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. 1998 Aug 18;31(8):502-510.
doi: 10.1021/ar9602462.

Recognition of DNA, RNA, and Proteins by Circular Oligonucleotides

Eric T Kool  1
Affiliations

Recognition of DNA, RNA, and Proteins by Circular Oligonucleotides

Eric T Kool. Acc Chem Res. .
No abstract available

PubMed Disclaimer

Figures

FIGURE 1
FIGURE 1
Illustration of how an oligonucleotide template or “splint” can be used to organize the ends of a precursor oligonucleotide for cyclization. Ligation chemistries (or ligase enzymes) can be used to close the circle under dilute conditions. Nontemplated cyclizations fare poorly for oligonucleotides greater than ca. 20 nucleotides in length.
FIGURE 2
FIGURE 2
Architecture of a pyrimidine–purine–pyrimidine triple helix, showing the base triads and the strand organization.
FIGURE 3
FIGURE 3
Strand orientation of a pyr-pur-pyr triplex and illustration of how a termolecular complex can be made bimolecular by use of various linking strategies. Dashes indicate Watson–Crick complementarity, and dots, Hoogsteen complementarity. Connecting two antiparallel-oriented strands makes a hairpinlike ligand, and connecting both ends makes a circular ligand.
FIGURE 4
FIGURE 4
Strategy for design of a cyclic oligonucleotide that can bind two different target sequences by conformation switching. Multisite binding can in principle lead to a broader spectrum of activity or application.
FIGURE 5
FIGURE 5
The strand orientation of a pur-pur-pyr triplex and illustration of how a termolecular complex can be made bimolecular by use of various linking strategies. This allows the efficient targeting of pyrimidine strands.
FIGURE 6
FIGURE 6
Illustrations of two of three possible complexes formed by a triplex-complementary circular oligonucleotide with duplex DNA. The third mode is illustrated in Figure 7.
FIGURE 7
FIGURE 7
Proposed mode of highest-affinity binding of duplex DNA by a circular oligonucleotide containing a triplex-forming domain. The oligonucleotide threads itself over the duplex, forming a pseudorotaxane complex.
FIGURE 8
FIGURE 8
Catenane formation by a triplex-forming 34mer circular oligonucleotide trapped on a 147-bp circular duplex DNA. The threading mode of binding (Figure 7) was proven by forming the catenane from a linear duplex on which the smaller circle was threaded.
FIGURE 9
FIGURE 9
Scheme for use of small synthetic circular oligonucleotides as catalysts for the synthesis of long repeating strands of DNA or RNA (“rolling circle synthesis”). Note that for rolling circle DNA synthesis a short primer is also required to initiate each repeating strand; for RNA synthesis, no primer is needed and the enzyme starts at a random “C” in the circle. If a cleavage site is engineered into the repeating strand, the reaction can yield unit-length oligonucleotides in amplified amounts.
Chart 1
Chart 1
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