Synthetic Repetitive DNA

A precision method for suppressing repetitive DNA sequences

Synthetic repetitive DNA can be used in lieu of Cot-1 DNA for repeat suppression in any hybridization experiment without distortion of hybridization signals Distortion of hybridization signals documented using Cot-1 DNA with its single copy impurities Available for any or all repetitive classes of DNA in human genome

Distortion of hybridization signal is seen in many genomic experiments, such as Southern blots, microarray, arrayCGH, etc, reported in the literature which utilize commercial suppressive DNA (ie Cot-1 DNA). The signal distortion leads to results that cannot be reproduced within and between labs using the same arrays and in many cases the same samples. Further the distortion causes many false results which make array data very difficult to interpret. This effect can be mitigated using the method of suppressing repetitive sequences using synthetic repetitive DNA purely comprised of repetitive sequences. Hybridization of probe or target sequences with synthetic repetitive DNA can effectively block repetitive sequences found in both the target DNA on an array or Southern blot or the probes used in the experiments. A pre-hybridization step using synthetic repetitive DNA instead of Cot-1 DNA is all that is required for background noise reduction and brighter probe hybridization signals.

Synthetic repetitive DNA can be included in any genomic hybridization experiment for effective suppression of repetitive sequences. For instance, in fluorescent in situ hybridization (FISH), hybridization probes can be incubated with synthetic repetitive DNA instead of Cot-1 DNA prior to hybridization to chromosomes fixed on slides. Often comparative experiments prepared with and without probe pre-hybridization using Cot-1 DNA show differing probe hybridization signals. The FISH experiment done without Cot-1 DNA probe pre-hybridization reveals a weaker probe signal on the chromosome as compared to the FISH experiment without Cot-1 DNA pre-hybridization. The weaker signal stems from hybridization of single copy sequences in the probe to single copy sequences present in the Cot-1 DNA. This reduces the amount of probe available for hybridization to the target sequence on the chromosomes and thus a weaker signal. However, as a consequence, the experiment without Cot-1 DNA pre-hybridization while brighter in probe signal intensity, typically shows more false positive prove hybridizations which results in a higher background level making analysis more labor intensive. By pre-hybridizing probes with a pure synthetic repetitive DNA fraction comprised of no single copy sequences, any repetitive sequences found in the probe are effectively suppressed leaving the single copy sequences available for hybridization to the chromosomes. Thus, probe signal intensity on the chromosome is not compromised and background (false positive hybridization signals) is effectively minimized.

Tim Wurst, CEO Eriban Wurst, Inc. 3101 Broadway, Suite 630 Kansas City, Missouri 64111 USA Phone 1.816.753.5329		Technology developed and patented by: