Uniformly modified 2'-deoxy-2'-fluoro-phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets

Kawasaki, Andrew M.; Casper, Martin D.; Freier, Susan M.; Lesnik, Elena A.; Zounes, Maryann; Cummins, Lendell L.; Gonzalez, C.; Cook, P. Dan

doi:10.1021/jm00059a007

Cited by 405 publications

(249 citation statements)

References 26 publications

(65 reference statements)

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“…the puckering of the branched-chain 5' sugars (rI(2`OH)SdT and rT(2 OMe)sdT) exceeds the 3'-endo distribution of the ribonucleosides, and by far that of 2'-deoxynucleosides, a property that makes them more 'compatible binders' of targeted RNA (31). Cook and co-workers have also suggested that increased affinity of an antisense oligomer for a complementary RNA target can be achieved by decreasing the entropic motion of the sugar while mantaining a preorganized structure with an RNA-like conformation (21,32). The second factor is base sequence.…”

Section: Resultsmentioning

confidence: 99%

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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INTRODUCTIONIn this report we describe the synthesis of oligonucleotides containing sulfide-linked dinucleoside units, namely rT(2'OH)dT, rT(2'0Me)5dT, dT8rU(2'OMe) and dT(2o0Me)5rU(2oMe). We also describe the interactions of such oligomers with complementary DNA and RNA targets, and provide the structural basis for their remarkable RNA binding selectivity. In all cases, the Tm values of the SIP-chimera duplexes were lower than those of the corresponding unmodified duplexes. We attribute this to steric interactions between the 5' sulfur and the atoms of the nearby base/sugar residues. The 2'-substituents (i.e., 2'OH or 2'OMe) vicinal to the alkylsulfide internucleoside linkage significantly perturb the structure and stability of the duplexes formed with DNA, and more so than with RNA. The introduction of three rT(2'OH)sdTp ( ' (5,6).Our research in the antisense field has focused on oligonucleotide analogues in which some of the phosphodiester groups are replaced by the dialkyl sulfide linkage 3'-CH2-CH2-S-CH2-5' (7-11). This linkage is non-hydrolyzable, non-ionic, and its length approximates that of a phosphodiester linkage reasonably well. More recently, we focused attention on the preparation of rT(20OH)SdT, rT(2 OMe)SdT, dTsrU(2'OMe) and rT(2'OMe)SrU(2'OMe) dimer units as well as their 3'-O-phosphoramidite derivatives for incorporation into oligonucleotides (11,12 (55°C, 16 h). The ammonia solution was collected by centrifuging the Eppendorf tube and then run through a Sephadex NAP-10 column which was pre-washed with 15 ml deionized water. The first eluting fractions (1.5 ml) were lyophilized to dryness and the resulting oligomer was redissolved in 1 ml of water. Purity of each oligomer was confmed by PAGE (26% polyacrylamide-7 M urea) run at 4°C, at a current of 10 mA, for 6-8 h (9). Melting experimentsMelting curves were measured in 10 mM NaH2PO4/Na2HPO4, 1 M NaCl buffer (pH 7.0) and analyzed the same way as described in reference 9. Circular dichroismThe CD spectrum ofeach sample was measured on a Jasco 500-C spectropolarimeter with a Jasco DP-J800/300 data processor. The cell temperature was kept at 50C. The concentration of the oligonucleotides were -2.5 jM (each strand).

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Section: Resultsmentioning

confidence: 99%

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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“…The 2′-position of the sugar moiety can also serve as a modification site. 2′-methoxy (2′-O-methyl) substituted oligonucleotides were found to form very stable double strands and exhibit significant nuclease resistance, which further facilitates in vivo administration [14][15][16][17][18][19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Tandem Mass Spectrometry of Modified and Platinated Oligoribonucleotides

Nyakas

Stucki

Schürch

2011

J. Am. Soc. Mass Spectrom.

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Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2′-O-methyl-and methylphosphonatederivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS n ). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2′-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2′-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3′-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to w x -ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2′-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2′-O-methyl-and 2′-O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.

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“…The 2'-position in the ribose moiety of RNA is prime target for chemical modifications. Extensive research work is going on towards the study of structural properties, biological applications and delivery strategies of oligonucleotides-incorporated with 2'-deoxy-2'fluoronucleotide in combination with other structural modifications [67][68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83][84]. Oligonucleotides containing 2'-deoxy-2'fluoronucleosides have been synthesized for regiospecific cleavage of RNA by RNase H [67].…”

Section: Application Of Fluorinated Oligonucleotide Analoguesmentioning

confidence: 99%

“…Oligonucleotides containing 2'-deoxy-2'fluoronucleosides have been synthesized for regiospecific cleavage of RNA by RNase H [67]. Incorporation of 2'-deoxy-2'-fluoronucleotide into oligonucleotides induces substantial enhancement in their binding affinities to RNA targets [68]. Damha On the other side, very interesting and novel studies have been carried out by Erande et al using 3'-deoxy-3'ribofluoro/xylofluoro uridine incorporated oligonucleotides (2'-5'-strand) [85].…”

Section: Application Of Fluorinated Oligonucleotide Analoguesmentioning

confidence: 99%

Nucleic Acid Based Fluorinated Derivatives: New Tools for Biomedical Applications

et al. 2012

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Nucleic acid-based fluorinated derivatives, e.g., nucleosides or oligonucleotides connected to highly fluorinated chains or labeled with one or more fluorine atoms, have been investigated recently due to their high potential for biomedical applications. This review deals with recent works on nucleoside and oligonucleotide fluorocarbon amphiphiles as well as with properties and applications of fluorine-labeled oligonucleotide analogues.

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Uniformly modified 2'-deoxy-2'-fluoro-phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets

Cited by 405 publications

References 26 publications

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

Tandem Mass Spectrometry of Modified and Platinated Oligoribonucleotides

Nucleic Acid Based Fluorinated Derivatives: New Tools for Biomedical Applications

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