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Parallel DNA double-helices with Watson-Crick base-pairing: Why do they not occur?

Parallel DNA double-helices with Watson-Crick base-pairing: Why do they not occur?



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I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can't they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.

The only specific suggestions that I could find was because of the DNA replication process and the negative polarity of hydoxyl group on the phosphates. Moreover, after flipping one strand, the DNA nucleotides form enantiomers. Are these possible reasons, or are there others?


“The only specific suggestions that I could find was because of the DNA replication process and… ”

No. The explanation can have nothing to do with DNA replication. If the structure does not exist, you can't replicate it, if it does, Nature will evolve a mechanism. (The related SE question, mentioned by @Gilleain, asked whether it could still replicate if it were parallel, i.e. using the enzymes that have evolved for parallel DNA.)

I know that parallel DNA helices exist…

Let us clarify this first. Perhaps the most extensive parallel duplex DNA, the structure of which has been determined, is that described by Parvathy et al.. The two parallel strands of this are shown below:

The following points should be noted:

  1. This parallel DNA (and the shorter examples that preceded it) is not a pure stretch of complementary base pairs.
  2. It is stabilized by what the authors refer to as “CC+ clamps” at either end. One is left to conclude that without these the duplex would not form.
  3. All the complementary base-pairs are of the type AT (actually reverse Watson-Crick base pairs). Presumably GC base-pairs would have destablized the structure.

(You can inspect this structure in three-dimensions here. Choose 'Licorice' style and colour 'by chain' and notice the non-planarity of the three base 'pairs' at each end.)

So although the question refers specifically to parallel DNA helices with Watson-Crick base pairs, it should be recognized that extended parallel DNA helices composed of any kind of complementary AT and GC base pairs are not found, and the question applies equally well to them.

“In the diagram if we were to flip one of the strands while keeping the other same, hydrogen bonding is still possible”

The diagram in the question is two-dimensional; DNA is three-dimensional. It is only by considering the three-dimensional structure of DNA can you approach this question.

So how would one do that? One must consider the free energy of alternative structures in the relevant millieu to determine which will occur (i.e. be more thermodynamically stable).

  1. This will tell you whether single DNA strands with parallel sequences will form a double-stranded (ds) structure or not.

  2. This will tell you whether ds-parallel DNA is more or less energetically stable than a ds-antiparallel DNA. Hence, even if both can form (which I doubt, without some special circumstances*) the lower thermodynamic free energy of the anti-parallel dsDNA would give organisms adopting it an evolutionary advantage.

And the answer to the question?

It seems unlikely that one single factor is responsible or it would have been pointed out in elementary text books such as Berg et al..

To answer would require a complete theoretical analysis of the structure or structures. First one would have to build a model of a proposed parallel structure that could accommodate Watson-Crick base pairs. This in itself is a problem because there are likely to be many alternative structures. Perhaps there are computer programs that can find the structure with the lowest energy. This would be calculated in the classic manner, calculating the positive contribution of hydrogen bonding (which depends on distance and angle), ionic interaction etc.* against the negative contribution of charge and steric repulsions.

*Etc? The two-dimensional diagram fails to consider the contribution of base stacking (how could it?), which contributes to a considerable extent to the stability of nucleic acid helices, as the original cover design of Stryer's Biochemistry is a constant reminder:


You can't see DNA unless you look properly

I'm not an angry man but a new analysis of the structure of DNA using electron microscopy made me cross yesterday. It wasn't the fault of the scientists involved, but the sloppy way the result was reported that got my scientific goat.

The structure of DNA was first determined almost 60 years ago by Watson's and Crick's famous analysis of the scattering patterns recorded by Maurice Wilkins and Rosalind Franklin as they fired beams of X-rays at narrow fibres of the stuff. We have had a long time to refine and digest this result so I was surprised to run across so much inaccurate information in the internet digests of the new finding, reported in the journal Nano Letters by an Italian group led by Enzo di Fabrizio.

The web-site io9.com headlined George Dvorsky's piece "Scientists snap a picture of DNA's double helix for the very first time." No, they hadn't. The accompanying article interspersed fact with fancy before finally concluding that the new imaging technique would enable us to see "how it interacts with proteins and RNA". No, it won't.

I'll explain why in a minute but first let's look at New Scientist's coverage of the same paper. This was a more measured and more accurate account of the new result but the piece got off to a bad start. Roland Pease's article claimed that "an electron microscope has captured the famous Watson-Crick double helix in all its glory." But it clearly hadn't. The accompanying image was fuzzy and did not show a double helix that resembled the one described by Watson and Crick.

Model and electron micrograph of a DNA fibre (published in Nano Letters)

Pease followed this up with the same ill-founded claim that the new method would allow researchers to see how other biomolecules interact with DNA. I'm not sure where this claim has come from because it's not in the paper. A faulty press release perhaps?

Finally Alex Wild blogged about the article at Scientific American. His post, riskily titled "What DNA actually looks like" claimed that the paper reports "the first ever microscope image of an isolated DNA molecule". If he had take the nanotrouble to type "electron micrograph DNA" into a Google search, he would have seen there are plenty of earlier microscope images of DNA. If he had looked more carefully at the abstract of the paper — helpfully illustrated in this instance (see above) — he would have seen that the sample was in fact a bundle of DNA molecules, not an isolated one. Sheesh.

Why make a fuss about this? OK, in part because I use X-ray crystallography rather than electron microscopy to look at the structures of interesting biological molecules in my research and the exaggerated claims made on behalf of electron microscopy by the science writers were fist-clenchingly annoying. We scientists are a territorial lot, you know.

