This HTML5 document contains 18 embedded RDF statements represented using HTML+Microdata notation.

The embedded RDF content will be recognized by any processor of HTML5 Microdata.

Subject Item

n2:w

rdf:type

rdac:C10001 bibo:Article

dcterms:isPartOf

n11:w

dcterms:subject

n13:methodsonline

dcterms:title

Free energy of DNA duplex formation on short oligonucleotide microarrays

rdaw:P10072

n6:print n6:web

vivo:relatedBy

n15:3 n15:4 n15:1 n15:2

marcrel:aut

n2:zhaohaitao n2:cartaroberto n2:wuchunlei n16:d0cd2693b3506677e4c55e91d6365bff

dcterms:abstract

DNA/DNA duplex formation is the basic mechanism that is used in genome tiling arrays and SNP arrays manufactured by Affymetrix. However, detailed knowledge of the physical process is still lacking. In this study, we show a free energy analysis of DNA/DNA duplex formation these arrays based on the positional-dependent nearest-neighbor (PDNN) model, which was developed previously for describing DNA/RNA duplex formation on expression microarrays. Our results showed that the two ends of a probe contribute less to the stability of the duplexes and that there is a microarray surface effect on binding affinities. We also showed that free energy cost of a single mismatch depends on the bases adjacent to the mismatch site and obtained a comprehensive table of the cost of a single mismatch under all possible combination of adjacent bases. The mismatch costs were found to be correlated with those determined in aqueous solution. We further demonstrate that the DNA copy number estimated from the SNP array correlates negatively with the target length; this is presumably caused by inefficient PCR amplification for long fragments. These results provide important insights into the molecular mechanisms of microarray technology and have implications for microarray design and the interpretation of observed data.

hub:articleType

n12:researcharticle

hub:isPartOfThisJournal

n10:w