Synthetic nucleic acid control molecules
The present invention provides synthetic DNA strands that find use as controls or in nucleic acid testing methods. In particular, provided herein are synthetic DNA strands of known composition for use as control molecules in stool DNA testing, e.g., of mutations and/or methylation of DNA isolated from stool samples.
1. A run control composition, comprising:
a) a number of copies of a first synthetic DNA fragment comprising a sequence of a portion of a human biomarker DNA, wherein the sequence is synthesized to comprise a sequence region containing a number and pattern of cytosines and cytosine-phosphate-guanosine (CpG) dinucleotides in which each of the cytosines in the CpG dinucleotides in the pattern comprises a 5-methyl;
b) a number of copies of a second synthetic DNA fragment comprising the same sequence of the same portion of the human biomarker DNA as the first synthetic DNA, and comprising a sequence region comprising the same number and pattern of cytosines and CpG dinucleotides as the sequence region in the first synthetic DNA fragment, wherein none of the cytosines in the pattern comprises a 5-methyl; and
c) fish DNA.
2. The run control composition of claim 1 , wherein the first synthetic DNA fragment and the second synthetic DNA fragment are double-stranded.
3. The run control composition of claim 1 , wherein the first and second synthetic DNA fragments each further comprise a second sequence region containing a CpG dinucleotide in which the cytosine does not comprise a 5-methyl.
4. The run control composition of claim 1 , wherein the composition comprises at least 50 μg/mL fish DNA.
5. The run control composition of claim 1 , further comprising a DNA stabilization buffer comprising Tris-HCl, EDTA, and NaCl.
6. The run control composition of claim 5 , wherein the DNA stabilization buffer is 80% of the volume of the composition, and wherein the DNA stabilization buffer comprises 500 mM Tris-HCl, 150 mM EDTA, and 10 mM NaCl, pH 9.
7. The run control composition of claim 1 , further comprising a synthetic DNA fragment comprising a sequence from a human reference gene.