I shouldn't get so worked up because the problem is largely due to the seductive power of the image, something I've puzzled over before. All three writers focused on the fact that the new paper reported a picture that you can see in contrast, although the X-ray method yields a much higher level of detail, its results are produced indirectly through mathematical analysis of the way that molecules scatter an X-ray beam. Dvorsky, Pease and Wild may not have fully grasped that the indirectness of X-ray crystallography in no way diminishes the quality of the information obtained — admittedly not something I would expect a non-specialist to know — but the allure of the image nevertheless seems to have dulled their vision. What frustrated me is that, in spite of having an image served up to them, they didn't look at it properly, and that allowed errors to creep in.

What is actually new in the paper is that the authors have been able to take a high-contrast image of a DNA fibre (made up of a bundle of DNA double-helices) using electron microscopy. They did this by drying out a drop of DNA dissolved in water over a layer of silicon that had been micro-fabricated to have an array of tiny pillars across its surface. As the water evaporated, strands of DNA were left stretched between the pillars. Because they are suspended above the silicon base, it was possible to get a good image of the DNA fibres (you get poorer contrast if the DNA is lying on a solid surface). In a nice touch, the authors note that their sample preparation is similar to the method used by Wilkins, but they got fibres that were about a thousand times finer than he was able to achieve.

And what do they see? There is certainly some fine structure in the image. There are repetitive features of the size expected for the helical structure in DNA. But it was clear to the Italian researchers and should have been clear to anyone looking at the picture in their online abstract, that the image is not of a single molecule of DNA but a bundle of them. Di Fabrizio and colleagues modelled the structure as a bunch of seven parallel DNA double-helices since that generated a structure with the same thickness as the imaged fibre.

However, is their model correct? If you look at the inset detail in the figure, you see that the indentations on the underside are much deeper than those on the DNA model (middle panel). Perhaps this is an artefact of the way that electron microscopes make images. I don't know because I am not an expert and the authors don't comment on the discrepancy.

The bundled nature of the DNA samples prepared for these experiments also helps to explain why the microscopy technique will be unsuitable for analysing the interactions of protein molecules with DNA, contrary to the claims of Dvorsky and Pease. DNA bundles do not occur naturally in living cells when DNA is being manipulated by proteins — to be copied or used to produce instructions for cellular processes — the double-helix has to be prised apart into separate strands so that the genetic code can be read. We are not likely to be able to investigate these processes using samples composed of tightly packed bundles of DNA double-helices.

Even if a single DNA strand could be isolated and imaged by electron microscopy, the fact that the method relies on largely drying out the sample makes it unsuitable for analysing any proteins bound, since these molecules depend critically on being immersed in water to work properly.

What all this tells you is that Nature is a bitch who likes to make life hard for scientists. Fair play to the Italians who have refined the techniques for preparing DNA fibres to a new level, but it remains to be seen whether their technique will reveal any interesting new biology. I wouldn't bet on it just yet. Scientists have more work to do, and so too, do science writers.

Update 7-12-2012 09:30 - Readers may be interested to know that in response to this article, George Dvorsky at io9.com and Alex Wild at Scientific American Blogs have both updated their articles with clarifications and corrections, while Roland Pease kindly wrote to me to explain his take on the article (see comment below).


3. Guanine Quadruplexes

4.1. The A-Form of RNA and DNA

19° against the helix axis, anti -conformation for all glycosyl torsion angles and C3’- endo sugar pucker of all nucleosides. The combination of these parameters gives the helix a stout appearance with a diameter of

23 Å, deep and narrow major groove and a shallow minor groove. Due to the deep major groove, the base pairs are pushed away from the helix, and the helix appears hollow when looking down its axis. A-RNA helices with 12 base pairs per turn (121 symmetry) have also been modeled based on fiber diffraction data [42].

4.2. The B-Form of DNA

20 Å and equally deep grooves, where the major groove is wider than the minor groove. The helix axis passes straight through the base pairs, allowing the helical periodicity to be read out by counting the spokes (the glycosyl bonds) connecting the base pairs to the sugar-phosphate backbone.

4.3. B-Like Forms of DNA

4.4. The Z-Form of DNA

–9° against the helix axis. A distinctive feature of Z-DNA is the syn -conformation of all purine nucleosides and the usual anti -conformation of pyrimidines. Purines have C3’- endo sugar pucker, while pyrimidines have C2’- endo pucker in Z-DNA. The combination of the dinucleotide stack repeat with the syn-anti alternation along each strand accounts for the wrinkled appearance of the sugar-phosphate backbone in Z-DNA that differs markedly from the smooth trajectory seen in A- and B-helices. The special backbone conformation is required to allow the formation of an antiparallel double helix, although the WC-paired nucleosides have syn and anti glycosyl bonds on their purines and pyrimidines, respectively. The Z-DNA helix appears unusually slender with a diameter of

18 Å, a shallow major groove and a deep minor groove. Because of the deep minor groove, the base pairs are displaced from the helix axis, and the helix reveals a small central opening when viewed along its axis.


