Synthetic Biology
Support and Educational Content

Tips for working with gBlocks® Gene Fragments

How to resuspend, quantify, and calculate copy number

We sell a lot of double-stranded DNA (dsDNA) fragments, our gBlocks® Gene Fragments. Researchers around the world are using them successfully for a wide range of applications, as you can see in our selected citations list. We frequently receive questions about the best way to handle these fragments, so we would like to share a few tips from the scientists in our synthetic biology group.

Resuspending gBlocks Gene Fragments

gBlocks Gene Fragments ordered in tubes are provided dry and must be resuspended. (Note: gBlocks Gene Fragments ordered in plates come in 25 µL of nuclease-free water at 10 ng/µL.) We have evidence of these dsDNAs occasionally adhering to the plastic tubes, and therefore, strongly recommend the 50°C incubation described below in step 4. Here is our recommended protocol for resuspension:

  1. Before opening the tube, spin it down in a microcentrifuge for 3–5 seconds to ensure the DNA is in the bottom of the tube. The pellet can become statically charged and, without this step, can either fly out of the tube or remain in the cap, resulting in loss of yield.
  2. Add molecular grade water, or a buffer such as IDTE, pH 8 (IDT), to reach a final concentration of 10 ng/µL. Our experiments have shown that storage concentrations <1 ng/µL result in loss of material due to adherence to the plastic tube in the absence of a carrier such as tRNA.
  3. Vortex briefly.
  4. Incubate at approximately 50°C for 15–20 min. Heating the tube will ensure the solvent comes in contact with the tiny pellet, even if it is stuck to the side of the tube. Thus, this step will increase the likelihood that the entire pellet will be resuspended.
  5. Briefly vortex and centrifuge.
  6. Verify the final concentration (see below).

  7. See the DECODED article, Tips for resuspending and diluting your oligonucleotides, for more advice on nucleic acid handling.


Quantifying gBlocks Gene Fragments

gBlocks Gene Fragments are delivered in amounts of 250–1000 ng. For quantification, we recommend using methods designed for small sample volumes, such as those using the NanoDrop™ (Thermo Fisher Scientific) or Qubit® instruments (Thermo Fisher Scientific). Note that when comparing resulting concentration values across instruments, variances may be seen due to the methods employed by each instrument. Ensure accurate measurements by performing the following steps:

  • Take the measurement as soon as the sample is prepared for the instrument.
  • Repeat quantification of each sample twice.
  • When using a Nanodrop instrument, test the sample resuspension solution alone between each sample measured. This ensures that there is nothing in the water or buffer that absorbs at A260 and would artificially inflate your sample readings.

Calculating copy number

It is often necessary to dilute the resuspended gBlocks Gene Fragment to a specific copy number/µL. The molecular weight and fmol/ng conversions for each gBlocks fragment are provided on the spec sheet provided with the fragment (Figure 1).

Figure 1. Specification sheet information needed for copy number calculation.


You can easily convert your concentration from ng/µL to copy number/µL by following the instructions in the following sidebar, Calculating copy number from concentration measurements.

Calculating copy number from concentration measurements


(C) (M) (1 x 10–15 mol/fmol) (Avogadro’s number) = copy number/µL 

Where C is the current concentration of the gBlocks® Gene Fragment in ng/µL, and M is the molecular weight in fmol/ng, as provided on the spec sheet.


Example: A gBlocks Gene Fragment, with the properties shown in Figure 1 (= 2.12 fmol/ng), is resuspended to 10 ng/µL:

(10 ng/µL) (2.12 fmol/ng) (1 x 10–15 mol/fmol) (6.022 x 1023) = 1.28 x 1010 copies/µL


Have you thought about these gBlocks fragment applications?

gBlocks Gene Fragments have been used in a wide range of applications including CRISPR-mediated genome editing, antibody research, codon optimization, mutagenesis, and aptamer expression. They can also be used for generating qPCR standards. With gBlocks Gene Fragments, IDT provides a tool that accelerates your research and makes synthetic biology easier and more accessible than ever, for any lab.

