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Discovery of the structure of DNA

The structure of DNA double helix and how it was discovered. Chargaff, Watson and Crick, and Wilkins and Franklin.


Today, the DNA double helix is probably the most iconic of all biological molecules. It's inspired staircases, decorations, pedestrian bridges (like the one in Singapore, shown below), and more.
I have to agree with the architects and designers: the double helix is a beautiful structure, one whose form fits its function in a remarkable way. But the double helix was not always part of our cultural lexicon. In fact, until the 1950s, the structure of DNA remained a mystery.
Image credit: "Double helix bridge," by William Cho, CC BY-SA 2.0
In this article, we'll briefly explore how the double-helical structure of DNA was discovered through the work of James Watson, Francis Crick, Rosalind Franklin, and other researchers. Then, we'll take a look at the properties of the double helix itself.

The components of DNA

From the work of biochemist Phoebus Levene and others, scientists in Watson and Crick's time knew that DNA was composed of subunits called nucleotidesstart superscript, 1, end superscript. A nucleotide is made up of a sugar (deoxyribose), a phosphate group, and one of four nitrogenous bases: adenine (A), thymine (T), guanine (G) or cytosine (C).
C and T bases, which have just one ring, are called pyrimidines, while A and G bases, which have two rings, are called purines.
Left panel: structure of a DNA nucleotide. The deoxyribose sugar is attached to a phosphate group and to a nitrogenous base. The base may be any one of four possible options: cytosine (C), thymine (T), adenine (A), and guanine (G). The four bases have differences in their structure and functional groups. Cytosine and thymine are pyrimidines and have just one ring in their chemical structures. Adenine and guanine are purines and have two rings in their structures.
Right panel: a strand of linked DNA nucleotides. The sugars are connected by phosphodiester bonds. A phosphodiester bond consists of a phosphate group in which two of the oxygen atoms are bonded to other atoms - in this case, to carbon atoms of the neighboring deoxyribose sugars. The DNA strand consists of alternating phosphate groups and deoxyribose sugars (sugar-phosphate backbone), with the nitrogenous bases sticking out from the deoxyribose sugars.
Image credits: left panel, image modified from "Nucleic acids: Figure 1," by OpenStax College, Biology (CC BY 3.0). Right panel, image modified from "DNA chemical structure," by Madeleine Price Ball (CC0/public domain).
DNA nucleotides assemble in chains linked by covalent bonds, which form between the deoxyribose sugar of one nucleotide and the phosphate group of the next. This arrangement makes an alternating chain of deoxyribose sugar and phosphate groups in the DNA polymer, a structure known as the sugar-phosphate backbone

Chargaff's rules

One other key piece of information related to the structure of DNA came from Austrian biochemist Erwin Chargaff. Chargaff analyzed the DNA of different species, determining its composition of A, T, C, and G bases. He made several key observations:
  • A, T, C, and G were not found in equal quantities (as some models at the time would have predicted)
  • The amounts of the bases varied among species, but not between individuals of the same species
  • The amount of A always equalled the amount of T, and the amount of C always equalled the amount of G (A = T and G = C)
These findings, called Chargaff's rules, turned out to be crucial to Watson and Crick's model of the DNA double helix.

Watson, Crick, and Rosalind Franklin

In the early 1950s, American biologist James Watson and British physicist Francis Crick came up with their famous model of the DNA double helix. They were the first to cross the finish line in this scientific "race," with others such as Linus Pauling (who discovered protein secondary structure) also trying to find the correct model.
Rather than carrying out new experiments in the lab, Watson and Crick mostly collected and analyzed existing pieces of data, putting them together in new and insightful wayssquared. Some of their most crucial clues to DNA's structure came from Rosalind Franklin, a chemist working in the lab of physicist Maurice Wilkins.
Franklin was an expert in a powerful technique for determining the structure of molecules, known as X-ray crystallography. When the crystallized form of a molecule such as DNA is exposed to X-rays, some of the rays are deflected by the atoms in the crystal, forming a diffraction pattern that gives clues about the molecule's structure.
X-ray diffraction image of DNA. The diffraction pattern has an X shape representative of the two-stranded, helical structure of DNA.
Image modified from "DNA structure and sequencing: Figure 2," by OpenStax College, Biology (CC BY 3.0)
Franklin’s crystallography gave Watson and Crick important clues to the structure of DNA. Some of these came from the famous “image 51,” a remarkably clear and striking X-ray diffraction image of DNA produced by Franklin and her graduate student. (A modern example of the diffraction pattern produced by DNA is shown above.) To Watson, the X-shaped diffraction pattern of Franklin's image immediately suggested a helical, two-stranded structure for DNAcubed.
Watson and Crick brought together data from a number of researchers (including Franklin, Wilkins, Chargaff, and others) to assemble their celebrated model of the 3D structure of DNA. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.

