Synthesis and properties of 3′-amino-2′,4′-BNA, a bridged nucleic acid with a N3′→P5′ phosphoramidate linkage

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…114 3 0 -Amino-LNA has been incorporated into oligonucleotides with a N3'-P5' phosphoramidate linkage. 34 The presence of the phosphoramidate linkage gave quite significant increases in thermal stabilities towards DNA, RNA and dsDNA, as well as nuclease resistance which was better than that found for phosphorothioate oligonucleotides. Base analogues that have been synthesised as LNA nucleotides include 5-methyl-dC used for miRNA detection, 138 and the analogues (27) and (28), both of which have successfully been used to aid triplex formation in the presence of a T:A interruption.…”

“…However, when (33) was incorporated into DNA it was destabilising by 5 1C per modification. 147 The tricyclic nucleoside (34) shows good RNA affinity, as well as high nuclease resistance, and a crystal structure of a duplex containing (34) shows the cyclopropane ring's importance in the overall conformational features that affect the affinity of the analogue for RNA. 148 The W-shaped nucleosides (35), previously shown to be effective at stabilising triplexes when present in the TFO, have been prepared bearing a p-amino group on the aromatic ring.…”

“…33 A phosphoramidate linkage has been introduced into an LNA oligomer (see section 1.2.2) which resulted in oligonucleotides with extraordinarily high resistance to nuclease digestion. 34 An important class of phosphoramidate modification is the morpholino nucleoside (PMO) (5), which have proven to be of particular interest in antisense applications. 35 Oligonucleotides containing PMO modifications have been prepared on a DNA synthesiser using phosphoramidite chemistry, and the resultant oligonucleotides showed good thermal stability with complementary DNA and RNA, albeit slightly reduced compared with DNA.…”

Synergistic Stabilization of Nucleic Acid Assembly by 2′-O,4′-C-Methylene-Bridged Nucleic Acid Modification and Additions of Comb-Type Cationic Copolymers

“…However, combinations of two stabilization methods have occasionally resulted in unexpectedly small effects. For example, while each of 2′-O,4′-C-methylene-bridged nucleic acid (2′,4′-BNA/LNA) modification (15-26) and N3′fP5′ phosphoramidate modification (27-33) of nucleic acid strands increases the thermal dissociation temperatures of duplex and triplex significantly, the combination of these two modifications results in less stabilizing activity than the 2′,4′-BNA modification alone (34,35). In another example, while †…”

“…However, combinations of two stabilization methods have occasionally resulted in unexpectedly small effects. For example, while each of 2′-O,4′-C-methylene-bridged nucleic acid (2′,4′-BNA/LNA) modification (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26) and N3′fP5′ phosphoramidate modification (27)(28)(29)(30)(31)(32)(33) of nucleic acid strands increases the thermal dissociation temperatures of duplex and triplex significantly, the combination of these two modifications results in less stabilizing activity than the 2′,4′-BNA modification alone (34,35). In another example, while 1 Abbreviations: TFO, triplex-forming oligonucleotide; PLL-g-Dex, poly(L-lysine)-graft-dextran; 2′,4′-BNA, 2′-O,4′-C-methylene-bridged nucleic acid; Bt, biotinylated; EMSA, electrophoretic mobility shift assay; T m , melting temperature; CD, circular dichroism; IAsys, interaction analysis system; k on , on-rate constant; k assoc , association rate constant; k off , off-rate constant; k dissoc , dissociation rate constant.…”