Efficient RNase H-Directed Cleavage of RNA Promoted by Antisense DNA or 2‘F-ANA Constructs Containing Acyclic Nucleotide Inserts

Mangos, Maria M.; Min, Kyoungdoug; Viazovkina, Ekaterina; Galarneau, Annie; Elzagheid, Mohamed I.; Parniak, Michael A.; Damha, Masad J.

doi:10.1021/ja025557o

Cited by 78 publications

(83 citation statements)

References 36 publications

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“…Furan-2-acrylic acid (0.5 g, 3.62 mmol) was dissolved in MeOH (25 mL). A concentrated NH 4 OH solution (270 μL) was added, followed by Pd/C (10%, 8.5 mg). Hydrogenation was performed under a slight positive hydrogen pressure for 18 h. Pd/C was removed by filtration through Celite.…”

Section: ' Conclusionmentioning

confidence: 99%

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Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

Beeck

Madder

2010

J. Am. Chem. Soc.

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Chemical reagents that form interstrand cross-links have been used for a long time in cancer therapy. They covalently link two strands of DNA, thereby blocking transcription. Cross-link repair enzymes, however, can restore the transcription processes, causing resistance to certain anti-cancer drugs. The mechanism of these cross-link repair processes has not yet been fully revealed. One of the obstacles in this study is the lack of sufficient amounts of well-defined, stable, cross-linked duplexes to study the pathways of cross-link repair enzymes. Our group has developed a cross-link strategy where a furan moiety is incorporated into oligodeoxynucleotides (ODNs). These furan-modified nucleic acids can form interstrand crosslinks upon selective furan oxidation with N-bromosuccinimide. We here report on the incorporation of the furan moiety at the 2 0 -position of a uridine through an amido or ureido linker. The resulting modified ODNs display an unprecedented selectivity for cross-linking toward a cytidine opposite the modified residue, forming one specific cross-linked duplex, which could be isolated in good yield. Furthermore, the structure of the formed cross-linked duplexes could be unambiguously characterized. ' INTRODUCTIONThe high specificity with which oligonucleotides recognize nucleic acids has led to considerable interest in the design of modified oligonucleotides. 1 These customized nucleic acid derivatives can be used for a range of therapeutic and analytical purposes, including the treatment of diseases (antisense, 2-4 siRNA 5-8 ), the regulation of gene expression (antigene, 9-11 decoy DNA 12,13 ), the investigation of RNA tertiary structures, 14-16 and the study of DNA damage and the resulting repair processes. [17][18][19][20][21] DNA is not indefinitely stable, and numerous sources of DNAdamaging agents of endogenous and exogenous origin contribute further to the instability of DNA. 22 DNA interstrand cross-links (ICLs) are among the most cytotoxic lesions known, the covalent bond between the two DNA strands prohibiting strand separation and thereby blocking vital aspects of DNA metabolism. ICLs are mostly formed by reaction of cellular DNA with bifunctional electrophilic compounds that are either formed endogenously (e.g., lipid peroxidation) or present through exogenous exposure. 23 Additionally, generation of an abasic site in the DNA upon depurination can also give rise to ICL formation. 20,24 The cytotoxic properties of such ICL-forming agents are exploited by cancer chemotherapeutics, where their toxicity ultimately leads to apoptosis of the malignant cells. 25 Development of resistance of the tumor cells to treatment with antitumor drugs can often be attributed to enhanced ICL repair. 23 These repair pathways find their evolutionary origin in the necessity to counteract the threat posed by endogenous and exogenous crosslinking compounds, and failure to repair these lesions can lead to inherited disorders such as Fanconi anemia. 23 Thus, although DNA repair is essential for a heal...

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Section: ' Conclusionmentioning

confidence: 99%

“…The desired product was extracted using ethyl acetate (4 Â 25 mL). The combined organic layers were dried on MgSO 4 and concentrated. The residue was purified by flash chromatography using isooctane:EtOAc 4:1.…”

Section: ' Conclusionmentioning

confidence: 99%

Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

Beeck

Madder

2010

J. Am. Chem. Soc.

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“…Although PS-FANA AONs showed only relatively weak inhibition of cellular target expression, mixed-backbone oligomers with PS-DNA cores flanked by PS-FANA stretches were found to have potent antisense activity (15). So-called FANA/DNA altimers, consisting of alternating FANA and DNA residues (16), and FANA constructs containing acyclic nucleotide inserts (17) were also capable of promoting efficient cleavage of RNA targets by RNase H.…”

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confidence: 99%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

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2′-Deoxy-2′-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A-and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A-and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

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“…[38] In this context, antisense molecules comprising entirely of F-ANA cannot effectively activate RNase H, but acquiring some flexibility, through flexible linkers, leads to triggering a very potent RNase H response. [39] With that said, more RNase H experiments concerning the 2′F-tc-ANA modification are underway. [32] Backbone torsion angles distribution (c, d, g, h) and preferred sugar pucker (e, f, I, j) for ON14/DNA and ON14/RNA duplexes extracted from 100 ns molecular dynamics trajectory.…”

Section: Rnase H Cleavagementioning

confidence: 99%

2′β‐Fluoro‐Tricyclo Nucleic Acids (2′F‐tc‐ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation

Istrate

Katolik

Leumann

2017

Chemistry A European J

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Abstract:We describe the synthesis, thermal stability, structural and RNase H activation properties of 2′β-fluoro-tricyclo nucleic acids (2'Ftc-ANA). Three 2'F-tc-ANA nucleosides (T, 5Me C and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements. However, an oligonucleotide with 5 contiguous 2'F-tc-ANA-T insertions exhibits increased affinity to complementary RNA. Moreover, a fully modified 10-mer 2′F-tc-ANA oligonucleotide paired to both DNA (+1.6°C/mod) and RNA (+2.5°C/mod) with significantly higher affinity compared to corresponding unmodified DNA, and similar affinity compared to corresponding tc-DNA. In addition, CD spectroscopy and molecular dynamics simulations indicate that the conformation of the 2′F-tc-ANA/RNA duplex is similar to that of a DNA/RNA duplex. Moreover, in some sequence contexts, 2′F-tc-ANA promotes RNase H-mediated cleavage of a complementary RNA strand. Taken together, 2′F-tc-ANA represents a nucleic acid analogue which offers the advantage of high RNA affinity while maintaining the ability to activate RNase H, and can be considered a prospective candidate for gene silencing applications.

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Efficient RNase H-Directed Cleavage of RNA Promoted by Antisense DNA or 2‘F-ANA Constructs Containing Acyclic Nucleotide Inserts

Cited by 78 publications

References 36 publications

Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2′β‐Fluoro‐Tricyclo Nucleic Acids (2′F‐tc‐ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation

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Efficient RNase H-Directed Cleavage of RNA Promoted by Antisense DNA or 2‘F-ANA Constructs Containing Acyclic Nucleotide Inserts

Cited by 78 publications

References 36 publications

Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

Unprecedented C-Selective Interstrand Cross-Linking through in Situ Oxidation of Furan-Modified Oligodeoxynucleotides

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

2′β‐Fluoro‐Tricyclo Nucleic Acids (2′F‐tc‐ANA): Thermal Duplex Stability, Structural Studies, and RNase H Activation

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2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,