A Novel Conversion Strategy Using an Expanded Genetic Alphabet to Assay Nucleic Acids. Yang, Z., Durante, M., Glushakova, L. G, Sharma, N., a Leal, N., Bradley, K. M, Chen, F., & a Benner, S. Analytical chemistry, April, 2013.
doi  abstract   bibtex   
Methods to detect DNA and RNA (collectively xNA) are easily plagued by noise, false positives, and false negatives, especially with increasing levels of multiplexing in increasing complex assay mixtures. We describe assay architectures that mitigate these problems, here by converting standard xNA analyte sequences into sequences that incorporate non-standard nucleotides (Z and P). Z and P are extra DNA building blocks that form tight non-standard base pairs without cross-binding to natural oligonucleotides containing G, A, C, and T (GACT). The resulting improvements are assessed in an assay that inverts the standard Luminex xTAG® architecture, placing a biotin on a primer (rather than on a triphosphate). This primer is extended on the target to create a standard GACT extension product that is captured by a CTGA oligonucleotide attached to a Luminex bead. Using conversion, a polymerase incorporates dZTP opposite template dG in the absence of dCTP. This creates a Z-containing extension product that is captured by a bead-bound oligonucleotide containing P, which binds selectively to Z. The assay with conversion produces higher signals than the assay without conversion, possibly because the Z:P pair is stronger than the C:G pair. These architectures improve the ability of the Luminex instruments to detect xNA analytes, producing higher signals without the possibility of competition from any natural oligonucleotides, even in complex biological samples.
@article{Yang2013,
  title = {A Novel Conversion Strategy Using an Expanded Genetic Alphabet to Assay Nucleic Acids.},
  author = {Yang, Zunyi and Durante, Michael and Glushakova, Lyudmyla G and Sharma, Nidhi and a Leal, Nicole and Bradley, Kevin M and Chen, Fei and a Benner, Steven},
  year = {2013},
  month = apr,
  journal = {Analytical chemistry},
  eprint = {23541235},
  eprinttype = {pubmed},
  issn = {1520-6882},
  doi = {10.1021/ac400422r},
  abstract = {Methods to detect DNA and RNA (collectively xNA) are easily plagued by noise, false positives, and false negatives, especially with increasing levels of multiplexing in increasing complex assay mixtures. We describe assay architectures that mitigate these problems, here by converting standard xNA analyte sequences into sequences that incorporate non-standard nucleotides (Z and P). Z and P are extra DNA building blocks that form tight non-standard base pairs without cross-binding to natural oligonucleotides containing G, A, C, and T (GACT). The resulting improvements are assessed in an assay that inverts the standard Luminex xTAG{\textregistered} architecture, placing a biotin on a primer (rather than on a triphosphate). This primer is extended on the target to create a standard GACT extension product that is captured by a CTGA oligonucleotide attached to a Luminex bead. Using conversion, a polymerase incorporates dZTP opposite template dG in the absence of dCTP. This creates a Z-containing extension product that is captured by a bead-bound oligonucleotide containing P, which binds selectively to Z. The assay with conversion produces higher signals than the assay without conversion, possibly because the Z:P pair is stronger than the C:G pair. These architectures improve the ability of the Luminex instruments to detect xNA analytes, producing higher signals without the possibility of competition from any natural oligonucleotides, even in complex biological samples.},
  pmid = {23541235},
  keywords = {\#nosource}
}
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