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Twist in the DNA double-helix

Twist in the DNA double-helix


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DNA, has a deoxyribose sugar - phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base-sugar molecules are nucleosides, and those with phosphate, nucleotides.) In the double helix structure of DNA the two strands are twisted and connected by hydrogen bonds between the bases.

How is this "twist" created in the cell, and why is it necessary?


First, your description is accurate. The only pedantic critique I would make is that the technical term for nucleotides in DNA is deoxyribonucleotide.

Second, I don't want to say that non-helical DNA never occurs since the structure of any macromolecule is dynamic, but I am specifically avoiding exceptions to the rule to avoid confusing the issue.

The helical structure of DNA is a low energy form which makes its formation thermodynamically favourable. Chemical bonds in DNA (and every molecule) have conformational flexibility which means that the molecule as a whole can adopt different structures. If you picture two DNA strands joined by hydrogen bonds but in a non-helical, straight form, you can simply twist the strands about their central axis to form a helical structure. This twisting is allowed because of the conformational flexibility of the chemical bonds. The helical structure is more stable than the "straight" form (because of base stacking interactions), and so it forms spontaneously. I struggled in vain to find a good animation of this, but came up short. You can skim through this video to see an example of what I'm talking about. It's subtle, but you may be able to see, or conceptualize, that as the two strands are twisted around each other, the adjacent bases in a strand come closer together. This permits stabilizing interactions between the adjacent bases which favours spontaneous helix formation (I briefly discuss this at the end of another answer).

As for how frequently the "rungs occur", this is dependent on the specific helix geometry. In B-form DNA, the geometry thought to occur predominantly in vivo, the helix completes one full turn approximately every 10.5 bases and the spacing between adjacent bases is ~3.4 Å, as shown below:


One key point for someone coming to structural biology from another disciple is to understand the basic thermodynamics underlying the concept of 'stable' structure. This is described in an introductory chapter of Berg et al. online. Although it is strictly necessary to consider the entropy of the total system, in many cases the most important factor is the (Gibbs) Free Energy of a structure. If one compares two (or more) structures, the most thermodynamically stable is the one with the lowest free energy.

Factors contributing to a low free energy state in a structure ('stabilizing it') are presence of chemical bonds and lack of steric or electrostatic repulsion. The double-helical structure is stabilized by hydrogen bonds between the bases of opposite strands, and stacking interactions between the aromatic rings above and below one another in the helix. This is mentioned by @canadiener, although the perspective of his diagram is not optimal for showing the stacking. Frame (a) of my diagram below views the DNA helix from 'above' with the purine bases red, the pyrimidine bases blue and the sugar-phosphate backbone white.(Frame (b) shows the hydrogen bonds as broken lines between the bases, although the blue half does not show up well.)

The reason for the 'twist' that is the basis of the helix in the DNA is simply that it is part of the structure that allows the strongest hydrogen bonding and base stacking with the lowest amount of steric or electrostatic repulsion. This will be the structure with the lowest free energy.

[See also the description of the double-helix in Berg et al., which includes a diagram of base stacking. I would very much advise refering to the biochemistry and molecular biology texts online at NCBI Bookshelf for standard material rather than Wikipedia. The scholarship, refereeing and consistency of the latter are generally much higher.]


Simple twist of DNA determines fate of placenta

The development of the mammalian placenta depends upon an unusual twist that separates DNA's classic double helix into a single-stranded form, Yale researchers report July 15 in the journal Nature.

The Yale team also identified the molecular regulator that acts upon this single strand to accelerate or stop placental development, a discovery with implications not only for diseases of pregnancy but also for understanding how cancer tumors proliferate.

"Placental tissue grows very fast, stimulates blood vessel formation, and invades into neighboring tissues, like a tumor," said senior author Andrew Xiao, associate professor of genetics and a researcher with the Yale Stem Cell Center. "Unlike a tumor, however, the placenta grows through a precise, coordinated, and well-controlled manner."

At the earliest stage of fetal development two linked processes begin simultaneously. As the fertilized egg begins developing specialized cells of the new life, another set of cells begins producing blood vessels in the placenta to nourish the growing fetus.

"In many ways, pregnancy is like a prolonged state of inflammation, as the placenta constantly invades the uterine tissue," Xiao said.

