Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (295K) Freely available
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 ISI Web of Science
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 (25)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Luebke, K. J.
Right arrow Articles by Garner, H. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Luebke, K. J.
Right arrow Articles by Garner, H. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 2 750-758
© 2003 Oxford University Press

Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts

Kevin J. Luebke*,1, Robert P. Balog1,2 and Harold R. Garner1,2

1 Center for Biomedical Inventions and 2 McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9185, USA

*To whom correspondence should be addressed. Tel: +1 214 648 4054; Fax: +1 214 648 4156; Email: kevin.luebke{at}utsouthwestern.edu

Only a small fraction of short oligonucleotide probes bind efficiently to complementary segments in long RNA transcripts. Technologies such as array-based transcript profiling and antisense control of gene expression would benefit greatly from a method for predicting probes that bind well to a given target RNA. To develop an algorithm for prioritizing selection of probes, we have analyzed predicted thermodynamic parameters for the binding of several large sets of probes to complementary RNA transcripts. The binding of five of these sets of probes to their RNA targets has been reported by others. In addition, we have used a method for light-directed synthesis of oligonucleotide arrays that we developed to generate two new arrays of surface-bound probes and measured the binding of these probes to their RNA targets. We considered predicted free energies for intramolecular base pairing of the oligonucleotide and its RNA target as well as the predicted free energy of intermolecular hybridization of probe and target. We find that a reliable predictor of probes that will hybridize significantly with their targeted transcripts is the predicted free energy of hybridization minus the predicted free energy for intramolecular folding of the probe.


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
 RNAHome page
U. Bissels, S. Wild, S. Tomiuk, A. Holste, M. Hafner, T. Tuschl, and A. Bosio
Absolute quantification of microRNAs by using a universal reference
RNA, December 1, 2009; 15(12): 2375 - 2384.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. G. Leparc, T. Tuchler, G. Striedner, K. Bayer, P. Sykacek, I. L. Hofacker, and D. P. Kreil
Model-based probe set optimization for high-performance microarrays
Nucleic Acids Res., February 1, 2009; 37(3): e18 - e18.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
S. M. Miller, D. M. Tourlousse, R. D. Stedtfeld, S. W. Baushke, A. B. Herzog, L. M. Wick, J. M. Rouillard, E. Gulari, J. M. Tiedje, and S. A. Hashsham
In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water
Appl. Envir. Microbiol., April 1, 2008; 74(7): 2200 - 2209.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Petersen, L. Poulsen, S. Petronis, H. Birgens, and M. Dufva
Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays
Nucleic Acids Res., February 2, 2008; 36(2): e10 - e10.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
A. E. Pozhitkov, D. Tautz, and P. A. Noble
Oligonucleotide microarrays: widely applied poorly understood
Brief Funct Genomic Proteomic, July 20, 2007; (2007) elm014v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Brukner, R. El-Ramahi, I. Gorska-Flipot, M. Krajinovic, and D. Labuda
An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences
Nucleic Acids Res., May 14, 2007; 35(9): e66 - e66.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Pozhitkov, P. A. Noble, T. Domazet-Loso, A. W. Nolte, R. Sonnenberg, P. Staehler, M. Beier, and D. Tautz
Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted.
Nucleic Acids Res., January 1, 2006; 34(9): e66 - e66.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
T. Nagaoka, T. Horii, T. Satoh, T. Ito, A. Monji, A. Takeshita, and M. Maekawa
Use of a Three-Dimensional Microarray System for Detection of Levofloxacin Resistance and the mecA Gene in Staphylococcus aureus
J. Clin. Microbiol., October 1, 2005; 43(10): 5187 - 5194.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. W. Karaman, S. Groshen, C.-C. Lee, B. L. Pike, and J. G. Hacia
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays
Nucleic Acids Res., February 18, 2005; 33(3): e33 - e33.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Nagpal, M. W. Karaman, M. M. Timmerman, V. V. Ho, B. L. Pike, and J. G. Hacia
Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks
Nucleic Acids Res., March 18, 2004; 32(5): e51 - e51.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. P. Bratu, B.-J. Cha, M. M. Mhlanga, F. R. Kramer, and S. Tyagi
Visualizing the distribution and transport of mRNAs in living cells
PNAS, November 11, 2003; 100(23): 13308 - 13313.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
Y. Cui and C. L. Denis
In Vivo Evidence that Defects in the Transcriptional Elongation Factors RPB2, TFIIS, and SPT5 Enhance Upstream Poly(A) Site Utilization
Mol. Cell. Biol., November 1, 2003; 23(21): 7887 - 7901.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. V. Matveeva, D. H. Mathews, A. D. Tsodikov, S. A. Shabalina, R. F. Gesteland, J. F. Atkins, and S. M. Freier
Thermodynamic criteria for high hit rate antisense oligonucleotide design
Nucleic Acids Res., September 1, 2003; 31(17): 4989 - 4994.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. V. Matveeva, S. A. Shabalina, V. A. Nemtsov, A. D. Tsodikov, R. F. Gesteland, and J. F. Atkins
Thermodynamic calculations and statistical correlations for oligo-probes design
Nucleic Acids Res., July 15, 2003; 31(14): 4211 - 4217.
[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.