Synthesis and Some Properties of Modified Oligonucleotides. II. Oligonucleotides Containing 2′-Deoxy-2′-fluoro-β-D-arabinofuranosyl Pyrimidine Nucleosides

Kois, Pavol; Točı́k, Zdeněk; Spassova, Maria; Ren, Wu-Yun; Rosenberg, Ivan; Soler, Jaume Farras; Watanabe, Kyoichi A.

doi:10.1080/07328319308016207

Cited by 26 publications

(27 citation statements)

References 20 publications

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“…Figure 3 shows the 16% denaturing PAGE gel autoradiograph of the Exo III digestion products obtained with unmodified and boron-containing oligonucleotides. Oligonucleotides that contain a boranophosphate at position 12 Temperature (°C) Figure 5. Nornalized absorbance at 260 nm versus temperatre forunmodified and boron-modified 14mer duplexes.…”

Section: Synthesis Of Boron-containing Dna Oligodeoxyribonucleotidesmentioning

confidence: 99%

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies

Porter

Huang

et al. 1995

Nucl Acids Res

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We have purified to homogeneity a DNase from a Crithidia fasciculata crude mitochondrial lysate. The enzyme is present in two forms, either as a 32 kDa polypeptide or as a multimer containing the 32 kDa polypeptide in association with a 56 kDa polypeptide. Native molecular weight measurements indicate that these forms are a monomer and possibly an alpha 2 beta 2 tetramer, respectively. The monomeric and multimeric forms of the enzyme are similar in their catalytic activities. Both digest double-stranded DNA about twice as efficiently as single-stranded DNA. They introduce single-strand breaks into a supercoiled plasmid but do not efficiently make double-strand breaks. They degrade a linearized plasmid more efficiently than a nickel plasmid. Both enzymes degrade a 5'-32P-labeled double-stranded oligonucleotide to completion, with the 5'-terminal nucleotide ultimately being released as a 5'-mononucleotide. One difference between the monomeric and multimeric forms of the enzyme, demonstrated by a band shift assay, is that the multimeric form binds tightly to double-stranded DNA, possibly aggregating it.

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Section: Synthesis Of Boron-containing Dna Oligodeoxyribonucleotidesmentioning

confidence: 99%

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies

Porter

Huang

et al. 1995

Nucl Acids Res

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“…[4,11] Inversion of the stereochemistry at the C2'-position of 2'-F-RNA results in 2'-deoxy-2'-fluoro-b-d-arabinonucleic acid (2'-F-ANA; Figure 1). [6,7,12,13] Introduction of 2'-F-ANA monomers into DNA ONs likewise induces increased thermal stability of duplexes formed with DNA and RNA complements. [14] 2'-F-ANA is a DNA mimic as the furanose moiety adopts an O4'-endo pucker; [13] this has stimulated its use in the antisense field as 2'-F-ANA-modified antisense ONs induce RNase H-mediated cleavage of a complementary RNA strand, although cleavage rates are generally lower than with unmodified DNA ONs.…”

Section: Introductionmentioning

confidence: 98%

Synthesis and Structural Characterization of 2′‐Fluoro‐α‐L‐RNA‐Modified Oligonucleotides

et al. 2011

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We describe the synthesis and binding properties of oligonucleotides that contain one or more 2'-fluoro-α-L-RNA thymine monomer(s). Incorporation of 2'-fluoro-α-L-RNA thymine into oligodeoxynucleotides decreased thermal binding stability slightly upon hybridization with complementary DNA and RNA with the smallest destabilization towards RNA. Thermodynamic data show that the duplex formation with 2'-fluoro-α-L-RNA nucleotides is enthalpically disfavored but entropically favored. 2'-Fluoro-α-L-RNA nucleotides exhibit very good base pairing specificity following Watson--Crick rules. The 2'-fluoro-α-L-RNA monomer was designed as a monocyclic mimic of the bicyclic α-L-LNA, and molecular modeling showed that this indeed is the case as the 2'-fluoro monomer adopts a C3'-endo/C2'-exo sugar pucker. Molecular modeling of modified duplexes show that the 2'-fluoro-α-L-RNA nucleotides partake in Watson--Crick base pairing and nucleobase stacking when incorporated in duplexes while the unnatural α-L-ribo configured geometry of the sugar is absorbed by changes in the sugar-phosphate backbone torsion angles. The duplex behavior of our new nucleotide follows that of α-L-LNA, by and large.

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“…Among the wide variety of nucleotide modifications available, arabinonucleic acid (ANA) and its 2¢-fluorinated derivative (2¢F-ANA) are particularly interesting (Fig. 1) [15][16][17][18][19]. In addition to closely mimicking DNA with respect to duplex structure [20,21], their hybrid duplexes with RNA display structure and flexibility patterns that make them effective mimics of the DNA-RNA hybrid [22][23][24][25][26].…”

Section: Introductionmentioning

confidence: 99%

Arabinonucleic Acids: 2′-Stereoisomeric Modulators of siRNA Activity

Anzahaee

Deleavey²,

Le³

et al. 2014

Nucleic Acid Therapeutics

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We have investigated, for the first time, short interfering duplexes containing arabinonucleotides (ANA; the 2'-stereoisomer of RNA), as well as combinations of ANA with RNA, and their 2'-fluorinated derivatives 2F-ANA and/or 2'F-RNA. The results show that ANA is especially well accommodated in the sense strand of small interfering RNA (siRNA) duplexes, which can be extensively modified with little effect on potency. Furthermore, combining ANA with RNA and 2'F-ANA in siRNA passenger strands, particularly in patterns that bias duplex thermal stability, produces duplexes with similar (and sometimes enhanced) potency compared with native siRNA. Effective patterns of modification were identified against firefly luciferase screens in HeLa cells and then applied to knockdown of down-regulated in renal cell carcinoma (DRR), a novel and clinically tractable target for the treatment of glioblastoma.

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Synthesis and Some Properties of Modified Oligonucleotides. II. Oligonucleotides Containing 2′-Deoxy-2′-fluoro-β-D-arabinofuranosyl Pyrimidine Nucleosides

Cited by 26 publications

References 20 publications

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies

Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies

Synthesis and Structural Characterization of 2′‐Fluoro‐α‐L‐RNA‐Modified Oligonucleotides

Arabinonucleic Acids: 2′-Stereoisomeric Modulators of siRNA Activity

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