Abstract
Deoxyribonucleic acid (DNA) is a macromolecule that contains the information for all living organisms to achieve important cellular processes such as growth and replication. DNA consists of two strands coiled around each other to form a double helix. Several interactions including Watson-Crick pairing and stacking between the bases stabilize the double helix. To ensure the integrity of genetic information, the bases are on the inside the double helix whereas the phosphate and sugar groups are on the outside. Thus, most DNA information is not accessible until DNA is unwound prior to replication or transcription. In cells, enzymes called helicases achieve DNA strands separation.
The anti-gene strategy aims to introduce a short single-stranded oligonucleotide (ON) to bind genomic DNA at a specific site to block the mRNA transcription. As a result, mRNA and protein expression for a specific gene are expected to be reduced, which could be beneficial in certain clinical contexts. However, this therapeutic strategy is hampered by the low stability of the DNA binding, the difficulty to reach the genomic target and to block the RNA polymerase, suggesting the needs for new DNA binding ONs.
In this thesis, we developed clamp-ONs, bis-locked nucleic (bisLNAs), binding via Hoogsteen and Watson-Crick interactions. In paper I, we assessed their binding characteristics and demonstrated their ability to invade supercoiled DNA at intranuclear pH and salt conditions. In paper II, we investigated the step-by-step mechanism for bisLNA invasion. Based on this mechanism, we designed a new generation of bisLNAs using non- natural modifications such as a stacking linker and 2 ́-glycylamino LNAs. In paper III, we investigated how the bisLNAs invade in a more complex environment using rolling circle amplification for detection.
