an overexpression and the development of Burkitt's lymphoma (BL). Sporadic BL constitutes one subgroup where one of the translocation sites is located at the 5'-vicinity of the two major MYC promoters P-1 and P-2. A non-B-DNA forming sequence within this region has been reported with the ability to form an intramolecular triplex (H-DNA) or a G-quadruplex. We have examined triplex formation at this site first by using a 17 bp triplex-forming oligonucleotide (TFO) and a double strand DNA (dsDNA) target corresponding to the MYC sequence. An antiparallel purine-motif triplex was detected using electrophoretic mobility shift assay. Furthermore, we probed for H-DNA formation using the BQQ-OP based triplex-specific cleavage assay, which indicated the formation of the structure in the supercoiled plasmid containing the corresponding region of the MYC promoter. Targeting non-B-DNA structures has therapeutic potential; therefore, we investigated their influence on strand-invasion of anti-gene oligonucleotides (ON)s. We show that in vitro, non-B-DNA formation at the vicinity of the ON target site facilitates dsDNA strand-invasion of the anti-gene ONs.
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