A Structural Comparision

Now lets review the kinds of structure adopted by the 3 major macromolecules, DNA, RNA and proteins. DNA predominately adopts the classic ds-BDNA structure, although this structure is wound around nucleosomes and "supercoiled" in cells since it must be packed into the nucleus. This extended helical form arise in part from the significant electrostatic repulsions of two strands of this polyanions (even in the presence of counterions). Given its high charge density, it is not surprising that it is complexed with positive proteins and does not adopt complex tertiary structures. RNA, on the other hand, can not form long B-type double-stranded helices (due to steric constraints of the 2'OH and the resulting 3'endo ribose pucker). Rather it can adopt complex tertiary conformations (albeit with significant counterion binding to stabilize the structure) and in doing so can form regions of secondary structure (ds-A RNA) in the form of stem/hairpin forms. Proteins, with their combination of polar charged, polar uncharged, and nonpolar side chains have little electrostatic hindrance in the adoption of secondary and tertiary structures. That RNA and proteins can both adopt tertiary structures with potential binding and catalytic sites makes them ideal catalysts for chemical reactions. RNA, given its 4 nucleotide motif can clearly also carry genetic information, making it an ideal candidate for the first evolved macromolecules enabling the development of life. Proteins with a great abundance of organic functionalities would eventually supplant RNA as a better choice for life's catalyst. DNA, with its greater stability, would supplant RNA as the choice for the main carrier of genetic information.


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Rohs, R. et al. Nature 461, 1248–1253 (2009).

Watson, J. D. & Crick, F. H. C. Nature 171, 737–738 (1953).

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Chemical structure of DNA discovered

On February 28, 1953, Cambridge University scientists James D. Watson and Francis H.C. Crick announce that they have determined the double-helix structure of DNA, the molecule containing human genes. The molecular biologists were aided significantly by the work of another DNA researcher, Rosalind Franklin, although she is not included in the announcement, nor did she share the subsequent Nobel Prize award for it.

Though DNA—short for deoxyribonucleic acid—was discovered in 1869, its crucial role in determining genetic inheritance wasn’t demonstrated until 1943. In the early 1950s, Watson and Crick were only two of many scientists working on figuring out the structure of DNA. California chemist Linus Pauling suggested an incorrect model at the beginning of 1953, prompting Watson and Crick to try and beat Pauling at his own game. 

On the morning of February 28, they determined that the structure of DNA was a double-helix polymer, or a spiral of two DNA strands, each containing a long chain of monomer nucleotides, wound around each other. According to their findings, DNA replicated itself by separating into individual strands, each of which became the template for a new double helix. In his best-selling book, The Double Helix (1968), Watson later claimed that Crick announced the discovery by walking into the nearby Eagle Pub and blurting out that “we had found the secret of life.” The truth wasn’t that far off, as Watson and Crick had solved a fundamental mystery of science–how it was possible for genetic instructions to be held inside organisms and passed from generation to generation.

Watson and Crick’s solution was formally announced on April 25, 1953, following its publication in that month’s issue of Nature magazine. The article revolutionized the study of biology and medicine. Among the developments that followed directly from it were pre-natal screening for disease genes genetically engineered foods the ability to identify human remains the rational design of treatments for diseases such as AIDS and the accurate testing of physical evidence in order to convict or exonerate criminals.

Crick and Watson later had a falling-out over Watson’s book, which Crick felt misrepresented their collaboration and betrayed their friendship. 

A larger controversy arose over the use Watson and Crick made of work done by another DNA researcher, Rosalind Franklin. Colleague Maurice Wilkins showed Watson and Crick Franklin&aposs X-ray photographic work to Watson just before he and Crick made their famous discovery. The imagery਎stablished that the DNA molecule existed in a helical conformation. When Crick and Watson won the Nobel Prize in 1962, they shared it with Wilkins. Franklin, who died in 1958 of ovarian cancer and was thus ineligible for the award, never learned of the role her photos played in the historic scientific breakthrough.


Parallel DNA double-helices with Watson-Crick base-pairing: Why do they not occur? - Biology

reprinted with permission from Nature magazine

A Structure for Deoxyribose Nucleic Acid
J. D. Watson and F. H. C. Crick (1)

April 25, 1953 (2), Nature (3) , 171, 737-738

We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.

A structure for nucleic acid has already been proposed by Pauling (4) and Corey 1 . They kindly made their manuscript available to us in advance of publication. Their model consists of three intertwined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory for two reasons:

(1) We believe that the material which gives the X-ray diagrams is the salt, not the free acid. Without the acidic hydrogen atoms it is not clear what forces would hold the structure together, especially as the negatively charged phosphates near the axis will repel each other.

(2) Some of the van der Waals distances appear to be too small.

Another three-chain structure has also been suggested by Fraser (in the press). In his model the phosphates are on the outside and the bases on the inside, linked together by hydrogen bonds. This structure as described is rather ill-defined, and for this reason we shall not comment on it.

We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid (5) . This structure has two helical chains each coiled round the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining beta-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions (6) . Each chain loosely resembles Furberg's 2 model No. 1 (7) that is, the bases are on the inside of the helix and the phosphates on the outside. The configuration of the sugar and the atoms near it is close to Furberg's "standard configuration," the sugar being roughly perpendicular to the attached base. There is a residue on each every 3.4 A. in the z-direction. We have assumed an angle of 36° between adjacent residues in the same chain, so that the structure repeats after 10 residues on each chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10 A. As the phosphates are on the outside, cations have easy access to them.

Figure 1
This figure is purely diagrammatic (8) . The two ribbons symbolize the two phophate-sugar chains, and the horizonal rods the pairs of bases holding the chains together. The vertical line marks the fibre axis.

The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more compact.

