Skip Navigation

This Article
Right arrow Print PDF (3896K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (114)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Tsai, D. E.
Right arrow Articles by Keene, J. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tsai, D. E.
Right arrow Articles by Keene, J. D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1991, Vol. 19, No. 18 4931-4936
© 1991

MOLECULAR BIOLOGY

U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts

Donald E. Tsai, David S. Harper and Jack D. Keene*

Department of Microbiology and Immunology, Duke University Medical Center Durham, NC 27710, USA

*To whom correspondence should be addressed

Received June 13, 1991. Accepted August 21, 1991.

The UlsnRNP-A (U1-A) protein was used to select specific RNA sequences from a degenerate pool of transcripts using direct RNA binding and polymerase chain reaction amplification (PCR). Sequences were randomized in loops of 10 or 13 nucleotides or as a linear stretch of 25 nucleotides. From all three structural contexts, an unpaired ten nucleotide consensus sequence was obtained. A selected stemloop structure that resembled the natural U1-A protein binding site on loop II of U1 RNA demonstrated the highest affinity of binding in comparison with the other structural contexts. A data profile of selected sequences Identified U1 RNA upon searching the GenBank database. Thus, this method was useful in determining the sequence specificity of an RNA binding protein and may complement the use of phylogenetic comparisons to predict conserved recognition elements. These findings also suggest that the evolutionary conservation of loop II of U1 RNA results from constraints imposed by protein binding.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
T. Saldi, C. Wilusz, M. MacMorris, and T. Blumenthal
Functional redundancy of worm spliceosomal proteins U1A and U2B''
PNAS, June 5, 2007; 104(23): 9753 - 9757.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. J. Law, A. J. Rice, P. Lin, and I. A. Laird-Offringa
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA
RNA, July 1, 2006; 12(7): 1168 - 1178.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. L. Ponthier, C. Schluepen, W. Chen, R. A. Lersch, S. L. Gee, V. C. Hou, A. J. Lo, S. A. Short, J. A. Chasis, J. C. Winkelmann, et al.
Fox-2 Splicing Factor Binds to a Conserved Intron Motif to Promote Inclusion of Protein 4.1R Alternative Exon 16
J. Biol. Chem., May 5, 2006; 281(18): 12468 - 12474.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. J. Law, M. E. Linde, E. J. Chambers, C. Oubridge, P. S. Katsamba, L. Nilsson, I. S. Haworth, and I. A. Laird-Offringa
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA
Nucleic Acids Res., January 10, 2006; 34(1): 275 - 285.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
T. S. BAYER, L. N. BOOTH, S. M. KNUDSEN, and A. D. ELLINGTON
Arginine-rich motifs present multiple interfaces for specific binding by RNA
RNA, December 1, 2005; 11(12): 1848 - 1857.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. J. Law, E. J. Chambers, P. S. Katsamba, I. S. Haworth, and I. A. Laird-Offringa
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction
Nucleic Acids Res., May 24, 2005; 33(9): 2917 - 2928.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Hori, Y. Taguchi, S. Uesugi, and Y. Kurihara
The RNA ligands for mouse proline-rich RNA-binding protein (mouse Prrp) contain two consensus sequences in separate loop structure
Nucleic Acids Res., January 12, 2005; 33(1): 190 - 200.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Miyanoiri, H. Kobayashi, T. Imai, M. Watanabe, T. Nagata, S. Uesugi, H. Okano, and M. Katahira
Origin of Higher Affinity to RNA of the N-terminal RNA-binding Domain than That of the C-terminal One of a Mouse Neural Protein, Musashi1, as Revealed by Comparison of Their Structures, Modes of Interaction, Surface Electrostatic Potentials, and Backbone Dynamics
J. Biol. Chem., October 17, 2003; 278(42): 41309 - 41315.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
L. O. F. Penalva and L. Sanchez
RNA Binding Protein Sex-Lethal (Sxl) and Control of Drosophila Sex Determination and Dosage Compensation
Microbiol. Mol. Biol. Rev., September 1, 2003; 67(3): 343 - 359.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. H. Lee, H. Kim, J. Ko, and Y. Lee
Interaction of C5 protein with RNA aptamers selected by SELEX
Nucleic Acids Res., December 15, 2002; 30(24): 5360 - 5368.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. C. Cox, A. Hayhurst, J. Hesselberth, T. S. Bayer, G. Georgiou, and A. D. Ellington
Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer
Nucleic Acids Res., October 15, 2002; 30(20): e108 - e108.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. S. Katsamba, M. Bayramyan, I. S. Haworth, D. G. Myszka, and I. A. Laird-Offringa
Complex role of the beta 2-beta 3 Loop in the Interaction of U1A with U1 Hairpin II RNA
J. Biol. Chem., August 30, 2002; 277(36): 33267 - 33274.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. C. Shiels, J. B. Tuite, S. J. Nolan, and A. M. Baranger
Investigation of a conserved stacking interaction in target site recognition by the U1A protein
Nucleic Acids Res., January 15, 2002; 30(2): 550 - 558.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
T. Imai, A. Tokunaga, T. Yoshida, M. Hashimoto, K. Mikoshiba, G. Weinmaster, M. Nakafuku, and H. Okano
The Neural RNA-Binding Protein Musashi1 Translationally Regulates Mammalian numb Gene Expression by Interacting with Its mRNA
Mol. Cell. Biol., June 15, 2001; 21(12): 3888 - 3900.
[Abstract] [Full Text]

