Inhibition of DNA Binding Proteins by Oligonucleotide-Directed Triple Helix Formation

Maher, L. James; Wold, B; Dervan, Peter B.

doi:10.1126/science.2549631

Cited by 434 publications

(268 citation statements)

References 46 publications

Supporting

Mentioning

265

Contrasting

Order By: Relevance

“…Such complexes can inhibit DNA binding proteins (11)(12)(13) and can repress eukaryotic promoters in vitro (14,15). Indirect evidence has been presented to suggest that triple helices can form and alter gene expression after exposure of intact cells to oligonucleotides (16)(17)(18).…”

Section: Hoogsteen Hydrogen Bonds [T-at (Or A-at) and G-gc Tripletmentioning

confidence: 99%

Recognition of duplex DNA by RNA polynucleotides

McDonald

Maher

1995

Nucl Acids Res

View full text Add to dashboard Cite

Section: Hoogsteen Hydrogen Bonds [T-at (Or A-at) and G-gc Tripletmentioning

confidence: 99%

Recognition of duplex DNA by RNA polynucleotides

McDonald

Maher

1995

Nucl Acids Res

View full text Add to dashboard Cite

“…Pyrimidine oligonucleotides were found to bind in a sequence-specific dependence to homopurine sites in duplex DNA by triple helix formation and had sufficient specificity and affinity to compete with sitespecific DNA binding proteins for occupancy of overlapping target sites (10). However, such oligonucleotide-directed triple helix formation has not been shown in cells in vitro or in vivo.…”

mentioning

confidence: 99%

Dual Blockade of Cyclic AMP Response Element- (CRE) and AP-1-directed Transcription by CRE-transcription Factor Decoy Oligonucleotide

Park

Nesterova

Agrawal³

et al. 1999

Journal of Biological Chemistry

119

116

View full text Add to dashboard Cite

Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins has important therapeutic potential. Synthetic double-stranded phosphorothioate oligonucleotides with high affinity for a target transcription factor can be introduced into cells as decoy cis-elements to bind the factors and alter gene expression. The CRE (cyclic AMP response element)-transcription factor complex is a pleiotropic activator that participates in the induction of a wide variety of cellular and viral genes. Because the CRE cis-element, TGACGTCA, is palindromic, a synthetic single-stranded oligonucleotide composed of the CRE sequence self-hybridizes to form a duplex/hairpin. Herein we report that the CRE-palindromic oligonucleotide can penetrate into cells, compete with CRE enhancers for binding transcription factors, and specifically interfere with CREand AP-1-directed transcription in vivo. These oligonucleotides restrained tumor cell proliferation, without affecting the growth of noncancerous cells. This decoy oligonucleotide approach offers great promise as a tool for defining cellular regulatory processes and treating cancer and other diseases.Eukaryotic transcription is regulated by the interplay of various protein factors at promoters (1, 2). It has been shown that prokaryotic repressors can function as negative regulators of eukaryotic promoters (3,4). This observation suggests that displacement of activating proteins might provide a general strategy for gene-specific repression in eukaryotes. Several approaches have been undertaken to control eukaryotic gene expression through such displacement.In one approach, trans-dominant mutants are generated that interfere with the function of transactivators. Mutants are generated that retain the ability to bind to cis-regulatory DNA sequences but that have dysfunctional transcriptional activation domains. These mutant transcription factors compete with their functional, wild-type counterparts for binding to the enhancer sequences and prevent the activation or repression of the target gene. Although this strategy has been successful, in vitro (5-8), the generation of such mutants is not always possible. The transcription factor must be well characterized such that the activation domain(s) is identified and can be mutated. Also, even with sufficient knowledge to generate such mutants, difficult gene therapy procedures would be required to express these proteins in vivo.Promoter competition strategy has also been utilized whereby plasmids containing cis-acting elements in common with the targeted gene are introduced in high copy number into cells (9). At high copy number, a majority of the transcription factors can be competitively bound away from the native enhancer sequences with gene expression accordingly regulated. Because these plasmids must be stably maintained at high copy number in target cells, a requirement that is difficult to achieve in vivo, this approach has also been limiting.Another alternative is to employ oligonucleotides to form triple heli...

show abstract

“…First of all, there are only two copies of a particular gene whereas there is a large continuous supply of the mRNA gene transcript. Moreover, blocking the transcription of the gene itself prevents repopulation of the mRNA pool, allowing a more efficient and lasting inhibition of gene expression [32,33]. The main disadvantage is that the ODN needs to cross the nuclear membrane and access its DNA target within the densely packed chromatin structure [34].…”

Section: Introductionmentioning

confidence: 99%

Contributions of the loops on the stability and targeting of DNA pseudoknots

Reiling¹,

Marky²

2014

Bio Chem Comp

View full text Add to dashboard Cite

Background: Pseudoknots have been found to play important roles in RNA function, examples include ribosomal frameshifting and in the 5' UTR of mRNA as riboswitches. In RNA frameshifting, there is a local formation of base-triplet stacks within the pseudoknot, increasing the stability of the terminal stem. The interaction of this triplex structure with the ribosome might help with the high-efficiency of frameshifting. The main objective of this work is to mimic RNA pseudoknots using DNA oligonucleotides for the control of gene expression. Specifically, we have designed a pair of DNA pseudoknots with different length in one of the loops to mimic the formation of a local triple helix, shown within RNA pseudoknots of the human telomerase. Methods: We have used a combination of temperature-dependent UV spectroscopy and calorimetric techniques to determine the thermodynamics for the unfolding of the pseudoknots and their targeting with complementary strands. The unfolding data is then used to create thermodynamic (Hess) cycles that correspond to each of the targeting reactions. The resulting data is then compared with the thermodynamic enthalpy data obtained directly from isothermal titration calorimetry. Results: UV melting curves of each pseudoknot show transitions with T M s independent of strand concentration, which confirms their intramolecular formation. Analysis of the differential scanning calorimetry (DSC) curves shows the pseudoknot with the longer thymine loop (PsK-9) to be more stable, by -5.7 kcal/mol, and to unfold with a higher enthalpy of 27.4 kcal/mol. The targeting of each pseudoknot yielded favorable reaction free energy contributions that were enthalpy driven. However, the disruption reaction of PsK-9 took place with a less favorable free energy term, by 0.7 kcal/mol, and less favorable enthalpy term, by 4.5 kcal/mol. Conclusion: The thermodynamic unfolding data showed that PsK-9 is more stable or more compact, due to the involvement of three loop thymines of PsK-9 in forming three T*AT base-triplets, or two T*AT/ T*AT base-triplet stacks, in the stem of this pseudoknot. The targeting thermodynamic data indicated that each complementary strand is able to disrupt the pseudoknots. However, the disruption of PsK-9 takes place with a less favorable free energy contribution, confirming the formation of a short and local triplex.

show abstract

Inhibition of DNA Binding Proteins by Oligonucleotide-Directed Triple Helix Formation

Cited by 434 publications

References 46 publications

Recognition of duplex DNA by RNA polynucleotides

Recognition of duplex DNA by RNA polynucleotides

Dual Blockade of Cyclic AMP Response Element- (CRE) and AP-1-directed Transcription by CRE-transcription Factor Decoy Oligonucleotide

Contributions of the loops on the stability and targeting of DNA pseudoknots

Contact Info

Product

Resources

About