The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases. The planes of the bases are perpendicular to the fibre axis. They are joined together in pairs, a single base from one chain being hydroden-bonded to a single base from the other chain, so that the two lie side by side with identical z-coordinates. One of the pair must be a purine and the other a pyrimidine for bonding to occur. The hydrogen bonds are made as follows: purine position 1 to pyrimidine position 1 purine position 6 to pyrimidine position 6.

If it is assumed that the bases only occur in the structure in the most plausible tautomeric forms (that is, with the keto rather than the enol configurations) it is found that only specific pairs of bases can bond together. These pairs are: adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine) (9) .

In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine similarly for guanine and cytosine. The sequence of bases on a single chain does not appear to be restricted in any way. However, if only specific pairs of bases can be formed, it follows that if the sequence of bases on one chain is given, then the sequence on the other chain is automatically determined.

It has been found experimentally 3,4 that the ratio of the amounts of adenine to thymine, and the ratio of guanine to cytosine, are always very close to unity for deoxyribose nucleic acid.

It is probably impossible to build this structure with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would make too close a van der Waals contact.

The previously published X-ray data 5,6 on deoxyribose nucleic acid are insufficient for a rigorous test of our structure. So far as we can tell, it is roughly compatible with the experimental data, but it must be regarded as unproved until it has been checked against more exact results. Some of these are given in the following communications (10) . We were not aware of the details of the results presented there when we devised our structure (11) , which rests mainly though not entirely on published experimental data and stereochemical arguments.

It has not escaped our notice (12) that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

Full details of the structure, including the conditions assumed in building it, together with a set of coordinates for the atoms, will be published elsewhere (13) .

We are much indebted to Dr. Jerry Donohue for constant advice and criticism, especially on interatomic distances. We have also been stimulated by a knowledge of the general nature of the unpublished experimental results and ideas of Dr. M. H. F. Wilkins, Dr. R. E. Franklin and their co-workers at King’s College, London. One of us (J. D. W.) has been aided by a fellowship from the National Foundation for Infantile Paralysis.


1 Pauling, L., and Corey, R. B., Nature, 171, 346 (1953) Proc. U.S. Nat. Acad. Sci., 39, 84 (1953).
2 Furberg, S., Acta Chem. Scand., 6, 634 (1952).
3 Chargaff, E., for references see Zamenhof, S., Brawerman, G., and Chargaff, E., Biochim. et Biophys. Acta, 9, 402 (1952).
4 Wyatt, G. R., J. Gen. Physiol., 36, 201 (1952).
5 Astbury, W. T., Symp. Soc. Exp. Biol. 1, Nucleic Acid, 66 (Camb. Univ. Press, 1947).
6 Wilkins, M. H. F., and Randall, J. T., Biochim. et Biophys. Acta, 10, 192 (1953).

Annotations
(1)
It’s no surprise that James D. Watson and Francis H. C. Crick spoke of finding the structure of DNA within minutes of their first meeting at the Cavendish Laboratory in Cambridge, England, in 1951. Watson, a 23-year-old geneticist, and Crick, a 35-year-old former physicist studying protein structure for his doctorate in biophysics, both saw DNA’s architecture as the biggest question in biology. Knowing the structure of this molecule would be the key to understanding how genetic information is copied. In turn, this would lead to finding cures for human diseases.

Aware of these profound implications, Watson and Crick were obsessed with the problem—and, perhaps more than any other scientists, they were determined to find the answer first. Their competitive spirit drove them to work quickly, and it undoubtedly helped them succeed in their quest.

Watson and Crick’s rapport led them to speedy insights as well. They incessantly discussed the problem, bouncing ideas off one another. This was especially helpful because each one was inspired by different evidence. When the visually sensitive Watson, for example, saw a cross-shaped pattern of spots in an X-ray photograph of DNA, he knew DNA had to be a double helix. From data on the symmetry of DNA crystals, Crick, an expert in crystal structure, saw that DNA’s two chains run in opposite directions.

Since the groundbreaking double helix discovery in 1953, Watson has used the same fast, competitive approach to propel a revolution in molecular biology. As a professor at Harvard in the 1950s and 1960s, and as past director and current president of Cold Spring Harbor Laboratory, he tirelessly built intellectual arenas—groups of scientists and laboratories—to apply the knowledge gained from the double helix discovery to protein synthesis, the genetic code, and other fields of biological research. By relentlessly pushing these fields forward, he also advanced the view among biologists that solving major health problems requires research at the most fundamental level of life.

(2) On this date, Nature published the paper you are reading.

According to science historian Victor McElheny of the Massachusetts Institute of Technology, this date was a turning point in a longstanding struggle between two camps of biology, vitalism and reductionism. While vitalists studied whole organisms and viewed genetics as too complex to understand fully, reductionists saw deciphering fundamental life processes as entirely possible—and critical to curing human diseases. The discovery of DNA’s double-helix structure was a major blow to the vitalist approach and gave momentum to the reductionist field of molecular biology.

Historians wonder how the timing of the DNA race affected its outcome. Science, after years of being diverted to the war effort, was able to focus more on problems such as those affecting human health. Yet, in the United States, it was threatened by a curb on the free exchange of ideas. Some think that American researcher Linus Pauling would have beaten Watson and Crick to the punch if Pauling’s ability to travel had not been hampered in 1952 by the overzealous House Un-American Activities Committee.

