Single strand targeted triplex-formation. Destabilization of guanine quadruplex structures by foldback triplex-forming oligonucleotides

Kandimalla, Ekambar R.; Agrawal, Sudhir

doi:10.1093/nar/23.6.1068

Cited by 24 publications

(12 citation statements)

References 39 publications

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“…5'-DMT-2'-t-Butyldimethylsilyl-and 2'-0-methyl-3'-~-cyanoethyl phosphoramidites for RNA and 2'-0-methyl-RNA synthesis, respectively, were purchased from Millipore and Chemgenes. Deprotection and purification of the oligonucleotides was carried out as described earlier (20). Oligonucleotides were quantified by measuring absorbance at 260 nm using extinction coefficients that were calculated by the nearest neighbor method (25).…”

Section: Methodsmentioning

confidence: 99%

“…Both FfFOs and circular oligonucleotides exhibit specific recognition and high affinity for the target sequence. FlFOs or oligonucleotide clamps strandinvade duplex DNA and form triple helices with the purine strand (18), disrupt guanine quadruplex structures (19,20), and arrest DNA synthesis in vitro (21).…”

Section: Introductionmentioning

confidence: 99%

“…We used 2'-0-methylribonucleotides for FlFOs and control duplex forming oligoribonucleotide because they are resistant to RNase and easy to handle. 2'-0-methylribonucleotides bind to the target sequences by duplex and triplex formation (20,22,23). We used, however, a normal RNA purine strand as target to mimic natural RNA.…”

Section: Introductionmentioning

confidence: 99%

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Single-Stranded DNA and RNA Targeted Triplex-Formation: UV, CD and Molecular Modeling Studies of Foldback Triplexes Containing Different RNA, 2′-OMe-RNA and DNA Strand Combinations

Kandimalla¹,

Venkataraman

Sasisekharan

et al. 1997

Journal of Biomolecular Structure and Dynamics

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We studied the influence of different 2'-OMe-RNA and DNA strand combinations on single strand targeted foldback triplex formation in the Py.Pu:Py motif using ultraviolet (UV) and circular dichroism (CD) spectroscopy, and molecular modeling. The study of eight combinations of triplexes (D.D:D, R*.D:D, D.D:R*, R*.D:R*, D.R:D, R*.R:D, D.R:R*, and R*.R:R*; where the first, middle, and last letters stand for the Hoogsteen Pyrimidine, Watson-Crick [WC] purine and WC pyrimidine strands, respectively, and D, R and R* stand for DNA, RNA and 2'-OMe-RNA strands, respectively) indicate more stable foldback triplex formation with a DNA purine strand than with an RNA purine strand. Of the four possible WC duplexes with RNA/DNA combinations, the duplex with a DNA purine strand and a 2'-O-Me-RNA pyrimidine strand forms the most thermally stable triplex, although its thermal stability is the lowest of all four duplexes. Irrespective of the duplex combination, a 2'-OMe-RNA Hoogsteen pyrimidine strand forms a stable foldback triplex over a DNA Hoogsteen pyrimidine strand confirming the earlier reports with conventional and circular triplexes. The CD studies suggest a B-type conformation for an all DNA homo-foldback triplex (D.D:D), while hetero-foldback triplex spectra suggest intermediate conformation to both A-type and B-type structures. A novel molecular modeling study has been carried out to understand the stereochemical feasibility of all the combinations of foldback triplexes using a geometric approach. The new approach allows use of different combinations of chain geometries depending on the nature of the chain (RNA vs. DNA).

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Single-Stranded DNA and RNA Targeted Triplex-Formation: UV, CD and Molecular Modeling Studies of Foldback Triplexes Containing Different RNA, 2′-OMe-RNA and DNA Strand Combinations

Kandimalla¹,

Venkataraman

Sasisekharan

et al. 1997

Journal of Biomolecular Structure and Dynamics

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“…These oligonucleotides containing Watson-Crick and Hoogsteen base pair-forming domains connected by a nucleotide loop (called foldback triplex-forming oligonucleotides; FTFOs) show increased affinity and specificity for target sequences compared to normal duplex-(antisense) and triplex-(antigene) forming oligonucleotides (11). The FTFOs destabilize quadruplex structures fonned by guanine-rich RNA and DNA (15,16). Circular oligonucleotides displace pyrimidine complementary strand and bind to the purine strand of a duplex DNA by triplex fonnation as in the case of PNA ( 17).…”

Section: Introductionmentioning

confidence: 99%

“…Circular oligonucleotides displace pyrimidine complementary strand and bind to the purine strand of a duplex DNA by triplex fonnation as in the case of PNA ( 17). 4 duplex DNA (15). Oligonucleotides 3-10 13 were designed to be T different lengths of Watson-Crick complementary sequences that bind to the target sequence and fonn duplexes of different lengths.…”

Section: Introductionmentioning

confidence: 99%

Single Strand Targeted Triplex Formation: Strand Displacement of Duplex DNA by Foldback Triplex-Forming Oligonucleotides

Kandimalla¹,

Manning²,

Agrawal³

1995

Journal of Biomolecular Structure and Dynamics

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Linear oligonucleotides that bind to single-stranded nucleic acid targets by formation of both Watson-Crick (duplex) and Hoogsteen (triplex) hydrogen bonds simultaneously (foldback triplex-forming oligonucleotides; FTFOs) were studied for their ability to disrupt duplex DNA. Recently, we reported that FTFOs interfere with quadruplex forming ability of guanine rich RNA and DNA sequences and indicated that they might also disrupt duplex structures binding to the purine target strand by foldback triplex formation (Kandimalla and Agrawal, Nucleic Acids Res. (1995) 23, 1068-1074). We now obtained evidence for strand displacement of duplex DNA by FTFOs using nuclease assays and thermal melting studies. UV melting studies revealed that complementary strands of 16 to 31 bases long were completely displaced. Results of DNase I assays showed that the FTFOs bound to purine site by strand displacement probably by preassociating with the duplex DNA in the major groove via Hoogsteen hydrogen bonding and subsequently displacing the complementary strand. Experiments with S1 nuclease, an enzyme specific for single-stranded nucleic acids, confirmed the strand displacement ability of the FTFOs.

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Thermodynamics of oligonucleotide triple helices

Plum

1997

Biopolymers

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Single strand targeted triplex-formation. Destabilization of guanine quadruplex structures by foldback triplex-forming oligonucleotides

Abstract: ABSTRACT

Cited by 24 publications

References 39 publications

Single-Stranded DNA and RNA Targeted Triplex-Formation: UV, CD and Molecular Modeling Studies of Foldback Triplexes Containing Different RNA, 2′-OMe-RNA and DNA Strand Combinations

Single-Stranded DNA and RNA Targeted Triplex-Formation: UV, CD and Molecular Modeling Studies of Foldback Triplexes Containing Different RNA, 2′-OMe-RNA and DNA Strand Combinations

Single Strand Targeted Triplex Formation: Strand Displacement of Duplex DNA by Foldback Triplex-Forming Oligonucleotides

Thermodynamics of oligonucleotide triple helices

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