Nucleic Acids Research, 2001, Vol. 29, No. 15 3248-3257
© 2001 Oxford University Press
Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA
Third Wave Technologies Inc., 502 South Rosa Road, Madison, WI 53719-1256, USA
DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific ‘bridge’ probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37°C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.
* To whom correspondence should be addressed. Tel: +1 608 663 7017; Fax: +1 608 273 8618; Email: vlyamichev{at}twt.com
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. J. Marshall, E. Reisdorf, G. Harms, E. Beaty, M. J. Moser, W.-M. Lee, J. E. Gern, F. S. Nolte, P. Shult, and J. R. Prudent Evaluation of a Multiplexed PCR Assay for Detection of Respiratory Viral Pathogens in a Public Health Laboratory Setting J. Clin. Microbiol., December 1, 2007; 45(12): 3875 - 3882. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W.-T. Liu, H. Guo, and J.-H. Wu Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays Appl. Envir. Microbiol., January 1, 2007; 73(1): 73 - 82. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Moser, D. R. Christensen, D. Norwood, and J. R. Prudent Multiplexed Detection of Anthrax-Related Toxin Genes J. Mol. Diagn., February 1, 2006; 8(1): 89 - 96. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Chavali, A. Mahajan, R. Tabassum, S. Maiti, and D. Bharadwaj Oligonucleotide properties determination and primer designing: a critical examination of predictions Bioinformatics, October 15, 2005; 21(20): 3918 - 3925. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 D. H. Atha, W. Kasprzak, C. D. O'Connell, and B. A. Shapiro Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling Nucleic Acids Res., November 15, 2001; 29(22): 4643 - 4653. [Abstract] [Full Text] [PDF]
|
|