Locked Nucleic Acids: Properties, Applications, and Perspectives

Abstract

A decade has passed since the introduction of locked nucleic acid (LNA) [1][2][3]. This chapter provides a review and a current status on the features and applications of LNA. Attention is focused on the structural chemistry of LNA and on its applications for therapeutics and probes. With regards to the latter point, the chapter is based on former comprehensive reviews on LNA applications [4][5][6] and, for that reason, is focused on results reported subsequently, with no intention of being comprehensive.The field of nucleic acid chemistry has evolved considerably during the past few decades, leading from synthetic developments via molecular recognition into nucleic acid-based therapeutics, powerful diagnostic probes, and modern nanobiotechnology. From the structural perspective, the central issue has been the thorough understanding of the basis for molecular recognition and the selective formation of nucleic acid complexes, initially the classic Watson-Crick-type double helix. The central creative challenge for synthetic chemists has been to design simple chemical perturbations of the natural duplex in order to increase our knowledge within nucleic acid chemical biology, and to bring this knowledge into applied nucleic acids research [7-9].The major motivation behind the design of nucleic acid analogues has, over the past two decades, been the antisense strategy aimed at the silencing of genes by strong binding towards mRNA, with or without associated RNA-cleavage. Two central problems have motivated the chemical effort: (1) the physiological instability of natural oligonucleotides; and (2) the relatively moderate affinity of short natural oligonucleotides for their RNA-targets [10,11]. If a solution to these problems -as well as to the delicate question of cellular delivery -can be found, then oligonucleotides will present unlimited therapeutic perspectives. Among the more than 1000 chemical analogues tested for these properties, a large part seems to induce a high degree of resistance towards nucleolytic degradation, although this is dependent on the sequence composition, the number and positioning of the chemical modifications within the sequence, and on the degree of perturbation compared to the natural chemical structure. On the other hand, significantly increasing the RNA-affinity of an Modified Nucleosides: in Biochemistry, Biotechnology and Medicine. Edited by Piet Herdewijn

Duplex and Triplex Formation of Mixed Pyrimidine Oligonucleotides with Stacking of Phenyl-triazole Moieties in the Major Groove

“…It adds to this importance that the stabilization increases with two consecutive modifications of 1 or 2 . For the development of antisense oligonucleotides, 1 and 2 can easily be combined with other modifications such as LNA and phosphorthioates that in combination has proven very promising in antisense research . LNA monomers induce a larger increase in thermal stability of DNA:RNA duplexes than the nucleobase substituents of 1 and 2 , but the two kinds of modifications show opposite behavior, as the impact of an LNA monomer is largest by one incorporation and then decreasing, relatively, by the number of consecutive incorporations.…”

“…The idea of regulating gene expression by chemically modified oligonucleotides has been pursued for three decades. , The therapeutic potential has been formulated in the so-called antisense , and antigene strategies, where the molecular target is RNA and genomic double stranded DNA, respectively. The chemically modified oligonucleotides should be physiologically stable and form thermally strong duplexes with RNA or triplexes with DNA. , A significant amount of chemical modifications have been presented, and among the most successful are 2′-modified nucleotides, conformationally restricted carbohydrate moieties, as in LNA, and base-modified analogues . As a prime example of the latter, nucleobases with extended ring systems have been found to give very strong duplexes due to increased π–π stacking.…”

Synthesis of Functionalized Carbocyclic Locked Nucleic Acid Analogues by Ring-Closing Diene and Enyne Metathesis and Their Influence on Nucleic Acid Stability and Structure

“…By introducing one or more LNA−nucleoside monomers into an otherwise unmodified oligodeoxynucleotide, unprecedented recognition of complementary RNA and DNA has been obtained. The increase in thermal stability (Δ T m ) of the formed duplexes compared to unmodified duplexes ranges from +3 to +8 °C for each incorporation of an LNA monomer. , It has been demonstrated that each LNA−nucleoside monomer is able to conformationally tune its neighboring unmodified 2′-deoxynucleosides from S - to N -type conformations (Figure ) . By this means, the overall duplex conformation is driven toward A-type or A-type-like duplex forms by the introduction of only a few LNA nucleosides.…”

“…Oligonucleotides that are conformationally restricted due to bicyclic nucleoside building blocks have demonstrated unique molecular recognition of complementary nucleic acid sequences and thus very promising properties as, e.g., antisense oligonucleotides (AOs), siRNA, or triplex-forming oligonucleotides (TFOs) . More than any other nucleic acid analogue, locked nucleic acid (LNA) has been recognized as the prime tool for engineering strong and specific nucleic acid recognition. , LNA constitutes only a small structural perturbation to natural nucleic acids, and its preparation is completely compatible with standard solid-phase DNA synthesis. The LNA nucleoside monomer (Figure , 1 ) is a bicyclic nucleoside that is locked in an N -type conformation due to an oxymethylene bridge between the 2′- and 4′-positions.…”