Inverted Motif for Oligonucleotide Triplexes: Adenosine-Pseudouridine-Adenosine (A-.PSI.-A)

Bandaru, Rajanikanth; Hashimoto, Harukichi; Switzer, Christopher

doi:10.1021/jo00109a002

Cited by 22 publications

(18 citation statements)

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“…to its own or a 5'-adjacent 5'-phosphate group (Arnez & Steitz, 1994) or intermolecularly, by triple-strand formation (Trapane et al, 1994;Bandaru et al, 1995). Stabilization could occur as a result of the increase in the 3'-endo conformation of the ribose moiety in C (Davis, 1995).…”

Section: Possible Functional Roles For Cmentioning

confidence: 99%

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

Ofengand

Bakin

1997

Journal of Molecular Biology

210

214

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Section: Possible Functional Roles For Cmentioning

confidence: 99%

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

Ofengand

Bakin

1997

Journal of Molecular Biology

210

214

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“…One of the most successful new strategies for the binding of single-stranded DNA has been the combined use of two oligonucleotide binding domains which form a triple helical complex with the target strand. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] In some cases this has been carried out using two physically separate strands, 4,16,18,19 and this can result in a binding advantage if the resulting triplex acts cooperatively. Examples of this behavior have been seen for peptide-derived nucleic acid backbones 4 and more recently for methylphosphonate DNA backbones.…”

Section: Introductionmentioning

confidence: 99%

“…[1][2][3] In one such approach, a double-length oligonucleotide can fold back to form a triplex bridge by a loop composed of nucleotides or of nonnucleotide linkers. 3,[7][8][9][10][11]14,15,19 Ligands of this type have been shown to bind a complementary target strand more tightly than standard Watson-Crick complements can. Such a binding advantage has been shown to result in improved inhibition of enzymatic DNA synthesis.…”

Section: Introductionmentioning

confidence: 99%

Very High Affinity DNA Recognition by Bicyclic and Cross-Linked Oligonucleotides

Chaudhuri

Kool²

1995

J. Am. Chem. Soc.

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We report the synthesis and DNA incorporation of a novel C-5 thiopropyne-substituted thymidine derivative which can be used to bring about covalent crosslinks between two noncomplementary DNA strands. This modified thymine pairs normally with adenine in duplex DNA and is shown not to be destabilizing to DNA double helices. Placement of the thiol-nucleotide near the center of opposing pyrimidine strands in pyr·pur·pyr triple helices results in crosslinking of the pyrimidine strands under aerobic conditions. Thermal melting studies at neutral pH show that such crosslinked ligands bind complementary purine strands with higher affinity than is possible with simple Watson-Crick recognition alone. In addition, we describe the construction of a triplex-forming circular oligonucleotide which contains a similar disulfide link across the center. This macrobicyclic ligand binds with extremely high affinity and sequence selectivity to a complementary purine DNA strand. The formation of crosslinks across two noncomplementary strands represents a new strategy for increasing affinity and selectivity of DNA recognition.

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“…Notable examples are the approaches described by Ts'o (see 20, 21), 44 by Agrawal (22, 23), 42 and by Switzer. 45 …”

Section: Binding Pyrimidine-rich Sequencesmentioning

confidence: 99%

Recognition of DNA, RNA, and Proteins by Circular Oligonucleotides

Kool

1998

Acc. Chem. Res.

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IntroductionWhile the backbone organization of DNA and RNA is normally quite regular, there are many structural forms which these molecules can adapt by undergoing various secondary and tertiary helical and folded interactions, by being subjected to twisting and bending, and by interconversion between various topological and knotted variations. Probably the most common structural form of DNA in nature is a long double helix in which the ends are joined into a circle. The genomes of most lower organisms are organized in this way, 1 and clearly this circular structure lends some important advantage to these organisms or evolution would not have selected for it.Most chemists are chiefly interested in structure and reactivity of molecules smaller than entire bacterial genomes; such large circular DNAs will not be discussed herein for that reason. Of particular interest, then, is the question: what are the smallest cyclic DNAs or RNAs which exist in nature? For DNA, the answer appears to be several hundred to perhaps 1500 nucleotides (nt), which is still rather large. For RNA, probably the smallest known circular structures are the viroid RNAs, which are single-stranded and as small as 246 nucleotides in size. 2 However, this is far from the smallest possible cyclic nucleic acid structure. Duplex DNA can exist in circles at least as small as 125 bp (base pairs); 3 cyclic structures smaller than this are difficult to achieve because of the rigidity of the double helix. 4 Single-stranded DNA and RNAs do not have this problem, and rings as small as two nucleotides are known. 5 Thus, the realm of possible cyclic DNA and RNA structures falls easily into the size range most palatable to chemists.Interestingly, although small synthetic circular DNAs had been reported a number of times as early as in 1968, 6 prior to 1990 there were no reported studies investigating the effect of this quite significant structural modification on DNA's molecular recognition properties. Despite this, there was quite reasonable precedent that such a structural alteration might have a large effect on such recognition properties. Indeed, in recent decades it has become widely recognized that macrocyclic molecular structures can have strong advantages in the formation of noncovalent complexes. 7 Among these advantages (relative to noncyclic molecules of similar structure) are tighter binding affinity and greater specificity for binding the target of interest. The advent of simple synthetic approaches to the construction of oligonucleotides has led to an explosion of studies aimed at studying and modifying their noncovalent binding properties. In our early work we proposed that the principle of macrocyclic recognition could also be applied to nucleic acids in small synthetic well-defined systems. The testing of that hypothesis is the subject of this Account. Recognition of Nucleic AcidsIn 1990 when we began our studies it was not trivial to synthesize a circular oligonucleotide from a linear precursor; however, the development of new synthetic meth...

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Inverted Motif for Oligonucleotide Triplexes: Adenosine-Pseudouridine-Adenosine (A-.PSI.-A)

Cited by 22 publications

References 0 publications

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

Very High Affinity DNA Recognition by Bicyclic and Cross-Linked Oligonucleotides

Recognition of DNA, RNA, and Proteins by Circular Oligonucleotides

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