The DNA of the cells that will make up the growing placenta share an unusual trait -- the double helix begins to twist. The resulting torsion causes certain sections of the genome break into a single strand. Although the primary sequences of the DNA are the same between the placenta and embryo, the different structure of the DNA between the two helps determine the fate of the cells.

The Yale team led by Xiao discovered placental growth is then regulated by the sixth base of DNA, N6-methyladenine. This base stabilizes the single-stranded regions of DNA and repels SATB1. SATB1 is protein critical for the organization of chromatin, the material that makes up chromosomes.

Placentas without N6-methyladenine grow uncontrollably while placentas with abnormally high levels of N6-methyladenine develop severe defects that eventually halt embryo development, the researchers found.

The findings could help researchers develop new therapies for conditions such as preeclampsia in pregnancy as well as certain types of cancer characterized by activity from single strands of DNA, the researchers said.

The research was primarily funded by National Institutes of Health and the Ludwig Family Foundation. A team of researchers led by Haitao Li in Tsinghua University also contributed to this study.


Contents

The double-helix model of DNA structure was first published in the journal Nature by James Watson and Francis Crick in 1953, [5] (X,Y,Z coordinates in 1954 [6] ) based on the work of Rosalind Franklin and her student Raymond Gosling, who took the crucial X-ray diffraction image of DNA labeled as "Photo 51", [7] [8] and Maurice Wilkins, Alexander Stokes, and Herbert Wilson, [9] and base-pairing chemical and biochemical information by Erwin Chargaff. [10] [11] [12] [13] [14] [15] The prior model was triple-stranded DNA. [16]

The realization that the structure of DNA is that of a double-helix elucidated the mechanism of base pairing by which genetic information is stored and copied in living organisms and is widely considered one of the most important scientific discoveries of the 20th century. Crick, Wilkins, and Watson each received one third of the 1962 Nobel Prize in Physiology or Medicine for their contributions to the discovery. [17]

Hybridization is the process of complementary base pairs binding to form a double helix. Melting is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes, or mechanical force. Melting occurs preferentially at certain points in the nucleic acid. [18] T and A rich regions are more easily melted than C and G rich regions. Some base steps (pairs) are also susceptible to DNA melting, such as T A and T G. [19] These mechanical features are reflected by the use of sequences such as TATA at the start of many genes to assist RNA polymerase in melting the DNA for transcription.

Strand separation by gentle heating, as used in polymerase chain reaction (PCR), is simple, providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. The cell avoids this problem by allowing its DNA-melting enzymes (helicases) to work concurrently with topoisomerases, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. Helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase.

The geometry of a base, or base pair step can be characterized by 6 coordinates: shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the helical structure of the molecule. In regions of DNA or RNA where the normal structure is disrupted, the change in these values can be used to describe such disruption.

For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider: [20] [21] [22]

  • Shear
  • Stretch
  • Stagger
  • Buckle
  • Propeller: rotation of one base with respect to the other in the same base pair.
  • Opening
  • Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
  • Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
  • Rise: displacement along the helix axis.
  • Tilt: rotation around the shift axis.
  • Roll: rotation around the slide axis.
  • Twist: rotation around the rise axis.
  • x-displacement
  • y-displacement
  • inclination
  • tip
  • pitch: the height per complete turn of the helix.

Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small.

Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. This corresponds to slide between a succession of base pairs, and in helix-based coordinates is properly termed "inclination".

At least three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The B form described by James Watson and Francis Crick is believed to predominate in cells. [23] It is 23.7 Å wide and extends 34 Å per 10 bp of sequence. The double helix makes one complete turn about its axis every 10.4–10.5 base pairs in solution. This frequency of twist (termed the helical pitch) depends largely on stacking forces that each base exerts on its neighbours in the chain. The absolute configuration of the bases determines the direction of the helical curve for a given conformation.

A-DNA and Z-DNA differ significantly in their geometry and dimensions to B-DNA, although still form helical structures. It was long thought that the A form only occurs in dehydrated samples of DNA in the laboratory, such as those used in crystallographic experiments, and in hybrid pairings of DNA and RNA strands, but DNA dehydration does occur in vivo, and A-DNA is now known to have biological functions. Segments of DNA that cells have methylated for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis the opposite way to A-DNA and B-DNA. There is also evidence of protein-DNA complexes forming Z-DNA structures.

