Abstract: Compositions, methods, and kits for reducing strand amplification bias using bisulfite treated gDNA are provided. Methods for detecting and for quantitating the amplified bisulfite treated gDNA and inferring the presence, absence, and/or degree of methylation of target cytosine(s) in the gDNA are also provided. Such methods typically employ tailed first primer pairs, which can, but need not comprise nucleotide analogs, and optionally second primer pairs.

Abstract: Various embodiments of the present teachings relate to methods for the methylation analysis of nucleic acids. The subject methods include methods that result in the preparation of mate-pair libraries suitable for highly multiplexed DNA sequencing. Embodiments include methods of preparing mate-pair libraries comprising a first tag sequence and a second tag sequence, wherein one of the tag sequences has been converted by a methylation conversion agent and the other tag sequence has not been converted by the methylation conversion agent. Other embodiments provided include intermediates for making the mate-pair library and kits for making the mate-pair libraries. Also provided is software and computer systems for analyzing the methylation levels of genomic DNA from which the tag sequences were derived.

Abstract: A method is provided for predicting an amount of methylation of at least one target region. The method includes establishing an observed size of a plurality of oligonucleotides relative to a size standard and correlating the observed size to a number of each of nucleotide base in each of the plurality of oligonucleotides. A mobility coefficient can be determined for each base of each respective oligonucleotide and the determined mobility coefficients can be applied to a predetermined number of polynucleotides subjected to methylation detection analysis. The plurality of oligonucleotides are treated with a modifying agent to obtain amplicons in methylated and unmethylated target regions and amplicons derived from methylated and unmethylated target regions are distinguished based on their relative mobilities. The degree of methylation can be predicted based on distinguished methylated regions.

Abstract: The present teachings generally relate to methods and materials for the detection of target nucleotides and/or the methylation state of target nucleotides.

Abstract: Methods and kits are disclosed for determining the degree of methylation of at least one target region. Typically a sample is exposed to a modifying agent to obtain a modified sample comprising a modified nucleotide. At least one target region in the modified sample is amplified. Some of the disclosed methods comprise at least one additional amplification reaction. In some embodiments, at least one mobility shifting analog is incorporated into an amplicon during an amplification reaction. The analogs are analyzed and the degree of methylation of at least one target region is determined.

Abstract: Compositions, methods, and kits for reducing strand amplification bias using bisulfite treated gDNA are provided. Methods for detecting and for quantitating the amplified bisulfite treated gDNA and inferring the presence, absence, and/or degree of methylation of target cytosine(s) in the gDNA are also provided. Such methods typically employ tailed first primer pairs, which can, but need not comprise nucleotide analogs, and optionally second primer pairs.

Abstract: The invention provides methods and materials for conversion of cytosine to uracil. In some embodiments, a nucleic acid, such as gDNA, is reacted with bisulfite and a polyamine catalyst, such as a triamine or tetra-amine. Optionally, the bisulfite comprises magnesium bisulfite. In other embodiments, a nucleic acid is reacted with magnesium bisulfite, optionally in the presence of a polyamine catalyst and/or a quaternary amine catalyst. Also provided are kits that can be used to carry out methods of the invention.

Abstract: The invention provides methods and materials for conversion of cytosine to uracil. In some embodiments, a nucleic acid, such as gDNA, is reacted with at least one bisulfite salt having the formula X+HSO3? or Y+2(HSO331)2; wherein X+ is ammonium ion, a tetraalkyl ammonium ion, or a group 1A ion other than sodium; and Y+2 is a group 2A ion or a group 7B ion; under conditions effective to convert at least one cytosine nucleobase to a uracil nucleobase. In some embodiments, X+ comprises at least one of lithium ion, potassium ion, ammonium ion, tetraalkylammonium ion, magnesium ion, manganese ion and calcium ion. In some embodiments, the reacting is performed optionally in the presence of a polyamine catalyst and/or a quaternary amine catalyst. Also provided are kits that can be used to carry out methods of the invention.

Abstract: The invention provides methods and materials for the conversion of cytosine to uracil. A nucleic acid, such a gDNA, is reacted with bisulfate, such as magnesium bisulfite, in the presence of a quaternary amine catalyst. Examples of suitable quaternary amine catalysts include but are not limited to quaternary ammonium compounds, quaternary alkyl ammonium salts, quaternary alkyl ammonium halides, quaternary methyl ammonium bromide, quaternary ammonium chloride, tetraethyl ammonium hydroxide, tetraethylammonium chloride, tetrabutyl ammonium chloride, tetrabutyl ammonium bromide. The invention also contemplates kits of premeasured ingredients for carrying out the methods of the invention either on an individual sample or on a plurality of samples.

Abstract: The invention provides methods for purifying bisulfite-treated nucleic acid samples.