(3) Nature (founded in 1869)——and hundreds of other scientific journals—help push science forward by providing a venue for researchers to publish and debate findings. Today, journals also validate the quality of this research through a rigorous evaluation called peer review. Generally at least two scientists, selected by the journal’s editors, judge the quality and originality of each paper, recommending whether or not it should be published.

Science publishing was a different game when Watson and Crick submitted this paper to Nature. With no formal review process at most journals, editors usually reached their own decisions on submissions, seeking advice informally only when they were unfamiliar with a subject.

(4) The effort to discover the structure of DNA was a race among several players. They were world-renowned chemist Linus Pauling at the California Institute of Technology, and X-ray crystallographers Maurice Wilkins and Rosalind Franklin at King’s College London, in addition to Watson and Crick at the Cavendish Laboratory, Cambridge University.

The competitive juices were flowing well before the DNA sprint was in full gear. In 1951, Pauling narrowly beat scientists at the Cavendish Lab, a top center for probing protein structure, to the discovery that certain proteins are helical. The defeat stung. When Pauling sent a paper to be published in early 1953 that proposed a three-stranded DNA structure, the head of the Cavendish gave Watson and Crick permission to work full-time on DNA’s structure. Cavendish was not about to lose twice to Pauling.

Pauling's proposed structure of DNA was a three-stranded helix with the bases facing out. While the model was wrong, Watson and Crick were sure Pauling would soon learn his error, and they estimated that he was six weeks away from the right answer. Electrified by the urgency—and by the prospect of beating a science superstar—Watson and Crick discovered the double helix after a four-week frenzy of model building.

Pauling was foiled in his attempts to see X-ray photos of DNA from King's College—crucial evidence that inspired Watson's vision of the double helix—and had to settle for inferior older photographs. In 1952, Wilkins and the head of the King's laboratory had denied Pauling's request to view their photos. Pauling was planning to attend a science meeting in London, where he most likely would have renewed his request in person, but the United States House Un-American Activities Committee halted Pauling’s trip, citing his antiwar activism. It was fitting, then, that Pauling, who won the Nobel Prize in Chemistry in 1954, also won the Nobel Peace Prize in 1962, the same year Watson and Crick won their Nobel Prize for discovering the double helix.

(5) Here, the young scientists Watson and Crick call their model “radically different” to strongly set it apart from the model proposed by science powerhouse Linus Pauling. This claim was justified. While Pauling’s model was a triple helix with the bases sticking out, the Watson-Crick model was a double helix with the bases pointing in and forming pairs of adenine (A) with thymine (T), and cytosine (C) with guanine (G).

(6) This central description of the double helix model still stands today—a monumental feat considering that the vast majority of research findings are either rejected or changed over time.

According to science historian Victor McElheny of the Massachusetts Institute of Technology, the staying power of the double helix theory puts it in a class with Newton’s laws of motion. Just as Newtonian physics has survived centuries of scientific scrutiny to become the foundation for today’s space programs, the double helix model has provided the bedrock for several research fields since 1953, including the biochemistry of DNA replication, the cracking of the genetic code, genetic engineering, and the sequencing of the human genome.

(7) Norwegian scientist Sven Furberg’s DNA model—which correctly put the bases on the inside of a helix—was one of many ideas about DNA that helped Watson and Crick to infer the molecule’s structure. To some extent, they were synthesizers of these ideas. Doing little laboratory work, they gathered clues and advice from other experts to find the answer. Watson and Crick’s extraordinary scientific preparation, passion, and collaboration made them uniquely capable of this synthesis.

(8) A visual representation of Watson and Crick’s model was crucial to show how the components of DNA fit together in a double helix. In 1953, Crick’s wife, Odile, drew the diagram used to represent DNA in this paper. Scientists use many different kinds of visual representations of DNA.

(9) The last hurdle for Watson and Crick was to figure out how DNA’s four bases paired without distorting the helix. To visualize the answer, Watson built cardboard cutouts of the bases. Early one morning, as Watson moved the cutouts around on a tabletop, he found that only one combination of base molecules made a DNA structure without bulges or strains. As Crick put it in his book What Mad Pursuit, Watson solved the puzzle “not by logic but serendipity.” Watson and Crick picked up this model-building approach from eminent chemist Linus Pauling, who had successfully used it to discover that some proteins have a helical structure.

(10) Alongside the Watson-Crick paper in the April 25, 1953, issue of Nature were separately published papers by scientists Maurice Wilkins and Rosalind Franklin of King’s College, who worked independently of each other. The Wilkins and Franklin papers described the X-ray crystallography evidence that helped Watson and Crick devise their structure. The authors of the three papers, their lab chiefs, and the editors of Nature agreed that all three would be published in the same issue.

The “following communications” that our authors are referring to are the papers by Franklin and Wilkins, published on the journal pages immediately after Watson and Crick’s paper. They (and other papers) can be downloaded as PDF files (Adobe Acrobat required) from Nature’s 50 Years of DNA website (http://www.nature.com/nature/dna50/archive.html).

Here are the direct links:

Molecular Configuration in Sodium Thymonucleate
Franklin, R., and Gosling, R. G.
Nature 171, 740-741 (1953)
URL: http://www.nature.com/nature/dna50/franklingosling.pdf

Molecular Structure of Deoxypentose Nucleic Acids
Wilkins, M. H. F., Stokes, A. R., & Wilson, H. R.
Nature 171, 738-740 (1953)
URL: http://www.nature.com/nature/dna50/wilkins.pdf

(11) This sentence marks what many consider to be an inexcusable failure to give proper credit to Rosalind Franklin, a King’s College scientist. Watson and Crick are saying here that they “were not aware of” Franklin’s unpublished data, yet Watson later admits in his book The Double Helix that these data were critical in solving the problem. Watson and Crick knew these data would be published in the same April 25 issue of Nature, but they did not formally acknowledge her in their paper.