Other conformations are possible A-DNA, B-DNA, C-DNA, E-DNA, [24] L-DNA (the enantiomeric form of D-DNA), [25] P-DNA, [26] S-DNA, Z-DNA, etc. have been described so far. [27] In fact, only the letters F, Q, U, V, and Y are now [update] available to describe any new DNA structure that may appear in the future. [28] [29] However, most of these forms have been created synthetically and have not been observed in naturally occurring biological systems. [ citation needed ] There are also triple-stranded DNA forms and quadruplex forms such as the G-quadruplex and the i-motif.

Structural features of the three major forms of DNA [30] [31] [32]
Geometry attribute A-DNA B-DNA Z-DNA
Helix sense right-handed right-handed left-handed
Repeating unit 1 bp 1 bp 2 bp
Rotation/bp 32.7° 34.3° 60°/2
bp/turn 11 10.5 12
Inclination of bp to axis +19° −1.2° −9°
Rise/bp along axis 2.3 Å (0.23 nm) 3.32 Å (0.332 nm) 3.8 Å (0.38 nm)
Pitch/turn of helix 28.2 Å (2.82 nm) 33.2 Å (3.32 nm) 45.6 Å (4.56 nm)
Mean propeller twist +18° +16°
Glycosyl angle anti anti C: anti,
G: syn
Sugar pucker C3'-endo C2'-endo C: C2'-endo,
G: C2'-exo
Diameter 23 Å (2.3 nm) 20 Å (2.0 nm) 18 Å (1.8 nm)

Grooves Edit

Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. [33] The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. [4] This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

Non-double helical forms Edit

Alternative non-helical models were briefly considered in the late 1970s as a potential solution to problems in DNA replication in plasmids and chromatin. However, the models were set aside in favor of the double-helical model due to subsequent experimental advances such as X-ray crystallography of DNA duplexes and later the nucleosome core particle, and the discovery of topoisomerases. Also, the non-double-helical models are not currently accepted by the mainstream scientific community. [34] [35]

DNA is a relatively rigid polymer, typically modelled as a worm-like chain. It has three significant degrees of freedom bending, twisting, and compression, each of which cause certain limits on what is possible with DNA within a cell. Twisting-torsional stiffness is important for the circularisation of DNA and the orientation of DNA bound proteins relative to each other and bending-axial stiffness is important for DNA wrapping and circularisation and protein interactions. Compression-extension is relatively unimportant in the absence of high tension.

Persistence length, axial stiffness Edit

DNA in solution does not take a rigid structure but is continually changing conformation due to thermal vibration and collisions with water molecules, which makes classical measures of rigidity impossible to apply. Hence, the bending stiffness of DNA is measured by the persistence length, defined as:

The length of DNA over which the time-averaged orientation of the polymer becomes uncorrelated by a factor of e. [ citation needed ]

This value may be directly measured using an atomic force microscope to directly image DNA molecules of various lengths. In an aqueous solution, the average persistence length is 46–50 nm or 140–150 base pairs (the diameter of DNA is 2 nm), although can vary significantly. This makes DNA a moderately stiff molecule.

The persistence length of a section of DNA is somewhat dependent on its sequence, and this can cause significant variation. The variation is largely due to base stacking energies and the residues which extend into the minor and major grooves.

Models for DNA bending Edit

Stacking stability of base steps (B DNA) [36]
Step Stacking ΔG
/kcal mol −1
T A -0.19
T G or C A -0.55
C G -0.91
A G or C T -1.06
A A or T T -1.11
A T -1.34
G A or T C -1.43
C C or G G -1.44
A C or G T -1.81
G C -2.17

At length-scales larger than the persistence length, the entropic flexibility of DNA is remarkably consistent with standard polymer physics models, such as the Kratky-Porod worm-like chain model. [37] Consistent with the worm-like chain model is the observation that bending DNA is also described by Hooke's law at very small (sub-piconewton) forces. For DNA segments less than the persistence length, the bending force is approximately constant and behaviour deviates from the worm-like chain predictions.

