Skip to content

How to Identify Supercoils, Nicks and Circles in Plasmid Preps

How to Identify Supercoils, Nicks and Circles in Plasmid Preps

One of my favorite things to do with a student the first time they work with DNA plasmid preps is to have them run an agarose gel containing 2 samples:  uncut plasmid DNA, and plasmid DNA that has been linearized with an restriction enzyme.  I love to have them try and figure out the banding pattern of uncut plasmid DNA (why do you see 2-3 bands?) versus the single band of linearized DNA (and why do all bands convert to 1 band when linearized?).

I like this exercise because understanding the forms they are seeing on the gel requires an understanding of the nature of DNA. In this article I will focus on the four most common species of plasmid DNA observed on a gel and how to recognize them. And in my next article I’ll cover how to increase recovery of the desired supercoiled species.

One Molecule, Many Forms

When plasmid DNA is isolated and run on an agarose gel, you may observe 2, 3 or even 4 or more bands.  Hopefully the majority of your isolated DNA will be supercoiled DNA, but other forms can also crop up. How these forms will show up on an agarose gel (in terms of relative migration speeds) is shown in the diagram below.

plasmid preps

And here’s where each form comes from:

Supercoiled Plasmid

Supercoiled DNA is the native confirmation found in vivo and occurs when extra twists are introduced into the double helix strand.  People often compare the forms of DNA to rubber bands or telephone cords (I know some you must still remember phones with cords!).  If you over twist a rubber band or telephone cord, coils stack up upon one another introducing tension.  In the case of plasmid preps, this superhelical tension cannot be relieved because the ends of the plasmid are joined together.  Supercoiled DNA migrates faster than predicted in an agarose gel due to its conformation.  Supercoiled DNA is the desired species when isolating plasmid DNA.

Nicked, Relaxed Circular Plasmid

DNA found in the supercoiled form is not easily accessed by replication machinery.  During replication, cellular topoisomerases nick one strand of the DNA helix and relax the superhelical tension, thus allowing polymerases to gain access to the DNA.  Using the rubber band analogy, nicked circle DNA is the rubber band without any twists introduced.  This large floppy circle is the slowest migrating form in an agarose gel.

Linear Plasmid

Linearized DNA occurs when the DNA helix is cut in both strands at the same place.  Linear DNA generally migrates between the nicked circle and the supercoiled forms.  However, it may also migrate the same distance as nicked circle — it migrates as predicted by the length of the DNA (as compared to the MW markers).  You can identify the linear DNA form on an agarose gel by comparing uncut plasmid DNA with a sample of the plasmid that has been linearized using a restriction enzyme.  If you get linear DNA when you are hoping for supercoiled (e.g. after a plasmid prep) it is due to nuclease contamination or harsh treatment during purification.

Circular, Single Stranded Plasmid

During alkaline lysis plasmid preps, plasmids are denatured because the hydrogen bonds are disrupted by the alkaline conditions. But the covalently-closed circular strands remain intact and topologically constrained and when the pH is returned to neutral the hydrogen bonds reform and the supercoiled DNA is re-formed. However, if the alkaline lysis step is overly harsh (e.g. it is incubated for too long) the DNA can become permanently denatured and give you useless single stranded closed circles that migrate ahead of all of the other forms of the plasmid in a gel.

Although DNA plasmid preps can return multiple forms of DNA, there is only one kind you want for successful cloning and transfection: supercoiled.  Make sure you know how to increase your recovery of good quality supercoiled DNA.

Image Credit: Theen Moy


  1. Gopal Jee on March 20, 2018 at 8:49 am

    Can you provide reference? How did you establish that front running band is of single stranded Circular plasmid?

    • Himanshu sharma on April 20, 2019 at 2:43 pm

      In agarose gel electrophoresis, DNA fragments are seperated on the basis of their size (Number of base pairs). Conventionally, the smaller the size of the DNA fragment the farthest it will move from the wells. In case of closed single stranded plasmid, the average size is the least (due to the loss of a chain of basepairs of one whole strand) as compared to closed nicked , linearised or supercoiled plasmid (all having two strands). Therefore it is justified why closed single stranded plasmid travels the farthest.

  2. Reena Bharti on March 6, 2018 at 1:32 pm

    It was useful as I was having many queries about this. Thanks

  3. Michael Labare on October 18, 2017 at 9:46 pm


  4. Sharon on March 12, 2017 at 2:22 pm

    “However, it may also migrate the same distance as nicked circle — it migrates as predicted by the length of the DNA (as compared to the MW markers). ”
    Can anyone explain what does this sentence mean? Why would the linear shaped DNA migrate the same distance as the circle one?

    • Marcino on July 10, 2018 at 9:53 am

      The author is in some partly right and wrong here. Firstly he means circular single stranded and circular double stranded pDNA that are travelling with the same speed in a gel. To get the picture just imagine a circle of pDNA travelling within a gel, and if it doesn’t have any extra twists, coils or nicks, it should not matter if it is a single stranded circular DNA or if it is comprised of 2 molecules (then it is travelling like 2 circles glued together).
      You might be confounding ssDNA with linear pDNA here, which clearly is migrating slower, in accordance with the length of pDNA, and this is also where the author is wrong.
      In the latter part of the sentence we read that circular pDNA ‘migrates as predicted by the length of the DNA’, which clearly is not observed in laboratory practice- linear pDNA is the only conformation that indicates DNA molecule length or approximates its MW (molecular weight).

  5. Route thala on October 8, 2016 at 5:22 am


  6. Adrienne Snyder on July 21, 2016 at 3:57 pm

    Hi, what exactly is covalently closed DNA on the image you provided and why does it run more quickly than nicked circular DNA?

  7. Phillip on July 21, 2016 at 3:02 am

    Hi Rebecka
    Your explanation was really amazing Actually I’m working with a plasmid from Aeromonas I would like to ask you how establish a difference between two forms of a plasmid and two different plasmid that cohabitate in a single bacteria?

  8. Yashar Khani on April 14, 2016 at 4:34 am

    It was one of the most well-writen scientific articles I’ve ever read.simple-complete-no big and useles words!!!
    Thanks Rebeca?

  9. YPT on February 4, 2016 at 2:00 am

    Loved it!
    I’m beginning my dissertation and I’m using CRISPR-Cas9
    So, the first steps is doing lots of minipreps!

    Greetings from Mexico.

  10. JackBean on May 14, 2014 at 5:34 pm

    Hasn’t this article been here already some time ago?

Leave a Comment

You must be logged in to post a comment.

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Scroll To Top
Share via
Copy link