Flexible and Frozen Sugar-Modified Nucleic Acids - Modulation of Biological Activity Through Furanose Ring Dynamics in the Antisense Strand

Abstract

A comparison of carbohydrate modified nucleic acids has identified key structural characteristics in antisense oligonucleotides (AON) that are necessary for sufficient clinical utility, including increased duplex stability towards RNA complements and improved hydrolytic resistance towards general serum and cellular nucleases. As such, the exogenous addition of short, synthetic oligonucleotides can influence cellular RNA metabolism at any or all levels of replication, transcription or translation by tight and specific hybridization with a chosen target and subsequently stop further function at that site. Furthermore, appropriate modification of the sugar residue may prove to be a vital design element in future AONs that operate by promoting enzyme assisted catalytic destruction of the mRNA target. Unfortunately, many of the current AON designs have provided little insight on the particular structural role of the AON towards enzymatic discrimination of the resultant hybrid. The use of RNase H as a cellular vehicle to assist the inhibitory potency of an AON as well as possible ways of enhancing activity in pre-existing antisense candidates are presented. Of the emerging criteria in this aspect, a balance between flexibility and rigidity within the AON appears to be a critical mediator of the RNase H assisted antisense effect. Accordingly, this review describes the conformational features and selected biological attributes of some of the more prominent AON contenders with a focus on the conformational criteria by which ribonuclease H activity is recruited to a particular hybrid target.

2-Modified Oligonucleotides for Antisense Therapeutics

“…In order to overcome these limitations several chemically modified antisense oligonucleotides have been designed and synthesized. These topics have been extensively reviewed in two recent articles [3,5]. Here we cover mainly our efforts since 2000 in this area.…”

“…This article focuses on the progress made in the design of antisense oligonucleotides that act via an RNase H mechanism of action. Recently several review articles have appeared in the literature dealing with this topic [3,4,5]. Therefore, the scope of this review is to summarize our work in this area in conjunction with related works from the literature.…”

Chemical Synthesis and Biological Application of Modified Oligonucleotides

“…2′OMe RNA has multiple advantages over RNA and DNA, such as improved ASO binding affinity, improved nuclease resistance, and reduced immune stimulation. − The stability is on the order of 0.2–0.8 °C Δ T m per modified nucleotide 2′OMe:RNA duplex/DNA:RNA duplex of the same sequence for uridine . The appealing properties of 2′OMe RNA inspired researchers to extensively test 2′- O -alkyl RNAs to determine the optimal alkyl substituent. − Of the tested alkyl substituents, 2′- O -methoxyethyl (2′MOE) , proved to be one of the best modifications for increased nuclease resistance and higher binding affinities for ASOs (0.9–1.7 °C Δ T m ). − The FDA approved antisense drugs Mipomersen, Nusinersen, Milasen, Inotersen, the EU approved Volanesorsen, , and several other ASO candidates currently in clinical trials featuring 2′MOE RNA, making it one of the most successful ribose modifications. Although 2′OMe and 2′MOE are somewhat interchangeable modifications, 2′MOE is more common in ASOs.…”

Comparing In Vitro and In Vivo Activity of 2′-O-[2-(Methylamino)-2-oxoethyl]- and 2′-O-Methoxyethyl-Modified Antisense Oligonucleotides

“…In order to improve the in vivo profile of antisense oligonucleotides (ASOs), hundreds of chemical modifications have been synthesized and evaluated for biophysical and biochemical properties. – Antisense molecules modified at the 2′- O -position of the sugar either at one or both termini (gapmers, Figure ) emerged as leading second-generation chemistries for clinical applications. – In particular, 2′- O -methoxyethyl (2′- O -MOE, Figure )-modified gapmer ASOs successfully demonstrated effective inhibition of many viral and cellular gene products, both in vitro and in vivo . Therefore, the 2′- O -MOE chemistry became one of the most successful modifications to advance to clinical use because of significant improvement in metabolic stability, cellular absorption, and protein binding properties.…”