What exactly were these data, and how did Watson and Crick gain access to them? While they were busy building their models, Franklin was at work on the DNA puzzle using X-ray crystallography, which involved taking X-ray photographs of DNA samples to infer their structure. By late February 1953, her analysis of these photos brought her close to the correct DNA model.

But Franklin was frustrated with an inhospitable environment at King’s, one that pitted her against her colleagues. And in an institution that barred women from the dining room and other social venues, she was denied access to the informal discourse that is essential to any scientist’s work. Seeing no chance for a tolerable professional life at King’s, Franklin decided to take another job. As she was preparing to leave, she turned her X-ray photographs over to her colleague Maurice Wilkins (a longtime friend of Crick).

Then, in perhaps the most pivotal moment in the search for DNA’s structure, Wilkins showed Watson one of Franklin’s photographs without Franklin’s permission. As Watson recalled, “The instant I saw the picture my mouth fell open and my pulse began to race.” To Watson, the cross-shaped pattern of spots in the photo meant that DNA had to be a double helix.

Was it unethical for Wilkins to reveal the photographs? Should Watson and Crick have recognized Franklin for her contribution to this paper? Why didn’t they? Would Watson and Crick have been able to make their discovery without Franklin’s data? For decades, scientists and historians have wrestled over these issues.

To read more about Rosalind Franklin and her history with Wilkins, Watson, and Crick, see the following:

“Light on a Dark Lady” by Anne Piper, a lifelong friend of Franklin’s
URL: http://www.physics.ucla.edu/

A review of Brenda Maddox’s recent book, Rosalind Franklin: The Dark Lady of DNA in The Guardian (UK)
URL: http://books.guardian.co.uk/whitbread2002/story/0,12605,842764,00.html

(12) This phrase and the sentence it begins may be one of the biggest understatements in biology. Watson and Crick realized at the time that their work had important scientific implications beyond a “pretty structure.” In this statement, the authors are saying that the base pairing in DNA (adenine links to thymine and guanine to cytosine) provides the mechanism by which genetic information carried in the double helix can be precisely copied. Knowledge of this copying mechanism started a scientific revolution that would lead to, among other advances in molecular biology, the ability to manipulate DNA for genetic engineering and medical research, and to decode the human genome, along with those of the mouse, yeast, fruit fly, and other research organisms.

(13) This paper is short because it was intended only to announce Watson and Crick’s discovery, and because they were in a competitive situation. In January 1954, they published the “full details” of their work in a longer paper (in Proceedings of the Royal Society). This “expound later” approach was usual in science in the 1950s as it continues to be. In fact, Rosalind Franklin did the same thing, supplementing her short April 25 paper with two longer articles.

Today, scientists publish their results in a variety of formats. They also present their work at conferences. Watson reported his and Crick’s results at the prestigious annual symposium at Cold Spring Harbor Laboratory in June 1953. As part of our recognition of the fiftieth anniversary of the double helix discovery, we will join scientists at Cold Spring Harbor as they present their papers at the “Biology of DNA” conference.


Watson and crick were wrong. dna is wrong. biology is wrong. we’re all wrong!

Even if they discount all in vitro work, there is plenty of in vivo data that only supports Watson/Crick pairing. For example, literally any paired-end deep sequencing experiment using cellular DNA shows us that each sequenced strand is paired with a reverse complement, so the pairing rules must be the same in vivo. Furthermore, high-resolution immunoprecipitation experiments that look at proteins bound to chromatin show the expected

10 bp twist of Watson/Crick paired B-DNA.

Not to mention the energetics: typical Watson/Crick base pairing is the most stable form under physiological conditions. They are basically asserting that some mystery force is preventing normal base pairing inside cells.

i keep laughing at the way they described artificially synthesized oligos as “certainly having utility.” i would hope so, they’re one of the greatest molecular biology innovations of our time

They must not have heard of FISH, siRNA, CRISPR Cas9 or dozens of tech that would not work if base pairing was different in vivo. And he “concedes” that Watson-Crick may only work in vitro method like PCR but not in vivo. If this were the case, almost none of the in vivo genetic manipulation we do would work because almost all of them contains a PCR step along the way.

R1: non watson and crick (aka non-canonical) base pairs do exist. wobble base pairs and hoogsteen base pairs are the first that come to mind. these have a biological role. this person is saying that when we observe DNA through high resolution structural biology methods, the base pairing is not true to what is occurring inside cells because we are synthesizing DNA to watson and crick’s “blueprint.” thus, watson and crick base pairing isn’t happening in vivo. this is false on many levels:

watson and crick did not invent the double helix, they discovered it

oligonucleotides that are synthesized by a machine are the same as oligonucleotides that are inside your cells, which is why we can use them for biology

watson and crick base pairing is observed during protein binding to dna, regardless of whether or not the oligonucleotide is from a cell or a machine. it’s also crucial to the function of many dna binding enzymes, such as the proofreading role of some dna polymerases, which “read” the hydrogen bonding between bases and remove incorrect pairs

this person’s theory goes against decades of knowledge and thousands of experiments, and they’ve been posting it in science related subreddits for the last year. it’s like a more intellectual version of flat earth lol

I also saw this spammed to several subreddits and considered posting this here. There's a mountain of badscience in some of the papers they've linked, much of it already debunked on biology and chemistry subreddits.

