Biopolym. Cell. 2012; 28(2):156-160 .
Bioinformatics analysis of the secondary structure of maize whp1 gene intron 1 transcripts
1Slishchuk G. I., 1Volkova N. E., 1Sivolap Yu. M.
  1. South Plant Biotechnology Center, NAAS of Ukraine
    3, Ovidiopolska doroga, Odesa, Ukraine, 65036


Aim. Analysis of the secondary structure of maize whp1 gene intron 1 transcripts. Methods. Alignment, in silico folding. Results. Novel complex microsatellites of the whp1 gene were discovered. 74 whp1 intron 1 transcripts secondary structures were predicted. Conclusions. The influence of whp1 gene intron 1 transcripts on restoration of CMS- S sterile maize fertility has been proposed.
Keywords: bioinformatics, whp1 gene, CMS, maize, intron, secondary structure


[1] Zabala G., Gabay-Laughnan S., Laughnan J. R. The nuclear gene Rf3 affects the expression of the mitochondrial chimeric sequence R implicated in S-type male sterility in maize. Genetics 1997 147, N 2:847–860.
[2] Gabay-Laughnan S., Chase C. D., Ortega V. M., Zhao L. Molecular-genetic characterization of CMS-S restorer-of-fertility alleles. Genetics 2004 166, N 2:959–970.
[3] Schaeffer M. L., Harper L. C., Gardiner J. M., Andorf C. M., Campbell D. A., Cannon E. K. S., Sen T. Z., Lawrence C. J. MaizeGDB: curation and outreach go hand-in-hand. J. Biol. Databases and Curation 2011.
[4] Franken P., Niesbach-Klosgen U., Weydemann U., MarechalDrouard L., Saedler H., Wienand U. The duplicated chalcone synthase genes C2 and Whp (white pollen) of Zea mays are independently regulated; evidence for translational control of Whp expression by the anthocyanin intensifying gene in. EMBO J 1991 10, N 2605–2612.
[5] Mount S. M., Gotea V., Lin C.-F., Hernandez K., Makalowski W. Spliceosomal small nuclear RNA genes in 11 insect genomes. RNA 2007 13, N 1:5–14.
[6] Zheng Q., Ryvkin P., Li F., Dragomir I., Valladares O., Yang J., Cao K., Wang L.-S., Gregory B. D. Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet 2010 6, N 9 e1001141.
[7] Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol 1970 48, N 3:443–453.
[8] Sneath P. H. A., Sokal R. R. Numerical taxonomy: The principles and practices of numerical classification San-Francisco: Freeman, 1973 573 p.
[9] Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981 9, N 1:133–148.
[10] SantaLucia J., Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 1998 95, N 4:1460–1465.
[11] Reuter J. S., Mathews D. H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010 N 11:129.
[12] Nguyen V. T., Kiss T., Michels A. A., Bensaude O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001 414, N 6861:322–325.
[13] Alexander M. R., Wheatley A. K., Center R. J., Purcell D. F. J. Efficient transcription through an intron requires the binding of an Sm-type U1 snRNP with intact stem loop II to the splice donor. Nucleic Acids Res 2010 38, N 9:3041–3053.