Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease.
Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1-7 nt) and sequence composition were formed in a 3' terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulges (up to 4 nt) were readily formed upon oligonucleotide hybridization, whereas hybridization of the RNA to the oligonucleotides designed to produce larger bulges resulted in formation of several alternative structures. A synthetic ribonuclease mimic displaying Pyr-Pu cleavage specificity cleaved CpA motifs located within bulges faster than similar motifs within the rest of the RNA. In the presence of 10 mM MgCl2, 75% of the cleavage products resulted from the attack of this motif. Thus, selective RNA cleavage at a single target phosphodiester bond was achieved by using bulge forming oligonucleotides and a small ribonuclease A mimic.
Kuznetsova
Irina L
IL
Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Avenue 8, Novosibirsk 630090, Russia.
Zenkova
Marina A
MA
Gross
Hans J
HJ
Vlassov
Valentin V
VV
D001483:Base Sequence; D002021:Buffers; D007093:Imidazoles / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
D002021:Buffers; D007093:Imidazoles; D009838:Oligodeoxyribonucleotides; D012367:RNA, Viral; D012313:RNA; C029899:imidazole; D012259:Ribonuclease, Pancreatic
Nucleic Acids Res. 1979 Sep 11;7(1):179-92
386279
Chem Rev. 1998 May 7;98(3):1045-1066
11848924
Biochemistry. 1990 Jan 9;29(1):278-85
2322546
Eur J Biochem. 1977 Feb;72(3):465-78
402264
Met Ions Biol Syst. 1996;33:561-92
8742856
Biochemistry. 1996 Dec 24;35(51):16591-600
8987994
Bioconjug Chem. 2004 Jan-Feb;15(1):174-84
14733598
Bioorg Khim. 2000 Nov;26(11):852-61
11696896
FEBS Lett. 1999 Aug 27;457(2):193-9
10471777
Biochemistry. 2002 Aug 20;41(33):10406-17
12173927
Nucleic Acids Res. 1992 Oct 11;20(19):5079-84
1408824
RNA. 2000 Apr;6(4):608-15
10786851
J Biol Chem. 1994 Aug 5;269(31):20090-4
8051096
J Am Chem Soc. 2004 Feb 11;126(5):1430-6
14759201
Cell Biochem Biophys. 2001;34(1):95-119
11394443
Methods Enzymol. 1979;59:58-109
220499
J Mol Biol. 1973 Aug 5;78(2):301-19
4747633
Nucleic Acids Res. 1977 Aug;4(8):2527-38
409999
Org Biomol Chem. 2004 Jan 7;2(1):66-73
14737661
Science. 1996 Sep 20;273(5282):1678-85
8781224
Nucleic Acids Res. 2002 Jan 15;30(2):468-74
11788709
Nucleic Acids Res. 1992 Feb 25;20(4):819-24
1371866
Science. 1996 Sep 20;273(5282):1696-9
8781229
Nature. 1990 Feb 1;343(6257):484-7
2300191
J Mol Biol. 1998 Jan 16;275(2):211-20
9466904
Chem Rev. 1998 May 7;98(3):961-990
11848921
J Mol Biol. 1985 Aug 5;184(3):455-71
3900415
Org Biomol Chem. 2003 Jul 21;1(14):2439-47
12956059
Biochemistry. 1994 Aug 16;33(32):9561-5
8068631
Biopolymers. 1977 Nov;16(11):2429-46
334280
Biochemistry. 1998 Sep 29;37(39):13486-98
9753434
Nucleosides Nucleotides. 1999 Jun-Jul;18(6-7):1463-5
10474226
Proc Natl Acad Sci U S A. 1971 Nov;68(11):2682-5
5288243
Nucleic Acids Res. 1996 Sep 15;24(18):3522-6
8836177
Biochemistry. 1995 May 16;34(19):6488-503
7756280
Biochemistry. 1996 Sep 10;35(36):11677-84
8794748
J Mol Biol. 2000 Jan 28;295(4):711-7
10656783
Methods Enzymol. 1989;180:51-62
2482430
J Am Chem Soc. 2002 Jun 19;124(24):6887-94
12059210
Nucleic Acids Res. 1999 Oct 1;27(19):3931-7
10481033
Org Biomol Chem. 2003 May 7;1(9):1461-5
12926273
Nucleic Acids Res. 1998 Jul 15;26(14):3392-6
9649624
Electrophoresis. 1989 May-Jun;10(5-6):360-5
2548839
Biochemistry. 1991 Apr 23;30(16):4042-7
2018770
Chem Rev. 1998 May 7;98(3):991-1026
11848922
Nucleic Acids Res. 1991 Nov 11;19(21):5901-5
1719483
Methods Enzymol. 2001;341:468-90
11582799
Nucleosides Nucleotides Nucleic Acids. 2000 May-Jun;19(5-6):977-94
10893716
Nucleic Acids Res. 1998 Mar 1;26(5):1345-51
9469847
Nucleic Acids Res. 1992 Oct 11;20(19):5073-7
1408823
Nucleic Acids Res. 1987 Nov 25;15(22):9109-28
2446263
J Mol Biol. 1995 Mar 31;247(3):486-500
7536250
RNA. 1999 Oct;5(10):1308-25
10573122
Dokl Akad Nauk. 1996 Jul;349(3):411-3
8963230
Chem Biol. 1996 Mar;3(3):173-84
8807843