But. the tertiary structure of DNA was resolved way before PCR was invented.

cries in Rosalind Franklin

Watson is wrong about a lot of things though.

Kary Mullis could barely tie his own shoes without hanging himself but I'm not gonna boycott PCR because of it.

watson and crick were wrong. dna is. - archive.org, archive.today

My understanding is that this individual believes that the 4 nucleotide bases were formed in the process of dissecting/examining DNA.

If that were true, there would be many steps within DNA synthesis that would have these "missing" nucleotides.

There are certain experiments that involved identifying sections of DNA with large amount of the same nucleotide natively, which was then centrifuged from the rest of the cell.

Essentially, there is a lot of documented research in which scientists systematically identified DNA's structure as it occurs within the cell.

Someone seems to have got the wrong end of the stick. and seems a bit triggered that I might dare consider a differing view and present work that poses difficult questions. It certainly matters whether Crick and Watson’s reading of Photo 51 is correct.

C/W rushed to publish, having settled on an arbitrary set of base-pairings - when there were many other theoretical contenders - and that these just so happened to turn out correct and canonical. Hmm…

By the way I am not disputing "Chargaff's second parity rule".

Jerry Donohue picked up on Hoogsteen in his 1960 paper Base Pairing in DNA.

He also takes issue with the “indirect evidence” supporting Watson and Crick's base pairing - which include:

“observations on rates of enzymatic synthesis of DNA in vitro with different deoxynucleoside triphosphates”

“The experiments on rates of synthesis, originally available only in abstract form have now been described more fully (Bessman et al. 1958), and it is clear that the rates observed reflect a great many different factors. In the words of the authors "it is not feasible at this time to attribute different rates of incorporation of (the different) deoxynucleoside triphosphates to conditions controlled simply by the hydrogen-bonding characteristics of the base pairs" and "the specificity of the enzyme toward a given substrate must be considered, as well as the unexplored influence of the DNA primer. "”

Plenty more below to chew on. The science is far from settled.

Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson–Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X‐ray structures of protein–DNA complexes. However, there are several examples of Hoogsteen bps in crystal structures that form Watson–Crick bps when examined under solution conditions. Furthermore, Hoogsteen bps can sometimes be difficult to resolve in DNA:protein complexes by X‐ray crystallography due to ambiguous electron density and by solution‐state NMR spectroscopy due to size limitations. Here, using infrared spectroscopy, we report the first direct solution‐state observation of a Hoogsteen (G–C+) bp in a DNA:protein complex under solution conditions with specific application to DNA‐bound TATA‐box binding protein. These results support a previous assignment of a G–C+ Hoogsteen bp in the complex, and indicate that Hoogsteen bps do indeed exist under solution conditions in DNA:protein complexes.

The detection and characterization of Hoogsteen bps can pose unique challenges to existing structural characterization techniques. There are now several studies documenting difficulties in distinguishing Hoogsteen from Watson–Crick bps by X-ray crystallography particularly for low-to-medium resolution maps. For example, a crystal structure of the Y-family DNA polymerase iota revealing Hoogsteen pairing during replication [25,26] was challenged [27] on the grounds that the weak electron density for the active site A-T bp makes it difficult to resolve a Watson–Crick from a Hoogsteen geometry. There have been other studies documenting difficulties in resolving Hoogsteen versus Watson–Crick bps in X-ray structures of DNA homeodomain [17] and DNA p73 [20] complexes. Because of these ambiguities [17], it is conceivable that Hoogsteen bps may have been mismodeled as Watson–Crick in existing X-ray structures of DNA complexes. The characterization of Hoogsteen bps by X-ray crystallography can also be complicated by potential effects arising due to crystal packing forces. For example, several AT-rich sequences form DNA duplexes composed of Hoogsteen bps by X-ray crystallography [28–32] but predominantly form canonical duplexes composed of Watson–Crick bps when examined using solution NMR. While solution NMR can be used to unambiguously characterize Hoogsteen bps, size limitations hinder application to large protein:DNA complexes. There have also been documented difficulties [4,6,33] in detecting Hoogsteen bps by NMR due to severe line broadening of resonances arising either because a fractional population of Hoogsteen (> 20%) exchanges with the Watson–Crick form on the microsecond-to-millisecond timescale or due to enhanced solvent exchange. Such broadening contributions can lead to a blind spot for NMR-based detection, even in small systems. Both NMR and X-ray also require significant amounts of nucleic acid material, and data collection and analysis can be significantly time-consuming.

At present, we have a few oligonucleotide crystal structures where Hoogsteen base pairs have been unambiguously established in the presence of quinoxaline antibiotics, but no clear probe is available to test its existence in solution. In the other case, the H-form, we have a model that fits nicely with most but not all of the experimental data, and so the H-form DNA, and the presence of Hoogsteen base pairs, remains as a hypothetical conformation.

A novel technique 2s for studying changes in DNA structure of the cell has recently become available in brief,the use of chemical probes (OsO4) in studies in vivo. However, proper controls are essential in order to determine whether or not the presence of this chemical reagent dramatically changes the structure and functions of the living cell. This technique could be of interest for analysing whether the H-form DNA could exist in the cell nucleus, and its biological role. Moreover, it could be also used to study DNA-antibiotic interactions 'in situ'.

