Selective binding of looped oligonucleotides to a single-stranded DNA and its influence on replicationin vitro

Abstract

Complexing of looped and circular oligonucleotides, composed of either 2'-deoxyribo- or 2'-O-methylribonucleoside units, with completely matching or partially mismatching complementary DNA sequences was studied. Melting experiments revealed considerable differences among the stabilities of these hybrid complexes. Maximum stability and selectivity was displayed by oligomers 2 and 5. It was concluded that a linear stretch, attached to 1'-O- of 3'-deoxypsicothymidine unit (Z) increases the selectivity of hybridisation and stability of the complex as a whole. This allows one to aim the target DNA very precisely at its polyadenine part as well as at adjacent sequence simultaneously. Experiments on termination of primer extension catalysed by different DNA-polymerases--Sequenase, Klenow fragment and Tth--have demonstrated that looped oligomer 5, composed of 2'-O-methylribonucleosides appears to be a highly selective and potent inhibitor of replication in vitro. Features of looped oligonucleotides, composed of 2'-O-methylribonucleosides seem to be useful for design of highly specific antigene oligonucleotides.

Synthesis and Triple‐Helix‐Stabilization Properties of Branched Oligonucleotides Carrying 8‐Aminoadenine Moieties

“…Most of the work on branched oligonucleotides was first focused on the study of these compounds as splicing intermediates of eukaryotic mRNAs [10 ± 12]. Moreover, branched nucleic acids have been prepared by using nucleoside branching points other than the 2'-and 3'-positions of the regular ribonucleoside such as those provided by 4'-C-(hydroxymethyl)thymidine [13] [14], arabino-uridine [15], or the nucleobase [16] [17]. The complexity of the synthesis of the branching molecules and the low yields obtained triggered the search for non-nucleoside branching molecules, such as derivatives of hexane-1,2,6-triol [18], 1,3-diaminopropanol [19], and pentaerythritol [20] [21].…”

“…This synthetic approach allows the preparation of parallel hairpins without the need of the reversed phosphoramidites, thus facilitating the preparation of parallel hairpins carrying modified bases and backbones. In most of the previous work in this area, nucleosides were used as branching units [13] [15] [17] [23] [24], as the conformational rigidity imparted by the sugar could be exploited to preorganize and induce triplex formation. We preferred the use of the non-nucleoside branching unit 11 because it is easy to prepare and it is free of possible side reactions described for the synthesis of branched RNA such as phosphoryl migration and/or chain cleavage [10 ± 12] [24].…”

“…{[(9H-Fluoren-9-ylmethoxy)carbonyl]oxy}-N-{2-hydroxy-3-{{4-[(4-methoxytrityl)oxy]-1-oxobutyl}ami-no}propyl}butanamide(13). A soln.…”

Selective Circular Oligonucleotide Probes Improve Detection of Point Mutations in DNA

“…Accordingly, detection of singlebase alterations within certain sequences may still be difficult and, even when possible, depends on time-consuming optimization of the probe length. Earlier, we reported the synthesis and highly selective binding of looped oligonucleotides to single-stranded DNA [9] [10] and also the interesting inhibitory properties of double-helix-forming circular oligomers [11]. More recently, we investigated the interaction of some doublehelix-forming circular oligonucleotide probes with various DNA targets, employing thermodynamic analysis.…”

Solid‐Phase Supports for Oligonucleotide Synthesis

“…The attachment of aminoalkyl‐tethered azacrown derivatives required overnight treatment with a 0.5 M aqueous solution of the reagent (Niittymäki et al, ). An ability to introduce cystamine at the terminus of oligonucleotides proved to be particularly convenient because it provided an expeditious access to 3′‐mercaptoalkylated oligonucleotides, useful intermediates in post‐synthetic cyclization of oligonucleotides (Azhayeva et al, ,b) and their immobilization on polymeric particles (Hakala and Lönnberg, ). Using the solid support 68 , oligonucleotide‐3′‐carboxylates may be generated by action of 0.05 M aqueous or methanolic K 2 CO 3 .…”