Watson and Crick's model of DNA

The structure of DNA, as represented in Watson and Crick's model, is a double-stranded, antiparallel, right-handed helix. The sugar-phosphate backbones of the DNA strands make up the outside of the helix, while the nitrogenous bases are found on the inside and form hydrogen-bonded pairs that hold the DNA strands together.
In the model below, the orange and red atoms mark the phosphates of the sugar-phosphate backbones, while the blue atoms on the interior of the helix belong to the nitrogenous bases.
Animation of DNA double helix 3D molecular structure.
Image credit: "Bdna cropped," by Jahobr, public domain.

Antiparallel orientation

Double-stranded DNA is an antiparallel molecule, meaning that it's composed of two strands that run alongside each other but point in opposite directions. In a double-stranded DNA molecule, the 5' end (phosphate-bearing end) of one strand aligns with the 3' end (hydroxyl-bearing end) of its partner, and vice versa.
Left panel: illustration of the antiparallel structure of DNA. A short segment of DNA double helix is shown, composed of two DNA strands held together by hydrogen bonds between the bases. The strand on the left has a phosphate group exposed at its top (5' end) and a hydroxyl group exposed at its bottom (3' end). The strand on the right has the opposite orientation, with a phosphate group exposed at its bottom (5' end) and a hydroxyl exposed at its top (3' end). The 5' end of one strand thus ends up next to the 3' end of the other, and vice versa.
Right panel: structure of a nucleotide, illustrating the 5' phosphate group and 3' hydroxyl group. These groups get their names from their positions on the deoxyribose sugar's ring. The ring carbons of the sugar are labeled from 1' (the carbon bearing the nitrogenous base) to 5' (the carbon bearing the phosphate group). The 3' carbon in the middle bears the hydroxyl group.
_Image modified from "DNA chemical structure," by Madeleine Price Ball (CC0/public domain)._

Right-handed helix

In Watson and Crick's model, the two strands of DNA twist around each other to form a right-handed helix. All helices have a handedness, which is a property that describes how their grooves are oriented in space.
Image of a DNA double helix, illustrating its right-handed structure. The major groove is a wider gap that spirals up the length of the molecule, while the minor groove is a smaller gap that runs in parallel to the major groove. The base pairs are found in the center of the helix, while the sugar-phosphate backbones run along the outside.
_Image modified from "DNA structure and sequencing: Figure 3," by OpenStax College, Biology (CC BY 3.0)._
The twisting of the DNA double helix and the geometry of the bases creates a wider gap (called the major groove) and a narrower gap (called the minor groove) that run along the length of the molecule, as shown in the figure above. These grooves are important binding sites for proteins that maintain DNA and regulate gene activity.

Base pairing

In Watson and Crick's model, the two strands of the DNA double helix are held together by hydrogen bonds between nitrogenous bases on opposite strands. Each pair of bases lies flat, forming a "rung" on the ladder of the DNA molecule.
Base pairs aren't made up of just any combination of bases. Instead, if there is an A found on one strand, it must be paired with a T on the other (and vice versa). Similarly, an G found on one strand must always have a C for a partner on the opposite strand. These A-T and G-C associations are known as complementary base pairs.
Diagram illustrating base pairing between A-T and G-C bases. A and T are found opposite to each other on the two strands of the helix, and their functional groups form two hydrogen bonds that hold the strands together. Similarly, G and C are found opposite to each other on the two strands, and their functional groups form three hydrogen bonds that hold the strands together.
_Image modified from "DNA structure and sequencing: Figure 3," by OpenStax College, Biology (CC BY 3.0)._
Base pairing explains Chargaff's rules, that is, why the composition of A always equals that of T, and the composition of C equals that of Gstart superscript, 11, end superscript. Where there is an A in one strand, there must be a T in the other, and the same is true for G and C. Because a large purine (A or G) is always paired with a small pyrimidine (T or C), the diameter of the helix is uniform, coming in at about 2 nanometers.
Although Watson and Crick's original model proposed that there were two hydrogen bonds between the bases of each pair, we know today that G and C form an additional bond (such that A-T pairs form two hydrogen bonds total, while G-C pairs form three)start superscript, 12, end superscript.

The impact of the double helix

The structure of DNA unlocked the door to understanding many aspects of DNA's function, such as how it was copied and how the information it carried was used by the cell to make proteins.
As we'll see in upcoming articles and videos, Watson and Crick's model ushered in a new era of discovery in molecular biology. The model and the discoveries that it enabled form the foundations for much of today's cutting-edge research in biology and biomedicine.

Explore outside of Khan Academy

Do you want to learn more about the DNA ladder? Check out this scrollable interactive from LabXchange.
LabXchange is a free online science education platform created at Harvard’s Faculty of Arts and Sciences and supported by the Amgen Foundation.

Want to join the conversation?

