Handling High Molecular Weight DNA

Introduction

Long-read sequencing, such as Oxford-Nanopore or PacBio sequencing, is becoming increasingly important for genome assembly and genomic research as reads stretching across repeats and mobile genetic elements can preserve structural information about the chromosome unavailable to short-read sequencing. For long-read sequencing high molecular weight DNA (HMW DNA), composed of long fragments generally greater than 50 kb, is necessary. Special care must be taken with these samples to preserve the size of the fragments: routine lab manipulations can break the DNA strands into smaller pieces, reducing the information they contain. As a general rule: minimize pipetting, vortexing, heat stress, and freezing when working with HMW DNA extracts. Ultra high molecular weight DNA (UHMW DNA) is even longer than HMW DNA, greater than 250 kb, and may require additional handling considerations.

N50 is a measure commonly used to compare the lengths of fragments in HMW samples. The N50 of a sample corresponds to the length of a fragment at which the fragments above and below it have equal total lengths. Or, more simply, if all the fragments were arranged in order from longest to shortest, the N50 would be the length of the fragment in the middle (see Figure).

Resuspension and Quantification

After extraction, HMW DNA frequently forms clumps and will not be well distributed within the sample. Resuspension requires incubation of the extract for periods ranging from an hour on a heat block to incubation overnight at room temperature or 4 °C for several days. Gently flicking the tube during resuspension can help disperse the DNA. At high concentrations the resuspended mixture becomes viscous and will pipette slowly.

HMW DNA extracts must be resuspended before quantification or the DNA will not be distributed evenly throughout the sample. While fluorescent dye-based quantification methods are typically preferred for quantifying DNA extracts they are less accurate when quantifying HMW DNA. Qubit quantification of HMW DNA can be off by more than 25% when using traditional standards [1]. Using genomic DNA extracts as standards may produce more reliable results.

Storage

If being used imminently, HMW extracts should be stored at 4 °C. For long-term storage HMW extracts can be frozen at -20 °C. Note that repeatedly freezing and thawing samples can lead to degradation of HMW DNA and lead to a decrease in N50 [2], so this should be used sparingly.

Shipping

HMW DNA can be damaged during shipping. To prevent this it is recommended to ship HMW DNA frozen on dry ice, as frozen samples are less likely to be damaged by jostling during transit [3].

References

[1] https://www.neb.com/en-us/tools-and-resources/usage-guidelines/measuring-analyzing-and-storing-high-molecular-weight-dna-hmw-dna-samples
[2] https://nanoporetech.com/document/requirements/dna-stability-f-t
[3] https://www.pacb.com/wp-content/uploads/Technical-Note-Preparing-DNA-for-PacBio-HiFi-Sequencing-Extraction-and-Quality-Control.pdf