Learn more about gBlocks Gene Fragments at www.idtdna.com/gBlocks.

Product focus—custom dsDNA fragments and codon optimization

gBlocks® Gene Fragments

These double-stranded, sequence-verified, DNA genomic blocks, 125–3000 bp in length, are designed by you, and are shipped in 2–5 working days for affordable and easy gene construction or modification, as well as in genome editing applications, and as standards in qPCR and NGS experiments.

Learn more about gBlocks Gene Fragments at www.idtdna.com/gBlocks.


gBlocks Gene Fragments Libraries

gBlocks Gene Fragments are also available as dsDNA fragment pools that contain up to 18 consecutive variable bases (N or K) for recombinant antibody generation or protein engineering.

Learn more about gBlocks Gene Fragments Libraries at www.idtdna.com/gBlocks.


Codon Optimization Tool

The IDT Codon Optimization Tool simplifies designing synthetic genes and gBlocks Gene Fragments for expression in a variety of organisms. It optimizes a DNA or protein sequence from one host organism for expression in another by reassigning codon usage. You can easily adjust a sequence that has difficult secondary structure, a repetitive motif, or high/low GC content for compatibility with gene or gBlocks Gene Fragments manufacturing requirements. Further, manual optimization allows you to make desired changes to individual codons by simply clicking on their locations.

Access IDT's free, online Codon Optimization Tool and get started.

Additional reading

Review these articles on applications for gBlocks® Gene Fragments:

Cloning strategies Part 1: Assembly PCR for novel gene synthesis—Learn how you can use single-stranded oligos or a mix of single- and double-stranded DNA to produce longer genes of up to several thousand base pairs. No restriction sites are needed, and the approach is beneficial for assembling constructs that contain modular elements, such as antibodies.

Easily-designed standard curves for qPCR—Adopt this easy way to combine control templates/multiple targets onto a single construct, and get the advantages that they provide for PCR experiments.

Pakistani iGEM team’s biosensor detects vehicle emission levels—Research profile: Learn how the first ever Pakistani iGEM team developed a portable, inexpensive vehicle emissions test to address air pollution. They used gBlocks Gene Fragments for construction of genetic circuits to detect carbon monoxide and nitrogen oxides. The colorimetric biosensor won this young research team a bronze medal at the 2016 iGEM International Jamboree.

Site-directed mutagenesis—improvements to established methods—Site-directed mutagenesis techniques have relied primarily on PCR and standard cloning methods. Read about some of the common cloning methods used for mutagenesis and how double-stranded DNA fragments (gBlocks Gene Fragments) can save you both time and money.

Functional nucleic acids as antibody alternatives for small molecule detection—Research profile: Learn how 2015 iGEM Team Heidelberg students applied functional nucleic acids to design high-affinity, ligand-specific aptamers, in just hours, and without SELEX. Read how the team applied these molecules in western blots, to repair a mutated mRNA, and in a date-rape-drug test strip. Their DNA aptamer sequence designs were synthesized as single-stranded DNA oligonucleotides by IDT.

Czech Republic iGEM team’s diagnostic for circulating tumor cells—Research profile: Read how students participating on the Czech Republic’s first iGEM team reprogrammed yeast cells to identify circulating tumor cells. Their project, the IOD Band, could become a general diagnostic test for early detection and mapping of tumor cell mobility. IDT gBlocks® Gene Fragments facilitated rapid, construct assembly of IOD Band receptor molecules.


Review other DECODED Online newsletter articles on synthetic biology applications.


You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.


Author: Heather Tyra, MS, is a product support specialist for the IDT synthetic biology group.

© 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.


gBlocks® Gene Fragments

Double-stranded DNA up to 3,000 kb—great for easy gene construction, CRISPR genome editing, and more.

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