Enhanced recognition of non-complementary hybridization by single-LNA-modified oligonucleotide probes.
ABSTRACT Locked nucleic acid (LNA) is a deoxyribonucleotide analogue with an unusual 'locked' furanose conformation. LNA-modified oligonucleotide probes have demonstrated an enhanced binding affinity towards their complementary strands; however, their potential to discriminate non-complementary hybridization of mismatches has not been explored. In this study, we investigated the effect of the chemical nature of LNA nucleobases on the hybridization stability and the capability of LNA-modified oligonucleotides to discriminate the LNA:DNA mismatched base pairs. It was observed that LNA modification indeed improves the discrimination capability of oligonucleotides by increasing the melting temperature differences between the complementary duplexes and hybrids containing mismatches. Particularly, LNA purines offer a greater potential to recognize the mismatches than LNA pyrimidines and DNA purines. Real-time PCR experiments further confirmed that LNA modifications at the 3'-end are more effective. The results and conclusions in this study provide useful information for hybridization-based nucleic acid analysis where designing sound oligonucleotide probes is crucial to the success of the analyses.
- SourceAvailable from: Krzysztof Sobczak[show abstract] [hide abstract]
ABSTRACT: Types 1 and 2 myotonic dystrophy are neuromuscular disorders caused by genomic expansions of simple sequence repeats. These mutations are unstable in somatic cells, which leads to an age-dependent increase of expansion length. Studies to determine whether changes in repeat size may influence disease severity are limited by the small amount of DNA that can be recovered from tissue biopsies samples. Here we used locked nucleic acid oligonucleotide probes and rolling circle amplification to determine length of the expanded repeat in sub-microgram quantities of genomic DNA. These methods can facilitate genetic analysis in cells and tissues obtained from individuals with myotonic dystrophy.Neuromuscular Disorders 09/2009; 19(11):759-62. · 3.46 Impact Factor
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ABSTRACT: A novel, highly sensitive technology for the detection, enrichment, and separation of trace amounts of target DNA was developed on the basis of amino-modified fluorescent magnetic composite nanoparticles (AFMN). In this study, the positively charged amino-modified composite nanoparticles conjugate with the negatively charged capture DNA through electrostatic binding. The optimal combination of AFMN and capture DNA was measured by dynamic light scattering (DLS) and UV-vis absorption spectroscopy. The highly sensitive detection of trace amounts of target DNA was achieved through enrichment by means of AFMN. The detection limit for target DNA is 0.4 pM, which could be further improved by using a more powerful magnet. Because of their different melting temperatures, single-base mismatched target DNA could be separated from perfectly complementary target DNA. In addition, the photoluminescence (PL) signals of perfectly complementary target DNA and single-base mismatched DNA as well as the hybridization kinetics of different concentrations of target DNA at different reaction times have also been studied. Most importantly, the detection, enrichment, and separation ability of AFMN was further verified with milk. Simple and satisfactory results were obtained, which show the great potential in the fields of mutation identification and clinical diagnosis.Analytical and Bioanalytical Chemistry 03/2010; 397(3):1251-8. · 3.66 Impact Factor