Doing research involves a lot more than just lab work. We also read a lot of papers from people who have done foundational research that we’re building from. Two such papers are “Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA” by Gansauge and Meyer (2013), and “Reducing microbial and human contamination in DNA extractions from ancient bones and teeth” by Korlević et al. (2015).
Gansauge and Meyer introduce and test a new method for improving the recovery of ancient DNA for DNA sequencing. In this method we take ancient DNA and add little bits of known DNA sequence to them that we can use later to copy the ancient DNA and sequence it. Many copies of the ancient DNA (with attached known sequences) are called a DNA library. In ancient DNA, many strands of DNA are often damaged and broken. DNA is present as two attached copies. Previous methods required both strands to be present and intact, but if they’re broken they get lost during processing. The thing that differs in this method versus others before it is that this method uses single-stranded DNA instead of double-stranded, so much more of the DNA is sequenceable. Another cool thing about this method is that they bind the DNA to magnetic beads so that they can be sure they aren’t losing any of it.
Korlević et al. talk about the contamination present in ancient DNA and how to decrease it. We don’t often think about it, but literally everything is covered with bacteria, and bacteria all have their own DNA. This means that any sample will be contaminated with bacterial DNA, and often with human DNA from handling. Korlevic et al. test three different methods of getting rid of the extra DNA: (1) using bleach on the samples, (2) incubating the samples in a phosphate buffer, and (3) re-extracting the DNA from the sample multiple times. Bleach was the best at getting rid of the contaminating DNA, but it also got rid of a lot of the target DNA, so it isn’t a good method for rare or precious samples. The phosphate treatment turned out to be the safest, since it preserved all of the target DNA, but it also didn’t get rid of as much contaminating DNA. The re-extraction method didn’t help significantly, and even made the contamination worse in some cases.
Reading papers like these is important for understanding the work that came before ours, and putting our own work into context. The papers can be difficult to read and understand, but reading them is an essential part of the research process. It’s also not too bad when you get to pet kitties while reading!