The realization that HG base pairing may provide an energetically viable route for key biological processes has fueled great interest in understanding the relative abundance of HG base pairs in diverse sequence and positional contexts, 38 as well as the molecular mechanism underlying the WC to HG switch. 39–42 A systematic survey of the DNA crystal structures deposited in the PDB database reveals that the repertoire of HG bonds is more extensive than previously thought, and the formation of HG base pairs can induce significant DNA bending.24

The possibility of different H-bond patterns for the A‚T pair (see Figure 1) has been known since the 1960s.22Accurate theoretical calculations23 showed that in fact the Watson-Crick pairing is not the best recognition mode for the A‚T pair and that all of the four recognition patterns shown in Figure 1 are accessible, at least in the gas phase. Molecular dynamics simulations have also shown that stable helices can be built for both duplexes10a and triplexes24 using Hoogsteen A‚T pairings. Experimentally, the Hoogsteen recognition mode is found in different structures of DNA and RNA,25 including the parallel triplexes,7,26 where it stabilizes both d(A-T‚T) and d(G-C‚C) triads. Very interestingly, Hoogsteen pairs are common in complexes between duplex DNA and drugs or proteins.18,27-29

In conjunction with the biological role of d(AT)n regions,27,30 these findings strongly suggest an important role for Hoogsteen pairings in the modulation of gene expression.18,27 In summary, recent theoretical and experimental information points out that the apparently exotic Hoogsteen interaction might be common and have a large biological significance.


TRNA: the assembly point of translation

The transfer RNA or tRNA is also single-stranded, but is folded, unlike the straight mRNA. It serves as a physical link between the mRNA and the amino acids by interpreting the mRNA and transferring the right amino acids to their place while making the protein. If the translation machinery was a factory, the tRNA would be the factory workers who interpret the instruction manual (the mRNA) to carefully put products in the specified order.

The tRNA are like factory workers that assemble the amino acids to form a polypeptide chain (Photo Credit : Lenam14/Wikimedia Commons)

The tRNA is structured in such a way that it has an anticodon loop on one end and an acceptor arm/stem on the opposite end.

The primary, secondary and tertiary structure of tRNA (Photo Credit : CNX OpenStax/Wikimedia Commons)

As the name suggests, the anticodon loop is complementary and antiparallel (3&rsquo to 5&rsquo) to the mRNA codons. That is, the tRNA consists of the 3 nucleotides that bind to the ones present on the mRNA. Thus, guanine (G) and cytosine (C) bind to each other and adenine (A) and uridine (U) bind to one another.

So, considering the codon for methionine, AUG, it would have a methionine tRNA with an anti-codon UAG.

This type of pairing is known as Watson-Crick base pairing. The pairing is like the attraction between highly specific magnets. Anti-codons on the tRNA ensure that it lines up against the correct codon on the mRNA. Furthermore, as codons are read in the 5&rsquo to 3&rsquo direction, anticodons present on the tRNA are positioned in the 3&rsquo to 5&rsquo direction.

The codon, anticodon and tRNA for the amino acid Alanine (Photo Credit : Yikrazuul/Wikimedia Commons)

This means that the 1st codon base binds to the 3rd anticodon base and so on. Note that each amino acid has its very own tRNA, which correctly positions it in the polypeptide chain due to the base-pairing between the codon and anticodon.

The codon for glutamic acid bound to the anticodon of the tRNA, which has glutamic acid on the acceptor arm. (Photo Credit : M. PATTHAWEE/Shutterstock)

However, like many things in biology, this is also a little more complicated. Each amino acid can be specified by more than one codon. Additionally, the base-pairing rules between the codon and anticodon are not equally binding for all bases. We will learn more about this peculiar phenomenon next!


Figure 3

Figure 3. (A) Effect of 10 μM metal ions (Ca 2+ , Sn 2+ , Fe 3+ , Al 3+ , Ba 2+ , Ag + , Cd 2+ , Co 2+ , Cu 2+ , Hg 2+ , Mn 2+ , Ni 2+ , Pb 2+ , Zn 2+ , and Mg 2+ ) on the HPIN fluorescence (1 μM) at pH 6.5 and 2 μM ps-DNA1. Inset: photographs of these solutions under UV illumination. (B) Ag + concentration-dependent fluorescence response of HPIN (1 μM) at pH 6.5 and 2 μM ps-DNA1 or aps-DNA1.

It is well-known that in G-quadruplex, the Hoogsteen hydrogen bonding between guanines is the driving force to form the quartet ingredients.(6) We found that the DNA and RNA G-quadruplexes with variant topologies including hybrid, chair, and parallel conformations (Table S1) are inefficient to turn on the HPIN fluorescence (Figure S9), suggesting the high selectivity of HPIN in fluorescently recognizing the ps-DNA duplex.

In conclusion, the strand polarity analysis in DNA duplex with an ideal selectivity is achieved using our synthesized HPIN as the fluorescent probe. The ps-DNA duplex held together by the Hoogsteen hydrogen bonding can efficiently turn on the HPIN fluorescence, as opposed to the nonfluorescent behavior when binding to the aps-DNA duplex. This hydrogen bonding pattern-specific discrimination using HPIN suggests the role of structurally adaptive recognition in the polarity analysis. This is the first report on the highly selective recognization of the duplex strand polarity. Our work will inspire more interest in developing the ps-DNA duplex-based sensors. The detailed binding mode is underway in this laboratory using theoretical computation.


Watch the video: Μοντέλο διπλής έλικας Watson - Crick (August 2022).