Home page
 Nucleic Acids ResHome page
X. Manival, L. Ghisolfi-Nieto, G. Joseph, P. Bouvet, and M. Erard
RNA-binding strategies common to cold-shock domain- and RNA recognition motif-containing proteins
Nucleic Acids Res., June 1, 2001; 29(11): 2223 - 2233.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Lin, N. Mizunuma, T.-m. Chen, S. M. Copur, G. F. Maley, J. Liu, F. Maley, and E. Chu
In vitro selection of an RNA sequence that interacts with high affinity with thymidylate synthase
Nucleic Acids Res., November 1, 2000; 28(21): 4266 - 4274.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
L. Perrin, P. Romby, P. Laurenti, H. Berenger, S. Kallenbach, H.-M. Bourbon, and J. Pradel
The Drosophila Modifier of Variegation modulo Gene Product Binds Specific RNA Sequences at the Nucleolus and Interacts with DNA and Chromatin in a Phosphorylation-dependent Manner
J. Biol. Chem., March 5, 1999; 274(10): 6315 - 6323.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
H. Kanamori, R. E. Dodson, and D. J. Shapiro
In Vitro Genetic Analysis of the RNA Binding Site of Vigilin, a Multi-KH-Domain Protein
Mol. Cell. Biol., July 1, 1998; 18(7): 3991 - 4003.
[Abstract] [Full Text]

Home page
 J. Virol.Home page
Z. Li, A. D. Bailey, J. Buchowski, and A. M. Weiner
A Tandem Array of Minimal U1 Small Nuclear RNA Genes Is Sufficient To Generate a New Adenovirus Type 12Inducible Chromosome Fragile Site
J. Virol., May 1, 1998; 72(5): 4205 - 4211.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
C. Baumann, S. Xirasagar, and P. Gollnick
The trp RNA-binding Attenuation Protein (TRAP) from Bacillus subtilis Binds to Unstacked trp Leader RNA
J. Biol. Chem., August 8, 1997; 272(32): 19863 - 19869.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. Bouvet, K. Matsumoto, and A. P. Wolffe
Sequence-specific RNA Recognition by the Xenopus Y-box Proteins
J. Biol. Chem., November 24, 1995; 270(47): 28297 - 28303.
[Abstract] [Full Text] [PDF]

Home page
 Genes Dev.Home page
T W Flickinger and H K Salz
The Drosophila sex determination gene snf encodes a nuclear protein with sequence and functional similarity to the mammalian U1A snRNP protein.
Genes & Dev., April 15, 1994; 8(8): 914 - 925.
[Abstract] [PDF]

Home page
 Genes Dev.Home page
C S Lutz and J C Alwine
Direct interaction of the U1 snRNP-A protein with the upstream efficiency element of the SV40 late polyadenylation signal.
Genes & Dev., March 1, 1994; 8(5): 576 - 586.
[Abstract] [PDF]

Home page
 Genes Dev.Home page
X C Liao, J Tang, and M Rosbash
An enhancer screen identifies a gene that encodes the yeast U1 snRNP A protein: implications for snRNP protein function in pre-mRNA splicing.
Genes & Dev., March 1, 1993; 7(3): 419 - 428.
[Abstract] [PDF]

Home page
 J. Biol. Chem.Home page
P. S. Katsamba, D. G. Myszka, and I. A. Laird-Offringa
Two Functionally Distinct Steps Mediate High Affinity Binding of U1A Protein to U1 Hairpin II RNA
J. Biol. Chem., June 8, 2001; 276(24): 21476 - 21481.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.