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Modified oligonucleotides, their preparation and their use

  • US 5,844,106 A
  • Filed: 11/06/1995
  • Issued: 12/01/1998
  • Est. Priority Date: 11/04/1994
  • Status: Expired due to Term
First Claim
Patent Images

1. An oligonucleotide of the formula I ##STR41## or a physiologically acceptable salt thereof, in which B is, independently of each other, a base which is customary in nucleotide chemistry, and at least one B is a base of the formula II ##STR42## in which R15 and R16 are, independently of each other, selected from the group of radicals consisting of:

  • (1) hydrogen(2) halogen,(3) (C1 -C10)-alkyl,(4) (C2 -C10) -alkenyl,(5) (C2 -C10) -alkynyl,(6) NO2,(7) NH2,(8) cyano,(9) --S--(C1 -C6) -alkyl,(10) (Cl-C6) -alkoxy,(11) (C6 -C20) -aryloxy,(12) SiH3, ##STR43## (14) radical (3), (4) or (5) substituted by one or more radicals selected from the group consisting of SH, S--(C1 -C6)-alkyl, (C1 -C6)-alkoxy, OH, --NR(c)R(d), --CO--R(b), --NH--CO--NR(c)R(d), --NR(c)R(g), --NR(e)R(f), and --NR(e)R(g), or by a polyalkyleneglycol radical of the formula -- O--(CH2)r !s --NR(c)R(d), where r and s are, independently of each other, an integer between 1 to 18, wherein any of the foregoing OH, SH, --CO--R(b), --NH--CO--NR(c)R(d), --NR(c)R(d), --NR(e)R(f), and --NR(e)R(g) or --NR(c)R(g) groups optionally is linked, via a further linker, to one or more groups which favor intracellular uptake or serve as labeling for a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving, and(15) radical (3), (4) or (5) in which from one to all the H atoms are substituted by halogen;

    with the provisos that;

    when R15 is hydrogen, R16 is selected from the group of radicals consisting of radicals (2)-(15), when R16 is hydrogen, R15 is selected from the group of radicals consisting of radicals (2), (6), (7), (9), (10), (11), (12), (13), (14), (15), ethyl, propyl, isobutyl, pentyl, hexyl, heptyl, 1-hexenyl and 1-heptenyl;

    and R15 and R16 cannot both be NO2, NH2, cyano or SiH3 ;

    R(a) is OH, (C1 -C6)-alkoxy, (C6 -C22)-aryloxy, NH2 or NH--T, where T is an alkylcarboxyl group or alkylamino group which is linked to one or more groups, via a further linker, which favor intracellular uptake or serve for labeling a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attack the latter while binding, cross-linking or cleaving,R(b) is hydroxyl, (C1 -C6)-alkoxy or --NR(c)R(d),R(c) and R(d) are, independently of each other, H or (C1 -C6) -alkyl which is unsubstituted or substituted by --NR(e)R(f) or --NR(e)R(g),R(e) and R(f) are, independently of each other, H or (C1 -C6)-alkyl,R(g) is (C1 -C6)-alkyl--COOH;

    E and F are, independently of each other, H, OH or NH2,R1 is hydrogen, C1 -C18 -alkyl, C2 -C18 -alkenyl, C2 -C18 -alkynyl, C2 -C18 -alkylcarbonyl, C3 -C19 -alkenylcarbonyl, C3 -C19 -alkynylcarbonyl, (C6 -C14)-aryl-(C1 -C8)-alkyl, a protective group which is customary in nucleotide chemistry, or a radical of the formula IIIa ##STR44## R1a i s hydrogen, C1 -C8 -alkyl, C2 -C18 -alkenyl, C2 -C18 -alkynyl, C2 -C18 -alkylcarbonyl, C3 -C19 -alkenylcarbonyl, C3 -C19 alkynylcarbonyl, (C6 -C14)-aryl-(C1 -C8)-alkyl, or a radical of the formula IIIb ##STR45## R2 is hydrogen, hydroxyl, C1 -C18 -alkoxy, C1 -C6 -alkenyloxy, halogen, azido or NH2 ;

    a is oxy, sulfanediyl or methylene;

    n is an integer ≧

    1;

    W is oxo, thioxo or selenoxo;

    V is oxy, sulfanediyl or imino;

    Y is oxy, sulfanediyl, imino or methylene;

    Y'"'"' is oxy, sulfanediyl, imino, (CH2)m or V(CH2)m, in which m is an integer from 1 to 18;

    X is hydroxyl or mercapto;

    U is hydroxyl, mercapto, SeH, C1 -C18 -alkoxy, C1 -C18 -alkyl, C6 -C20 -aryl, (C6 -C14)-aryl-(C1 -C8)-alkyl, NHR3, NR3 R4 or a radical of the formula IV
    
    
    space="preserve" listing-type="equation">OCH.sub.2 CH.sub.2).sub.p O(CH.sub.2).sub.q CH.sub.2 R.sup.5 (IV) in whichR3 i s C1 -C18 -alkyl, C6 -C20 -aryl, (C6 -C14)-aryl-(C1 -C3)-alkyl,--(CH2)-- NH(CH2) !d-NR 6 R, in which c is an integer from 2 to 6 and d is an integer from 0 to 6, and each R6 is, independently, hydrogen or C1 -C6 -alkyl or C1 -C4 -alkoxy-C1 -C6 -alkyl;

    R4 is C1 -C18 -alkyl, C6 -C20 -aryl or (C6 -C10)-aryl-C1 -C8)-alkyl, or, in the case of NR3 R4, is, together with R3 and the nitrogen atom carrying them, a 5-6-membered heterocyclic ring which can additionally contain a further O, S or N, heteroatom,p is an integer from 1 to 100,q is an integer from 0 to 22,R5 is hydrogen or is a substituent selected from the group consisting of hydroxyl, amino, C1 -C18 -alkylamino, COOH, CONH2, COO(C1 -C4) -alkyl and halogen;

    Z and Z'"'"' are, independently of each other, hydroxyl, mercapto, SeH, C1 -C22 -alkoxy, --O--(CH2)b -NR6 R7, in which b is an integer from 1 to 6, and R7 is C1 -C6 -alkyl or R6 and R7, together with the nitrogen atom carrying them, form a 3-6-membered ring, C1 -C18 -alkyl, C6 -C20 -alkyl, (C4 -C14)-aryl-(C1 -C8)-alkyl, (C6 -C14)-aryl-(C1 -C8) -alkoxy, where aryl includes heteroaryl and any aryl is optionally substituted by 1,2 or 3 identical or different radicals selected from the group consisting of carboxyl, amino, nitro, C1 -C4 -alkylamino, C1 -C4 -alkoxy, hydroxyl, halogen and cyano, C1 -C18 -alkylmercapto, NHR3, NR3 R4, a radical of the formula IV, or a group which favors intracellular uptake or serves for labeling a DNA or RNA probe or, when the oligonucleotide analog hybridizes to the target nucleic acid, attacks the latter while binding, cross-linking or cleaving, and the curved bracket indicates that R2 and the adjacent phosphoryl or --Y'"'"'--R1a radical can either be located in the 2'"'"' and 3'"'"' position or else, conversely, in the 3'"'"' and 2'"'"' position, with it being possible for each nucleotide to be present in its D or L configuration, and for the base B to be located in the α

    or β

    position.

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