This effect results in unusual ease in circularising small DNA molecules and a higher probability of finding highly bent sections of DNA. [38]

Bending preference Edit

DNA molecules often have a preferred direction to bend, i.e., anisotropic bending. This is, again, due to the properties of the bases which make up the DNA sequence - a random sequence will have no preferred bend direction, i.e., isotropic bending.

Preferred DNA bend direction is determined by the stability of stacking each base on top of the next. If unstable base stacking steps are always found on one side of the DNA helix then the DNA will preferentially bend away from that direction. As bend angle increases then steric hindrances and ability to roll the residues relative to each other also play a role, especially in the minor groove. A and T residues will be preferentially be found in the minor grooves on the inside of bends. This effect is particularly seen in DNA-protein binding where tight DNA bending is induced, such as in nucleosome particles. See base step distortions above.

DNA molecules with exceptional bending preference can become intrinsically bent. This was first observed in trypanosomatid kinetoplast DNA. Typical sequences which cause this contain stretches of 4-6 T and A residues separated by G and C rich sections which keep the A and T residues in phase with the minor groove on one side of the molecule. For example:

¦ ¦ ¦ ¦ ¦ ¦
G A T T C C C A A A A A T G T C A A A A A A T A G G C A A A A A A T G C C A A A A A A T C C C A A A C

The intrinsically bent structure is induced by the 'propeller twist' of base pairs relative to each other allowing unusual bifurcated Hydrogen-bonds between base steps. At higher temperatures this structure is denatured, and so the intrinsic bend is lost.

All DNA which bends anisotropically has, on average, a longer persistence length and greater axial stiffness. This increased rigidity is required to prevent random bending which would make the molecule act isotropically.

Circularization Edit

DNA circularization depends on both the axial (bending) stiffness and torsional (rotational) stiffness of the molecule. For a DNA molecule to successfully circularize it must be long enough to easily bend into the full circle and must have the correct number of bases so the ends are in the correct rotation to allow bonding to occur. The optimum length for circularization of DNA is around 400 base pairs (136 nm) [ citation needed ] , with an integral number of turns of the DNA helix, i.e., multiples of 10.4 base pairs. Having a non integral number of turns presents a significant energy barrier for circularization, for example a 10.4 x 30 = 312 base pair molecule will circularize hundreds of times faster than 10.4 x 30.5 ≈ 317 base pair molecule. [39]

The bending of short circularized DNA segments is non-uniform. Rather, for circularized DNA segments less than the persistence length, DNA bending is localised to 1-2 kinks that form preferentially in AT-rich segments. If a nick is present, bending will be localised to the nick site. [38]

Elastic stretching regime Edit

Longer stretches of DNA are entropically elastic under tension. When DNA is in solution, it undergoes continuous structural variations due to the energy available in the thermal bath of the solvent. This is due to the thermal vibration of the molecule combined with continual collisions with water molecules. For entropic reasons, more compact relaxed states are thermally accessible than stretched out states, and so DNA molecules are almost universally found in a tangled relaxed layouts. For this reason, one molecule of DNA will stretch under a force, straightening it out. Using optical tweezers, the entropic stretching behavior of DNA has been studied and analyzed from a polymer physics perspective, and it has been found that DNA behaves largely like the Kratky-Porod worm-like chain model under physiologically accessible energy scales.

Phase transitions under stretching Edit

Under sufficient tension and positive torque, DNA is thought to undergo a phase transition with the bases splaying outwards and the phosphates moving to the middle. This proposed structure for overstretched DNA has been called P-form DNA, in honor of Linus Pauling who originally presented it as a possible structure of DNA. [26]

Evidence from mechanical stretching of DNA in the absence of imposed torque points to a transition or transitions leading to further structures which are generally referred to as S-form DNA. These structures have not yet been definitively characterised due to the difficulty of carrying out atomic-resolution imaging in solution while under applied force although many computer simulation studies have been made (for example, [40] [41] ).

Proposed S-DNA structures include those which preserve base-pair stacking and hydrogen bonding (GC-rich), while releasing extension by tilting, as well as structures in which partial melting of the base-stack takes place, while base-base association is nonetheless overall preserved (AT-rich).

