Silencing of HIV by hairpin‐loop‐structured DNA oligonucleotide

Moelling, Karin; Abels, Susanne; Jendis, Joerg; Matskevich, Alexey A.; Heinrich, Jochen

doi:10.1016/j.febslet.2006.05.033

Cited by 29 publications

(30 citation statements)

References 26 publications

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“…This structure was superior to single-stranded asDNA, which may have been due to improved stability and possibly to secondary structures, which contributed to the antiviral effect (18,20). 3 Most asDNAs and ODNs activate RNases H, which cleave and degrade the RNA of DNA-RNA hybrids (15,20,52,53). AsDNA can also block translation by steric hindrance of the ribosomes (14,54,55), and miRs primarily inhibit translation of proteins (13,56).…”

Section: Discussionmentioning

confidence: 99%

“…The second strand was designed based on an HIV ODN (20) whereby the second strand was partially complementary to the antisense strand. This structure was superior to single-stranded asDNA, which may have been due to improved stability and possibly to secondary structures, which contributed to the antiviral effect (18,20). 3 Most asDNAs and ODNs activate RNases H, which cleave and degrade the RNA of DNA-RNA hybrids (15,20,52,53).…”

Section: Discussionmentioning

confidence: 99%

“…The cellular effects of short hairpin-looped ODNs are less well characterized but can affect viral mRNA levels, especially in the presence of a viral RNase H (18)(19)(20). We asked what effect on protein expression could be observed after transfection of ODN-Raf.…”

Section: Effect Of Mir-125b On C-raf Protein Expressionmentioning

confidence: 99%

“…Inhibition of translation has also been described for asDNA as secondary effect (14,15). ODNs are a special class of short hairpin-looped DNAs that can induce cleavage of viral RNAs via a retroviral or cellular RNase H and therefore are active as antiviral agents (16)(17)(18)(19)(20).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, ODNRaf is a multifunctional molecule that reduces proliferation by inhibition of oncogene expression and induces cell death. (1,8,17,19,20,31,32). The 3′UTRs of mRNAs are preferred target sites for miRs and play an essential role in translational control and in the stability of transcripts (13,33).…”

Section: Introductionmentioning

confidence: 99%

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A Short Hairpin DNA Analogous to miR-125b Inhibits C-Raf Expression, Proliferation, and Survival of Breast Cancer Cells

Hofmann

Heinrich

Radziwil

et al. 2009

Molecular Cancer Research

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The noncoding RNA miR-125b has been described to reduce ErbB2 protein expression as well as proliferation and migration of cancer cell lines. As additional target of miR-125b, we identified the c-raf-1 mRNA by sequence analysis. We designed a short hairpin-looped oligodeoxynucleotide (ODN) targeted to the same 3′ untranslated region of c-raf-1 mRNA as miR-125b. The fully complementary ODN antisense strand is linked to a second strand constituting a partially double-stranded structure of the ODN. Transfection of the c-raf-1-specific ODN (ODN-Raf) in a breast cancer cell line reduced the protein levels of C-Raf, ErbB2, and their downstream effector cyclin D1 similar to miR-125b. MiR-125b as well as ODN-Raf showed no effect on the c-raf-1 mRNA level in contrast to small interfering RNA. Unlike miR-125b, ODN-Raf induced a cytopathic effect. This may be explained by the structural properties of ODN-Raf, which can form G-tetrads. Thus, the short hairpin-looped ODN-Raf, targeting the same region of c-raf-1 as miR-125b, is a multifunctional molecule reducing the expression of oncoproteins and stimulating cell death. Both features may be useful to interfere with tumor growth. (Mol Cancer Res 2009;7(10):1635-44)

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Effect Of Mir-125b On C-raf Protein Expressionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A Short Hairpin DNA Analogous to miR-125b Inhibits C-Raf Expression, Proliferation, and Survival of Breast Cancer Cells

Hofmann

Heinrich

Radziwil

et al. 2009

Molecular Cancer Research

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Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny

et al. 2010

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The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. ¹H and ³¹P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D(298 K) = (2.0 ± 0.07) × 10⁻¹⁰ m² s⁻¹ was evaluated across all hexamers except for d(GCGAGC) (D(298 K) = 1.7 × 10⁻¹⁰ m² s⁻¹) and d(GCGGGC) (D(298 K) = 1.2 × 10⁻¹⁰ m² s⁻¹). Melting under VT analysis (T(m) = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 10⁵M⁻¹. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies.

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RNase H: Specificity, Mechanisms of Action, and Antiviral Target

Moelling

Broecker

Kerrigan

2014

Methods in Molecular Biology

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The Ribonuclease (RNase) H is one of the four enzymes encoded by all retroviruses, including HIV. Its main activity is the hydrolysis of the RNA moiety in RNA-DNA hybrids. The RNase H ribonuclease is essential in the retroviral life cycle, since it generates and removes primers needed by the Reverse Transcriptase (RT) for initiation of DNA synthesis. Retroviruses lacking RNase H activity are noninfectious. Despite its importance, RNase H is the only enzyme of HIV not yet targeted by antiretroviral therapy. Here, we describe functions and mechanisms of RNase H during the HIV life cycle and describe a cleavage assay, which is suitable to determine RNase H activity in samples of various kinds. In this assay, an artificial, fluorescence-labeled RNA-DNA hybrid is cleaved in vitro by an RT/RNase H enzyme. Cleavage products are analyzed by denaturing polyacrylamide gel electrophoresis (PAGE). This assay may be used to detect the RNase H, assess the effect of inhibitors, or even activators, of the RNase H, as we have described, as candidates for novel antiretroviral agents.

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Silencing of HIV by hairpin‐loop‐structured DNA oligonucleotide

Cited by 29 publications

References 26 publications

A Short Hairpin DNA Analogous to miR-125b Inhibits C-Raf Expression, Proliferation, and Survival of Breast Cancer Cells

A Short Hairpin DNA Analogous to miR-125b Inhibits C-Raf Expression, Proliferation, and Survival of Breast Cancer Cells

Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny

RNase H: Specificity, Mechanisms of Action, and Antiviral Target

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