Computational generation and screening of RNA motifs in large nucleotide sequence pools.
Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.
Kim
Namhee
N
Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA.
Izzo
Joseph A
JA
Elmetwaly
Shereef
S
Gan
Hin Hark
HH
Schlick
Tamar
T
D000465:Algorithms; D052157:Aptamers, Nucleotide / Q000737:chemistry; D019729:Carbon-Oxygen Ligases / Q000737:chemistry; D019295:Computational Biology; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry; D017423:Sequence Analysis, RNA
D052157:Aptamers, Nucleotide; D016337:RNA, Catalytic; D012313:RNA; D019729:Carbon-Oxygen Ligases
Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13750-5
15365187
Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14712-7
10611278
Chem Biol. 1995 Aug;2(8):543-52
9383458
Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15288-93
17878292
Curr Mol Med. 2004 Aug;4(5):489-506
15267221
Front Biosci. 2006 Jan 01;11:89-112
16146716
Comput Appl Biosci. 1990 Oct;6(4):309-18
1701685
Nucleic Acids Res. 1999 Nov 15;27(22):4457-67
10536156
Nature. 2008 Mar 6;452(7183):51-5
18322526
Structure. 1999 Jul 15;7(7):817-27
10425683
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18902-7
16357200
Curr Opin Struct Biol. 2000 Jun;10(3):318-25
10851196
Curr Opin Struct Biol. 2006 Jun;16(3):270-8
16713706
Science. 2000 Feb 4;287(5454):820-5
10657289
Annu Rev Biochem. 2004;73:791-836
15189159
RNA. 2005 Nov;11(11):1701-9
16177137
RNA. 2007 Apr;13(4):478-92
17322501
FEBS Lett. 2004 Jun 1;567(1):55-62
15165893
Chem Biol. 1997 Nov;4(11):833-43
9384530
Comput Appl Biosci. 1990 Oct;6(4):325-31
1701686
Methods Enzymol. 2004;383:66-93
15063647
Trends Biotechnol. 2002 Nov;20(11):462-6
12413820
Science. 2009 Nov 27;326(5957):1271-5
19965478
Nature. 1993 Aug 5;364(6437):550-3
7687750
Nucleic Acids Res. 2005 Oct 27;33(18):6057-69
16254081
J Mol Biol. 1991 Dec 5;222(3):739-61
1721092
Trends Biotechnol. 1999 Dec;17(12):469-76
10557159
Bioinformatics. 2007 Nov 1;23(21):2959-60
17855416
Science. 1990 Aug 3;249(4968):505-10
2200121
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
12824340
Rev Med Virol. 2004 Jan-Feb;14(1):47-64
14716691
Nucleic Acids Res. 2001 Nov 15;29(22):4724-35
11713323
J Mol Biol. 1996 May 17;258(4):650-60
8636999
Nucleic Acids Res. 2009 Jul;37(12):e87
19465396
BMC Biol. 2006 Feb 15;4:5
16480488
Bioinformatics. 2006 Feb 15;22(4):500-3
16357029
Comput Biol Chem. 2007 Feb;31(1):11-35
17218151
Nature. 1990 Aug 30;346(6287):818-22
1697402
RNA. 2005 Jun;11(6):853-63
15923372
RNA. 2004 Dec;10(12):1900-6
15525711
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3584-9
10097080
Arch Biochem Biophys. 2009 Oct 15;490(2):163-70
19728985
J Am Chem Soc. 2004 Apr 28;126(16):5130-7
15099096
Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14664-9
17726102
Nucleic Acids Res. 2005 Oct 19;33(18):5924-35
16237127
RNA. 1998 Jan;4(1):112-23
9436913
Annu Rev Biochem. 1999;68:611-47
10872462