DNA Recognition by Hybrid Oligoether–Oligodeoxynucleotide Macrocycles

Abstract

The sequence-specific binding of RNA and DNA by synthetic oligonucleotides and analogues is important as a diagnostic tool in the study of naturally ocurring polynucleotides and is the subject of intense research as a potential therapeutic strategy as well. [1][2][3] Two limitations of natural DNA oligomers in these applications are their low binding affinity [2] and also their limited stability, due to cleavage by exo-and endonucleases which occur in natural systems. [4,5] We report here the construction of circular hybrid molecules which contain two oligonucleotide domains bridged by two oligoethylene glycol chains. These molecules bind with high affinity to complementary strands of RNA and DNA and display exceptional resistance to degradation by nucleases.Oligoethylene glycol chains have been successfully used as simple linking groups which replace nucleotide units in linear oligonucleotide chains [6] and in hairpin-shaped oligonucleotides in duplexes and triplexes as well. [7] We wished to determine whether such spacers could be incorporated into circular structures and what the effect on their recognition properties and stability would be. We have previously shown that circular oligonucleotides can display very strong binding affinity [8] and high sequence selectivity [9] for singlestranded DNA and RNA by forming bimolecular triple helices. These macrocycles bind by forming bonds on two sides of a linear target strand, and their unusual recognition characteristics arise from the preorganized circular structure. [10] Examination of models [11] and published data on DNA triple helices [12] revealed that a group 19-21 Å long would be ideal for bridging the outer pyrimidine strands, and that fivebase nucleotide loops might be replaced with penta-or hexaethylene glycol chains. In addition to confirming our model for the binding, such a replacement might lead to favorable properties, such as lower cost and higher synthesis yield (by decreasing the number of nucleotide units), longer lifetimes in biological media, and possibly, improved membrane permeability (by decreasing total negative charge).The linear precursors to the compounds investigated in this study 1-3 were constructed by automated DNA synthesis methods [13] (Experimental Procedure) with the introduction of the synthetic dimethoxytrityl hexa-or pentaethylene glycol (HEG or PEG) phosphoramidites [7] at two positions. The oligomers d(A) 12 (for 1) and

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

“…Circular oligonucleotides have no ends and thus can be considerably more resistant to such degradation. 108,85,111 c. Cross-Linked Oligonucleotides: The clamp and circular oligonucleotide approaches are strategies in which two DNA-binding domains are linked at their end or ends. Another approach would be to link them across the center.…”

Structural Optimization of Non-Nucleotide Loop Replacements for Duplex and Triplex DNAs

“…Studies in modification of these structures have led to the development of nonnucleotide linking groups which replace several nucleotides bridging a folded duplex or triplex structure. [3][4][5][6][7][8][9][10][11][12] Nonnucleotide groups have also been used as linkers in nonfolded structures as well. [13][14][15][16][17] Such linking groups are potentially useful replacements of natural nucleotides for several reasons.…”

Strong, Specific Binding of Six Different DNA Sequences by a Single Conformation‐Switching DNA Macrocycle

“…200 mM imidazole · HCl (titrated to pH 7.0 as a stock solution prior to addition to the reaction mixture). 100 mM NiCl 2 , and 125 mM BrCN for 12 h at 23°C, as described previously [11,16]. Workup and isolation were as described previously [11,17].…”