The preparation of a high quality sequencing library plays an important role in next-generation sequencing (NGS). The first main step in preparing nucleic acid for NGS is fragmentation. In the next series of blog posts we will present important challenges and things to consider as you isolate nucleic acid samples and prepare your own libraries.
Next Generation Sequencing, will give you a plethora of reads, but they will be short. Illumina and Ion read lengths are currently under 600 bases. Roche 454 outputs reads at less than 1kb and PacBio less than 9kb in length. This makes sizing your input DNA or RNA important prior to library construction. There are three main ways to shorten your long nucleic acid material into something compatible for next-gen sequencing: 1) Physical, 2) Enzymatic and 3) Chemical shearing.
1) Acoustic shearing
3) Hydrodynamic shear
Acoustic shearing and sonication are the main physical methods used to shear DNA. The Covaris® instrument (Woburn, MA) is an acoustic device for breaking DNA into 100-5kb bp. Covaris also manufactures tubes (gTubes) which will process samples in the 6-20 kb for Mate-Pair libraries. The Bioruptor® (Denville, NJ) is a sonication device utilized for shearing chromatin, DNA and disrupting tissues. Small volumes of DNA can be sheared to 150-1kb in length. Hydroshear from Digilab (Marlborough, MA) utilizes hydrodynamic forces to shear DNA. Nebulizers (Life Tech, Grand Island, NY) can also be used to atomize liquid using compressed air, shearing DNA into 100-3kb fragments in seconds. While nebulization is low cost and doesn’t require the purchase of an instrument, it is not recommended if you have limited starting material. You can lose up to 30% of your DNA with a nebulizer. The other sonication and acoustic shearing devices described above are better designed for smaller volumes and retain the entire amount of your DNA more efficiently.
4) DNase I or other restriction endonuclease, non-specific nuclease
Enzymatic methods to shear DNA into small pieces include DNAse I, a combination of maltose binding protein (MBP)-T7 Endo I and a non-specific nuclease Vibrio vulnificus (Vvn), NEB’s (Ipswich, MA) Fragmentase and Nextera tagmentation technology (Illumina, San Diego, CA). The combination of non-specific nuclease and T7 Endo synergistically work to produce non-specific nicks and counter nicks, generating fragments that disassociate 8 nucleotides or less from the nick site. Tagmentation uses a transposase to simultaneously fragment and insert adapters onto dsDNA. Generally enzymatic fragmentation has shown to be consistent, but worse when compared to physical shear methods when it comes to bias and detecting insertions and deletions (indels) (Knierim et al., 2011). Depending on your specific application, de novo genome sequencing vs. small genome re-sequencing, biases associated with enzymatic fragmentation may not be as important.
RNAse III is an endonuclease that cleaves RNA into small fragments with 5’phosphate and 3’hydroxyl groups. While these end groups are needed for RNA ligation, making the assay convenient, RNAse III cleavage does have sequence preference which makes the cleavage biased. Heat / chemical methods described below, while they leave 3’phosphate and 5’hydroxyl ends, show less sequence bias and are generally preferred methods in library preparation.
6) Heat and divalent metal cation
Chemical shear is typically reserved for the breakup of long RNA fragments. This is typically performed through the heat digestion of RNA with a divalent metal cation (magnesium or zinc). The length of your RNA (115 bp – 350 nt) can be adjusted by increasing or decreasing the time of incubation.
The size of your DNA or RNA insert is a key factor for library construction and sequencing. You’ll need to choose an instrument and read length that is compatible with your insert length. You can choose this by entering project parameters in the Shop by Project page and filtering according to read length (estimated insert length). If you’re not sure, we can help. Send us a request through our consultation form .
Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing
Ellen Knierim, Barbara Lucke, Jana Marie Schwarz, Markus Schuelke, Dominik Seelow