Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid.
Biotechniques
; 39(1): 89-96, 2005 Jul.
Article
em En
| MEDLINE
| ID: mdl-16060373
ABSTRACT
The hybridization behavior of small oligonucleotides arrayed on glass slides is currently unpredictable. In order to examine the hybridization efficiency of capture probes along target nucleic acid, 20-mer oligonucleotide probes were designed to hybridize at different distances from the 5' end of two overlapping 402- and 432-bp ermB products amplified from the target DNA. These probes were immobilized via their 5' end onto glass slides and hybridized with the two labeled products. Evaluation of the hybridization signal for each probe revealed an inverse correlation with the length of the 5' overhanging end of the captured strand and the hybridization signal intensity. Further experiments demonstrated that this phenomenon is dependent on the reassociation kinetics of the free overhanging tail of the captured DNA strand with its complementary strand. This study delineates key predictable parameters that govern the hybridization efficiency of short capture probes arrayed on glass slides. This should be most useful for designing arrays for detection of PCR products and nucleotide polymorphisms.
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Base de dados:
MEDLINE
Assunto principal:
Sondas de DNA
/
Análise de Sequência de DNA
/
Hibridização In Situ
/
Benchmarking
/
Análise de Sequência com Séries de Oligonucleotídeos
Tipo de estudo:
Diagnostic_studies
/
Evaluation_studies
/
Prognostic_studies
Idioma:
En
Ano de publicação:
2005
Tipo de documento:
Article