Selective Circular Oligonucleotide Probes Improve Detection of Point Mutations in DNA

Abstract

The synthesis of disulfide-cross-linked circular oligonucleotides, employing two different approaches, was accomplished. Several circular oligomers, which bear a C(5)-aminoalkyl-tethered thymidine unit, were labeled with photoluminescent europium(III) chelates. All circular structures were thoroughly characterized with denaturing PAGE and electrospray-ionization mass spectrometry. It was demonstrated that the disulfide cross-linking, resulting in circularization, considerably increases the enzymatic stability of phosphodiester oligonucleotides. In addition, UV melting experiments, followed, where possible, by extraction of thermodynamic parameters, revealed that several circular oligomers appear to be more selective towards their complementary targets than their corresponding linear precursors. Finally, the mixed-phase hybridization experiments have demonstrated that use of circular probes indeed improves the selectivity in the detection of DNA point mutations.

Allosteric Control of Oligonucleotide Hybridization by Metal-Induced Cyclization

“…Formation of a 1:1 complex between 1 and Fe(II) is confirmed by electrospray MS (negative mode, m/z 1796 [M + Fe(II)], 4- indicates smooth formation of a product (1)Fe (confirmed by elution and MALDI-TOF MS of the spot), which has a somewhat higher mobility than the linear probe 1, as expected for a relatively small circular DNA. 26 A band of similar retention factor is observed in the gel for a (1)Ni(II) 1:1 mixture (Figure 1, lane 3). In contrast, the intermolecular complex (2) 2 Fe formed with the mono-tpy compound 2 has a very low mobility (lane 1) due to its double DNA chain length.…”

“…This observation is consistent with the strong destabilization of a 25mer DNA duplex when one of the strands is circularized by a covalent linker. 26 Addition of the strong chelator EDTA does not increase the fluorescence of 5.…”

Circular DNA by “Bis‐Click” Ligation: Template‐Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides

“…In the case of the circular products, the mobility also depends on the length of the oligonucleotides. For the 9‐ and 18‐mers, the circular products migrate faster, whereas the circular 36‐mers move slower …”

“…For the 9-and 18-mers, the circularproducts migrate faster,whereas the circular 36-mers move slower. [23] Because circularD NA forms strongerd uplexes than those of their linear counterparts, [3a] we wondered if this would still the case when ab is-triazolyl linkage was present within the hybridization element. To this end, hybridization experiments to detect UV duplex melting were performed with 36-mers cODN-10 and cODN-12 and the short complementary strand ODN-3 overlapping the bis-nucleoside linker.A ll species showeds igmoidal melting curves ( Figure S7 in the Supporting Information).…”

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. [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.…”