Looped oligonucleotides form stable hybrid complexes with a single-stranded DNA

Abstract

Several new branched (1, 2), circular (9) and looped oligonucleotides (14-17) were synthesized. 3'-Deoxypsicothymidine was employed to create the site of branching when required. The circular and looped structures were obtained by oxidative disulfide bond formation between mercaptoalkyl tether groups. All the oligonucleotides prepared contained two T11 sequences, and the branched and looped oligomers an additional alternating CT sequence. The melting experiments revealed that the branched oligonucleotides form relatively weak hybrid (double/triple helix) complexes with the single-stranded oligodeoxyribonucleotide, showing a considerable destabilizing effect produced by the structure at the point of branching. The data obtained with looped oligonucleotides demonstrated considerable stabilization of the hybrid (double/triple helix) complexes with the complement. The data reported may be useful in attempting to design new antisense or antigene oligonucleotides capable of forming selective and stable bimolecular hybrid complexes with nucleic acids.

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.…”

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

“…All the oligodeoxyribonucleotides used in the present study were synthesised and characterised as reported (32). Oligo-2'-O-methylribonucleotides were assembled using the ABI standard RNA coupling cycle and monomers from Glen Research.…”

“…A number of recent investigations have also been devoted to in vitro inhibition of important biochemical processes, such as replication (27,28), transcription (29,30) and reverse transcription (31) by triplex formation. We have recently reported a new strategy for DNA recognition based on a bimolecular hybrid complex (double/triple helix) formation (32). In that study we found that looped oligonucleotides undergo simultaneous binding to a polyadenine region and an adjacent sequence of a single-stranded DNA target.…”

Phthalimide–Oxy Derivatives for 3′‐ or 5′‐Conjugation of Oligonucleotides by Oxime Ligation and Circularization of DNA by “Bis‐ or Tris‐Click” Oxime Ligation

“…[1][2][3][4][5] The first cyclic DNAs were synthesized in the late 1980s, [1,[6][7][8][9] and new syntheses of cyclic DNAs and RNAs have been reported along the years. Their synthesis has been performed by using enzymatic and chemical methods to afford phosphodiester, [1,[10][11][12][13] phosphorothiolate diester, [14][15][16][17] disulfide [18][19][20] oxime, [17,21] and, more recently, triazole linkers. [22][23][24][25][26][27][28][29] As a rule, cyclic oligonucleotides can be synthesized as a result of the complementary chemical functions borne on both ends of the sequence.…”