How To - Writing a Methods Section of a Scientific Paper

The best advice is to read the methods section of papers similar to your paper. Here are a few examples of aptamer papers with well written methods section:

Stoltenburg, R, Reinemann, C, and Strehlitz, B: FluMag-SELEXas an advantageous method for DNA aptamer selection. Analytical and Bioanalytical Chemistry 2005, 383(1):83-91.

Wilner, SE, Wengerter, Br, Maier, K, de Lourdes Borba Magalhaes, M, Del Amo, DS, Pai, S, Opazo, F, Rizzoli, SO, Yan, A, Levy, M: AnRNA Alternative To Human Transferrin: ANew Tool for Targeting Human Cells. Molecular Therapy-Nucleic Acids 2012, 1,e21. doi: 10.1038/mtna.2012.14.

Advice on writing research papers:

Whitesides, GM: Whitesides’ Group: Writing a Paper. Advanced Materials 2004, 16(15):1375-1377.

Here is some more specific advice for writing the methods section of one of your first aptamer papers:

Experimental Design, Methods, and Materials (no more than 1 page)

1. Describe how the selection will be performed and the specific options and parameters. Pay attention to how others have used your target, their buffers and conditions, etc.
2. DO NOT ..
   1. DO NOT REHASH THE PROTOCOL.
   2. DO NOT list the steps of selection here, but rather talk about the options of the selection, negative selection, activity assays, etc.
      1. If for instance, your protein has a GST tag, then you would want to do a GST negative selection to remove sequences that bind to GST.
      2. If it is an F/C chimera, this means it is attached to a portion of the IgG antibody and you should include this in the negative selections.
3. Use first person sparingly.
4. Do not use bullet points. It should be a narrative (story) of what happened to the items you were working with, describing the overall process you performed.
5. Include the conditions and why those conditions were selected. For example,
   1. If you want a diagnostic to differentiate between two closely related targets, then you should consider doing the negative selection with that related target.
   2. If you want a therapeutic agent, then you should consider incubations at body temperature (37̊C).
6. Please specify all of these conditions.
   1. What buffer do you plan to use and at what concentration and pH? PBS, Tris, and HEPES buffers are the regularly used.
   2. What salts will you add to your buffer? KCL, NaCl, MgCl₂, etc. Review the Selection protocol to help you decide.
   3. What negative selections will you perform?
   4. Is the protein stable frozen for long periods?
   5. Is the protein stable at neutral pH? Does it require something special?
   6. What is the predicted protein information such as isoelectric point (pI), amino acid sequence, protein structure, charge, absorbtivity, etc.

Predicting the Isoelectric Point (pI)

Predicting the isoelectric point and other information is easy with online tools. First, find the amino acid sequence with a search at the protein database on the NCBI website (http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein). In the example for endostatin, Wikipedia mentioned that endostatin was derived from type XVIII collagen, so the 2^nd link down is “endostatin [synthetic construct]” and the fourth link down is collagen from Homo sapiens (humans). Both could be predicted. Note: Mus is mouse, Danio is the zebrafish, Drosophila is the fruit fly, etc.

1 hshrdfqpvl hlvalnspls ggmrgirgad fqcfqqarav glagtfrafl ssrlqdlysi

61 vrradraavp ivnlkdellf pswealfsgs egplkpgari fsfdgkdvlr hptwpqksvw

121 hgsdpngrrl tesycetwrt eapsatgqas sllggrllgq saaschhayi vlciensfmt

181 ask

Next copy the amino acid sequence located at the bottom of the link under ORIGIN into a web based predictor program such as the one from Scripps Institute (http://www.scripps.edu/~cdputnam/protcalc.html). The web form includes input for the sequence, with option boxes to calculate information such as molecular weight, isoelectric point, charge at pH 7 and other pH and absorbance conversion in M-1 cm-1. All of this information is useful for suggesting buffer conditions. Ideally, an isoelectric point above 7 will be positively charged at neutral pH and therefore more likely that the nucleic acid will bind. If it is much lower, then the salts should be increased to bridge the negative charges.