Assessing incomplete deprotection of microarray oligonucleotides in situ
نویسندگان
چکیده
منابع مشابه
Assessing incomplete deprotection of microarray oligonucleotides in situ
En masse analysis of gene structure and function by array technologies will have a lasting and profound effect on biology and medicine. This impact can be compromised by low quality of probes within arrays, which we show can be caused by incomplete removal of chemical protecting groups. To solve this quality control problem, we present a sensitive, specific and facile method to detect these gro...
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Deprotection of methylphosphonate oligonucleotides with ethylenediamine was evaluated in a model system. Methylphosphonate sequences of the form 5'-TTTNNTTT, where N was either N4-bz-dC, N4-ibu-dC, N2-ibu-O6-DPC-dG, N2-ibu-dG, N6-bz-dA, or T, were used to determine the extent of modifications that occur during deprotection. Up to 15% of N4-bz-dC was found to transaminate at the C4 position when...
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Barrett and Kawasaki's recent review [1] of the three forms of probe (short oligonucleotides, long oligonucleotides and cDNAs) used on microarrays raised several points of discussion. None was more important than their assertion that the microarray field is in great need of standardization. Many would point to the nomenclature, annotation and sequence of array probes as being the prime example ...
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Assessing statistical significance of over-representation of exceptional words is becoming an important task in computational biology. We show on two problems how large deviation methodology applies. First, when some oligomer H occurs more often than expected, e.g. may be overrepresented, large deviations allow for a very efficient computation of the so-called p-value. The second problem we add...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2006
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkl713