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The A, B, Z’s of DNA

Today (4/25) is national DNA day.  Digital World Biology™ is celebrating by sharing some of our favorite structures of DNA. We created these photos with Molecule World™ a new iPad app for viewing molecular structures.

As we are taught in school, the double stranded DNA molecule is a right-handed helix as determined by Watson and Crick using Franklin’s x-ray diffraction images [1]. This B-form of DNA has approximately 10 nucleotides per turn of the helix and is the most common form of DNA found in nature.

B-DNA

Classic structure with the elements colored.

B-DNA

Classic structure with the bases colored.

B-DNA

Classic structure with the strands colored.

However, we’ve heard it said that the first crystal structure of DNA was not right-handed (pers. communication S. Elgin, Washington University). Instead, the high salt and GC base-pairs, used to form the DNA crystals caused the helix to twist in a left-handed way, creating a structure called  Z-DNA. Z-DNA occurs in nature, but is most frequently used by marketing departments to [incorrectly] create company logos.

Z-DNA

Z-DNA with the elements colored.

Z-DNA

Z-DNA with the bases colored.

Z-DNA

Z-DNA with the stands colored.

In addition to B- and Z-DNA, DNA can exist in another form known as A-DNA. A-DNA occurs when DNA is dehydrated, but also in DNA/RNA hybrids and double stranded RNA.

A-DNA

A-DNA with the elements colored.

A-DNA

A-DNA with the bases colored.

A-DNA with the strands colored.

A-DNA with the strands colored.

Here’s another look at the same molecules, this time head on with the structures rendered in tubes and the bases colored.

B-DNA

B-DNA “on end,” showing the double helix.

Z-DNA

Z-DNA “on end,” showing the double helix.

A-DNA

A-DNA “on end,” showing the double helix.

References

Double Helix – Watson, J. D., & Crick, F. H. (1953). Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356), 737-8.

B-DNA Structure (PDB:1BNA) – Drew, H., Wing, R., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Sciences, 78 (4), 2179-2183 DOI: 10.1073/pnas.78.4.2179

First Z-DNA Crystal – Wang, A., Quigley, G., Kolpak, F., Crawford, J., van Boom, J., van der Marel, G., & Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution Nature, 282 (5740), 680-686 DOI: 10.1038/282680a0

Z-DNA Structure (PDB:1D48) – Egli, M., Williams, L., Gao, Q., & Rich, A. (1991). Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-.ANG. resolution Biochemistry, 30 (48), 11388-11402 DOI: 10.1021/bi00112a005

A-DNA Structure (PDB:371D) – Fernandez, L., Subirana, J., Verdaguer, N., Pyshnyi, D., Campos, L., & Malinina, L. (1997). Structural Variability of A-DNA in Crystals of the Octamer d(pCpCpCpGpCpGpGpG) Journal of Biomolecular Structure and Dynamics, 15 (1), 151-163 DOI: 10.1080/07391102.1997.10508954

 

Molecule World™ was developed with funding from the National Science Foundation (SBIR IIP 1315426).  Any opinions, findings, conclusions, or recommendations expressed on this website are those of the authors and do not necessarily represent the official views, opinions, or policy of the National Science Foundation.

Comments

  1. #1 qetzal
    April 25, 2014

    What about 3- and 4-stranded DNA?

  2. #2 @finchtalk
    April 26, 2014

    Good point, we’ll include some in a future post.

  3. #3 u14043042
    Pretoria,hatfield, South Africa
    April 26, 2014

    Why is the 25th of April chosen to be the national DNA day

  4. #4 Sandra Porter
    April 26, 2014

    DNA day is April 25th because that’s the day that the DNA structure papers were published in Nature.

  5. #5 u14043042
    Pretoria,Hatfield,South Africa
    April 26, 2014

    In nature? can you please explain

  6. #6 @finchtalk
    April 26, 2014

    Nature is referring to the scientific journal: “Nature.”

  7. […] Today (4/25) is national DNA day. Digital World Biology™ is celebrating by sharing some of our favorite structures of DNA. We created these photos with Molecule World™ a new iPad app for viewing molecular structures.  […]

  8. #8 u14043042
    Pretoria,Hatfield,South Africa
    April 26, 2014

    Thank you.As a student in Biotechnology.It would be great to know important dates like this.

  9. #9 u13044657
    Hatfield, Pretoria, South Africa
    April 27, 2014

    The information in this post is very interesting. I have never learnt of any other DNA other than the original structure. It really creates a urge to do further research about the different structures of DNA.

  10. #10 u14043042
    Pretoria
    April 28, 2014

    That is true we only know the right handed helix, at least now we know that it is not the only one.

  11. #11 u14053706
    Pretoria
    April 28, 2014

    This is all new information since at first year level we have only been taught the basics such as the basic structure , replication models etc. So to most of us , including myself , this is new information which makes it exciting to know how much else there is to learn about . Especially as a student, to be studying genetics and physiology.

  12. #12 A. Smit 14023190
    April 28, 2014

    I would like to ask what exactly is A, B and Z DNA? and what are the difference’s and similarity’s of these DNA?

  13. #13 Sandra Porter
    April 28, 2014

    They are different three dimensional forms that DNA can assume depending on the environment. Conditions that affect the form are the salt concentration, the sequence, and the amount of water. You can look at the pictures above to see how the forms change.

  14. #14 U14066582
    South Africa
    April 29, 2014

    I am a first year student studying Biochemistry and I find this article useful as well as the images provided that help the reader to visualize the actual three dimensional structure of DNA

  15. #15 Westley Ferguson
    University of Pretoria
    April 29, 2014

    Perhaps a more accurate description of the right or left handed forming of the helix structure would be describing the way the structure forms due to the polarity of the base-pairs. The DNA helix structure has an anti-parallel configuration, meaning that one strand connects to the other anti-parallel with one strand running from 5′ to 3′ and the other strand running from 3′ to 5′. This also serves as an important base for DNA replication.

    u14060290

  16. #16 u14220751
    University of Pretoria, Hatfield
    April 29, 2014

    This post is very informative. It is astonishing that there are different structures of DNA other than the original. It is also interesting to learn that April 25th is a National DNA day.

  17. #17 u13044657
    Hatfield, Pretoria, South Africa
    April 29, 2014

    After reading this new information I went and did some further research to find the purpose of these different structures and what I found was quite intersting.

    The A- structure is actually necassary for the reproduction of B-DNA, the commonly found structure. A conformational switch happens from the B- to underwound A-form starting at the point of nucleotide incorporation and extending to four bases upwards.

    And then the Z-structure’s purpose is less infamous. It is found to be used as a basin where the torsional tension in supercoiled DNA collects.

    I hope you find this information as intersting as I did

  18. #18 u14236967
    Hatfield, Pretoria, South Africa
    April 29, 2014

    This is indeed an eye opening information which gives explanation to one of the concepts in that have been generalized in Biology as a whole. Such generalisations have led to the limitation of our knowledge and raised misconceptions.

    It is of great value that the digital world can help us to resolve such misconceptions.

    Does the difference in structure play any significance in the role played by the DNA?

  19. #19 u14014905
    Hatfield, Pretoria, South Africa
    May 1, 2014

    As a student we are currently studying genetics and I would like to ask if these different tipes of DNA can all be found in the genetic composition of one organism?

  20. #20 u14013097
    Hatfield,m Pretoria, South Africa
    May 1, 2014

    As a first year studying Biochemistry I found this topic interesting, useful and highly informative. I did not know that there were so many types of DNA structures.

    This just shows you how little we actually know, and how much studying lies before us. Not to mention al the discoveries that can still be made, as I am sure that scientist do not know absolutely everything yet, they are still researching and studying the structures.

    This is the reason I love this field of studying, it is so fascinating and it is always developing and making new discoveries. I will definitely go read up more on these DNA structures and do some research to broaden my knowledge.

  21. #21 u14013097
    Hatfield, Pretoria, South Africa
    May 1, 2014

    What is the major importance in the roles of these structures? How many structures’ existences are we aware of, is it currently only these 3? lastly what in the body exactly triggers them to form these different structures?

  22. #22 Sandra Porter
    May 1, 2014

    Just curious, is this some kind of class assignment?

  23. #23 u13044657
    Hatfield, Pretoria, South Africa
    May 2, 2014

    Hi Sandra
    Yes, we have an assignment to follow a blog. I must say it took me some time to find a blog post that was of interest. Must be why my fellow classmates also contribute to it so eagerly.

    Thank you for your contribution to science and helping us understand science better and further our studies.

  24. #24 u14014905
    May 2, 2014

    “In addition to B- and Z-DNA, DNA can exist in another form known as A-DNA. A-DNA occurs when DNA is dehydrated, but also in DNA/RNA hybrids and double stranded RNA.” Does this only state that a number of DNA strands can have the same composition just different names?

  25. #25 Sandra Porter
    May 2, 2014

    The physical shape is different. The different names are used to describe the different shapes.

    Let’s say I have I have two samples of DNA, with the identical sequence. I keep one in water (hydrated) and let the other one dry out (it becomes dehydrated), then I analyze the crystal structure. One would be in the B form, the other would be in the A form.

  26. #26 u14071348
    University of pretoria, South Africa
    May 2, 2014

    This blog post gives great insight into the world of DNA. It is informative and aims to broaden the perspectives of people such as myself (a first year BSc Student).

    I am definitely inspired by this post because of the interest it ignites in me. I did not realise the complexity in which DNA can exist but after reading this post I appreciate the human body and the essence of its systematic processes.

  27. #27 @finchtalk
    May 2, 2014

    On comment #23, Just wanted to add that we really appreciate that you like the post. Also, if you want to play with the structures yourself, and have an iPad, you can get the app https://itunes.apple.com/us/app/molecule-world/id863565223?ls=1&mt=8 — The references above include the PDB IDs so you can use Molecule World’s search to get them from MMDB or PDB. Enjoy.

  28. #28 u14014905
    UP
    May 3, 2014

    Thank you Sandra for this very interesting piece on DNA. I truly appreciate the link for the structures.

  29. #29 u14130263
    May 3, 2014

    After reading this post I actually went and did some more research on the topic because we are only being taught the basics at the moment. This has definitely sparked a level of interest in the field of genetics

  30. #30 u14359678
    May 4, 2014

    It feels good knowing that there’s an application that enables us to view such educational information. This can really help us(students) to learn while we are having fun

  31. #31 Daniel D'Emmerez de Charmoy u14152232
    TUKS
    May 4, 2014

    This article leads me to question whether or not other possible forms of DNA could exist and how the change in structure would affect its function as well as its phenotypic expression of the genes? Also what is meant by “but is most frequently used by marketing departments to [incorrectly] create company logos.”?

  32. #32 @finchtalk
    May 4, 2014

    Daniel, as an assignment perhaps you can look at company logos that use a DNA helix and see if the helix is right handed or left handed.

    For comment #30 – check out the app and tell us what you think. Thanks.

  33. […] recent post on DNA structures inspired an entire group of students to ask questions and comment. Some wanted to know about […]

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