RNA and DNA Extraction Protocols and Papers

This page will contain resources and open source links to RNA and DNA extraction methods for research. Will update regularly. This page will contain standard wet lab methods, kit protocols, and manuscripts describing novel and older techniques. Email catherin@bu.edu with additions/corrections.

Klapperich Lab Papers

• Paper Based RNA Extraction from Clinical Flu A Samples:  open access link  “Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens.”, Rodriguez NM¹, Linnes JC¹, Fan A¹, Ellenson CK¹, Pollock NR², Klapperich CM¹. Anal Chem. 2015 Aug 4;87(15):7872-9. doi: 10.1021/acs.analchem.5b01594. Epub 2015 Jul 15.
• Paper Based RNA Extraction from HIV and Malaria in Blood.
  SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood
  Nikunja Kolluri, Nikolas Albarran, Andy Fan, Alex Olson, Manish Sagar, Anna Young, José Gomez-Marquez, Catherine M. Klapperich
  bioRxiv 2020.03.14.991893; doi: https://doi.org/10.1101/2020.03.14.991893
• Nucleic Acid Extraction (DNA) Using a Pipette Tip Packed with Filter Paper (we’ve never tried for RNA): open access link “Paper-based molecular diagnostic for Chlamydia trachomatis.” Linnes JC, Fan A, Rodriguez NM, Lemieux B, Kong H, Klapperich CM. RSC Adv. 2014 Jan 1;4(80):42245-42251.
• Paper Based DNA Extraction from Clinical Cervical Swab Samples: open access link  “A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples.”Rodriguez NM, Wong WS, Liu L, Dewar R, Klapperich CM., Lab Chip. 2016 Feb 21;16(4):753-63. doi: 10.1039/c5lc01392e. Epub 2016 Jan 20.
• How to make our BoomD Lysis Buffer: BoomD Lysis Buffer Protocol
• How to use BoomD with PES Membrane and Filter Paper to Extract RNA for Downstream qPCR. Lysis_precipitation Protocol on Membrane Using BoomD

Other Protocols

• Chomczynski and Sacchi: Hard to spell, easier to do! Start here if you are thinking of trying out Boom on your own (Boom is what the Qiagen kits are based on). Chomczynski, P., Sacchi, N. The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on. Nat Protoc 1, 581–585 (2006). https://doi.org/10.1038/nprot.2006.83 pdf
• TRIzol, tried but true, for those who like efficient, don’t mind smelly, and are careful with pellets!
• BOOM! The Boom Method. Can basically use any silica solid substrate for this one (including glass wool) – What Chomczynski is all about. open access link “Rapid and simple method for purification of nucleic acids.” Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J., J Clin Microbiol. 1990 Mar;28(3):495-503.
• Phenol/Chloroform. For those who don’t want to pay full freight retail for TRIzol.
  • https://www.neb.com/protocols/0001/01/01/purification-of-synthesized-rna-e2040

• Detailed DNA extraction on Silica Beads you can buy from Sigma. using Davisil 643 amorphous silica particles (Sigma-Aldrich, St. Louis, MO, USA), Here is the open access link to paper with protocol. 
• What if they run out of Davisil?!: Davisil is great because it comes cleaned by Sigma. If you can’t get Davsil any more, you can use any glass/silica beads, but you need to acid clean them first to get off impurities and optimize bind and release. Our protocol is here: Silica_Prep_for_extraction