ArticleNucleic acids research2001
Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Amplification-free, OR-gated CRISPR-Cascade reaction for pathogen detection in blood samples.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Rapid Detection of COVID-19 Viral RNA in Human Saliva Using Electrical Double Layer-Gated Field-Effect Transistor-Based Biosensors.Advanced materials technologies · 2022Article
- A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes.Nature communications · 2021Article
- The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex.Nucleic acids research · 2021Article
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- Genetic and biochemical evidences reveal novel insights into the mechanism underlyingJournal of biosciences · 2016Article
- Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions.Nucleic acids research · 2014Article
- Processing of DNA double-stranded breaks and intermediates of recombination and repair by Saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins.The Journal of biological chemistry · 2013Article
- Multipurpose instantaneous microarray detection of acute encephalitis causing viruses and their expression profiles.Current microbiology · 2012Review
- RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.Bioinformation · 2012Article
- Vertical transmission of Chlamydia trachomatis in Chongqing China.Current microbiology · 2009Article
- Novel computational methods for increasing PCR primer design effectiveness in directed sequencing.BMC bioinformatics · 2008Article
- Evaluation of a multiplexed PCR assay for detection of respiratory viral pathogens in a public health laboratory setting.Journal of clinical microbiology · 2007Article
- Effects of target length on the hybridization efficiency and specificity of rRNA-based oligonucleotide microarrays.Applied and environmental microbiology · 2007Article
- Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.Biophysical journal · 2006Article
- Multiplexed detection of anthrax-related toxin genes.The Journal of molecular diagnostics : JMD · 2006Article
- Use of a three-dimensional microarray system for detection of levofloxacin resistance and the mec A gene in Staphylococcus aureus.Journal of clinical microbiology · 2005Article
- Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling.Nucleic acids research · 2001Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.
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