2′-O- and 3′-O- pyrimidine aminotether-containing oligonucleotides: Synthesis and conjugation chemistry

Manoharan, Muthiah; Tivel, Kathleen L.; Andrade, Laura K.; Cook, P. Dan

doi:10.1016/0040-4039(95)00596-5

Cited by 27 publications

(14 citation statements)

References 17 publications

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“…35). In the case of zwitterionic nucleic acid analogues it remains to be determined how the substituent length affects the nuclease resistance [e.g., aminopentyl (36) or aminohexyl (37)]. Using structural information that takes into account both the nuclease and the nucleic acid analogue should be helpful in the design of new modifications with improved nuclease resistance.…”

Section: Discussionmentioning

confidence: 99%

Structural origins of the exonuclease resistance of a zwitterionic RNA

Teplova

Wallace

Tereshko

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1°C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3 ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3-5 exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-Å resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 Å and compared with the structure of the complex between oligo(dT) and the D355A͞E357A KF mutant. The structural models suggest that interference of the positively charged 2-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.antisense ͉ cationic oligonucleotides ͉ exonuclease inhibitor ͉ hydration ͉ x-ray crystallography S econd-generation oligonucleotide analogues for use as antisense (AS) therapeutics are now emerging (1, 2). Two improvements over the first-generation DNA phosphorothioates (PS-DNA) are of particular importance. First, several of the modifications confer increased affinity toward target RNA. Second and perhaps more importantly, they have increased ability to evade nuclease degradation. In the quest to achieve both goals, a large number of compounds with modifications located in the backbone, sugar, or base portion of the nucleic acid framework were introduced (3). Among the sites available for modification, the 2Ј position of the deoxyribose sugar has shown particular promise (4). Attachment of electron withdrawing moieties at the 2Ј carbon shifts the conformational equilibrium of the sugar toward the C3Ј-endo pucker, thus preorganizing the AS oligonucleotide for binding to the RNA target (5-7). The 2Ј-modified class of compounds also has proven to be valuable because of its enhanced nuclease resistance (4). Examples are the 2Ј-O-alkoxyalkyl compounds (8-11) and 2Ј-O-aminopropyl (AP) RNA (4, 12) (Fig. 1).Protection of AS oligodeoxynucleotides (ODNs) against 3Ј exonucleases appears to be of particular concern in view of practical applications in vivo or in cell cultures (9). The nuclease resistance conferred by simple 2Ј-O-alkyl substituents is correlated with the length of the alkyl chain (3,13,14). Longer and more bulky substituents lead to improved protection and the resistance of the 2Ј-O-pentyl modification is similar to that of PS-DNA. Howeve...

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Section: Discussionmentioning

confidence: 99%

Structural origins of the exonuclease resistance of a zwitterionic RNA

Teplova

Wallace

Tereshko

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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“…As shown in Scheme 2, (S)-()-ibuprofen (Sigma) was attached to 3'-O-(6-aminohexyl)-5'-O-dimethoxytrityluridine [20,21] by using the pentafluorophenyl ester derivative of ibuprofen. The resulting conjugate was hemisuccinylated at the 2'-position and attached to long chain aminoalkyl controlled pore glass (LCAA-CPG).…”

Section: Improving Antisense Oligonucleotide Binding To Human Serum Amentioning

confidence: 99%

Improving Antisense Oligonucleotide Binding to Human Serum Albumin: Dramatic Effect of Ibuprofen Conjugation

et al. 2002

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“…Several studies on cationic ONs, both with positively charged backbones and with positively charged groups attached have been reported. 15,[26][27][28] Several ONs modified with cationic groups in the 2¢-position exhibit efficient binding affinity to target RNA, enhanced chemical stability and increased nuclease resistance. 29 In this paper, we present various structures based on a 2¢amino-LNA/DNA mixmer scaffold.…”

Section: Introductionmentioning

confidence: 99%

Amino acids attached to 2′-amino-LNA: synthesis and excellent duplex stability

et al. 2011

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The synthesis of 2'-amino-LNA (the 2'-amino derivative of locked nucleic acid) has opened up a number of exciting possibilities with respect to modified nucleic acids. While maintaining the excellent duplex stability inferred by LNA-type oligonucleotides, the nitrogen in the 2'-position of 2'-amino-LNA monomers provides an excellent handle for functionalisation. Herein, the synthesis of amino acid functionalised 2'-amino-LNA derivatives is described. Following ON synthesis, a glycyl unit attached to the N2'-position of 2'-amino-LNA monomers was further acylated with a variety of amino acids. On binding to DNA/RNA complements, the modified ONs induce a marked increase in thermal stability, which is particularly apparent in a buffer system with a low salt concentration. The increase in thermal stability is thought to be caused, at least in part, by decreased electrostatic repulsion between the negatively charged phosphate backbones when positively charged amino acid residues are appended. Upon incorporation of more than one 2'-amino-LNA modification, the effects are found to be nearly additive. For comparison, 2'-amino-LNA derivatives modified with uncharged groups have been synthesised and their effect on duplex thermal stability likewise investigated.

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2′-O- and 3′-O- pyrimidine aminotether-containing oligonucleotides: Synthesis and conjugation chemistry

Cited by 27 publications

References 17 publications

Structural origins of the exonuclease resistance of a zwitterionic RNA

Structural origins of the exonuclease resistance of a zwitterionic RNA

Improving Antisense Oligonucleotide Binding to Human Serum Albumin: Dramatic Effect of Ibuprofen Conjugation

Amino acids attached to 2′-amino-LNA: synthesis and excellent duplex stability

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