  • piceratops seed style avatar for user jakduir1
    What is a codon and how does it relate to a DNA function and structure ?
    (15 votes)
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    • duskpin ultimate style avatar for user Natassja Ellen Brien
      A codon is the name for a group of three subsequent nucleotides in RNA. Since RNA is transcribed from DNA, the DNA sequence will determine the sequence of RNA, the codons, and ultimately what amino acids come together to form a protein. If a DNA sequence (template strand) goes CTTAGG, the corresponding RNA will read GAAUCC. In this sequence there are two codons: GAA followed by UCC, which will code for amino acids.
      (48 votes)
  • blobby green style avatar for user samarth6899
    well I have 2 doubts:
    1) in the second para under the topic 'right hand helix' i couldn't understand as to why DNA is a right handed helix
    2) in the second para under the topic 'base pairing' how exactly is the bigger size of purines and small size of pyramidines affecting the bond length?
    (7 votes)
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    • aqualine ultimate style avatar for user Sanjana
      As far as the 2nd question is concerned , it is because the double helix should have a uniform diameter all throughout otherwise there might be problems during the supercoiling . Now if , purine is bonded to purine , both being bigger , would end up in a diameter that would be larger than that formed by the 2 pyrimidines and thus the diameter would be uneven . The fact that A will pair T and G with C was found experimentally .
      (7 votes)
  • blobby green style avatar for user Manar Al-Masri
    I want to make sure I have these ideas true!
    It may have nothing to do with the article but I found it relevant.
    Starting from zero:
    We all have 2 copies of chromosomes; one from the mother and the second from the father.
    Each chromosome is formed of DNA and proteins ( basically histamin) .
    DNA is a double helix; 2 strands, each one has coding areas ( which are 2% and maybe less) and non-coding areas . Within the gene itself there are non-coding sequences which their name is “ introns “.
    The non-coding area (outside the gene) of DNA strand has different types of sequences ; satellites and repeated sequencing .
    Is that true for now?
    (5 votes)
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    • female robot grace style avatar for user tyersome
      Seems mostly correct.

      The one mistake I notice is that I think the word you were looking for was histones (not histamin).
      Chromatin is composed of DNA plus associated proteins and RNAs. These other molecules organize, fold, protect, and control the DNA.
      A major component of chromatin are nucleosomes — a twist of DNA wrapped around an octamer of histones.

      Note that the non-coding DNA between genes is very diverse and much of it is composed of many different families of repeated sequences including multiple types of transposons and inserted retroviral genomes.
      (9 votes)
  • blobby green style avatar for user choui003
    Am I understanding this correctly? The amount of the total bases in a cell's DNA is always the same in each organism in a species, but the amount of each type of base (A,T,G, and C) in a cell's DNA can vary between organisms in the same species.

    And is the double-helix form of DNA its condensed or decondensed form?

    (6 votes)
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    • winston baby style avatar for user Ivana - Science trainee
      Not exactly.

      The amount of each type of base in a cell's DNA is the same in all cells in the whole organism. Genetic code is the same, but gene expression is different.

      What is different is proprotion of AG to CT for each species and defined as a different number (CHargaff's rule).

      The condensed form is chromosomes. The double helix is always double helix, regardless of being part of Euchromatin or Heterochromatin.

      So, in metaphase, you can only see the condensed form of chromosomes. But you can isolate DNA (extract) by various methods and see t by the naked eye as well.

      Hope this helps :D
      (5 votes)
  • duskpin seed style avatar for user Katherine Butseev
    Why is adenine a purine base?
    (4 votes)
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    • piceratops ultimate style avatar for user RowanH
      I'm not sure it is the NH2 group which accepts protons most readily to make it a base. I think it could be the nitrogens in the rings, which I think also have lone pairs of electrons that could accept a H+. I think on the other hand the NH2 nitrogens the lone pair electrons are delocaslised so wouldn't make it very basic.
      (3 votes)
  • blobby green style avatar for user SorensenAbigail
    How can you tell the helix is right handed?
    (4 votes)
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  • blobby green style avatar for user Brittany Jean Czarnecki
    What do the data show about the make-up from different species? Before concluding that the pattern seen in the data is universal, which other types of organisms should tested? Why?
    (4 votes)
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  • blobby green style avatar for user vilceusjimmy
    What are the four different kinds of nitrogen bases?
    (2 votes)
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  • blobby green style avatar for user Ema Gaidan
    What is the order of the nitrogenous bases of the DNA if I have to put up a 3d model?
    (2 votes)
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    • female robot grace style avatar for user tyersome
      There isn't a single order — all combinations along a strand are possible. The only thing that is fixed in DNA is that A pairs with T, and G pairs with C.

      The sequence of bases is a very complex code that we are still working to understand. You can think of DNA as being the instructions for building, operating, and maintaining a cell. The order of the letters is used to encode how, when, and where proteins and RNAs are made. This affects every process within that cell and often in neighboring cells as well.

      So, for a structural model of DNA the order doesn't actually matter, but if you could pick the sequence associated with something well known like the restriction enzyme EcoRI ...

      Does that help?
      (3 votes)
  • female robot grace style avatar for user Aakanksha yadav
    Can you elucidate the role of major and minor grooves in DNA?
    (2 votes)
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