Periodic fracture of the base-pair stack with a break occurring once per three bp (therefore one out of every three bp-bp steps) has been proposed as a regular structure which preserves planarity of the base-stacking and releases the appropriate amount of extension, [42] with the term "Σ-DNA" introduced as a mnemonic, with the three right-facing points of the Sigma character serving as a reminder of the three grouped base pairs. The Σ form has been shown to have a sequence preference for GNC motifs which are believed under the GNC hypothesis to be of evolutionary importance. [43]

The B form of the DNA helix twists 360° per 10.4-10.5 bp in the absence of torsional strain. But many molecular biological processes can induce torsional strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively supercoiled. DNA in vivo is typically negatively supercoiled, which facilitates the unwinding (melting) of the double-helix required for RNA transcription.

Within the cell most DNA is topologically restricted. DNA is typically found in closed loops (such as plasmids in prokaryotes) which are topologically closed, or as very long molecules whose diffusion coefficients produce effectively topologically closed domains. Linear sections of DNA are also commonly bound to proteins or physical structures (such as membranes) to form closed topological loops.

Francis Crick was one of the first to propose the importance of linking numbers when considering DNA supercoils. In a paper published in 1976, Crick outlined the problem as follows:

In considering supercoils formed by closed double-stranded molecules of DNA certain mathematical concepts, such as the linking number and the twist, are needed. The meaning of these for a closed ribbon is explained and also that of the writhing number of a closed curve. Some simple examples are given, some of which may be relevant to the structure of chromatin. [44]

Analysis of DNA topology uses three values:

  • L = linking number - the number of times one DNA strand wraps around the other. It is an integer for a closed loop and constant for a closed topological domain.
  • T = twist - total number of turns in the double stranded DNA helix. This will normally tend to approach the number of turns that a topologically open double stranded DNA helix makes free in solution: number of bases/10.5, assuming there are no intercalating agents (e.g., ethidium bromide) or other elements modifying the stiffness of the DNA.
  • W = writhe - number of turns of the double stranded DNA helix around the superhelical axis
  • L = T + W and ΔL = ΔT + ΔW

Any change of T in a closed topological domain must be balanced by a change in W, and vice versa. This results in higher order structure of DNA. A circular DNA molecule with a writhe of 0 will be circular. If the twist of this molecule is subsequently increased or decreased by supercoiling then the writhe will be appropriately altered, making the molecule undergo plectonemic or toroidal superhelical coiling.

When the ends of a piece of double stranded helical DNA are joined so that it forms a circle the strands are topologically knotted. This means the single strands cannot be separated any process that does not involve breaking a strand (such as heating). The task of un-knotting topologically linked strands of DNA falls to enzymes termed topoisomerases. These enzymes are dedicated to un-knotting circular DNA by cleaving one or both strands so that another double or single stranded segment can pass through. This un-knotting is required for the replication of circular DNA and various types of recombination in linear DNA which have similar topological constraints.

The linking number paradox Edit

For many years, the origin of residual supercoiling in eukaryotic genomes remained unclear. This topological puzzle was referred to by some as the "linking number paradox". [45] However, when experimentally determined structures of the nucleosome displayed an over-twisted left-handed wrap of DNA around the histone octamer, [46] [47] this paradox was considered to be solved by the scientific community.


4. Specific sequences of nitrogenous bases that code for particular proteins or regulatory RNA molecules are called genes.

Each strand of DNA is like a recipe book for synthesizing proteins. Certain sequences of nitrogenous bases along the strand encode particular RNA molecules. These sequences are called genes. mRNA molecules transcribed from genes are translated into proteins later.

Chromosomes can vary widely in their number of base pairs and genes. The longest chromosome in human cells, Chromosome 1, is around 249 million base pairs long and has between 2000 and 2100 distinct genes. Chromosome 21, the shortest human chromosome, consists of 48 million base pairs and contains between 200 and 300 genes. Overall, prokaryotic cells have shorter chromosomes with fewer genes. For example, the bacterium Carsonella rudii has only 159,662 base pairs and 182 genes in its entire genome.

Although genes get most of the credit for what DNA does, they make up only about 1% of DNA (in humans). Genes are separated from one another by sequences of nitrogenous bases that don’t provide instructions for RNA synthesis. These are called intergenic regions. Even within genes, there are regions of noncoding DNA called introns.

Noncoding regions of DNA are important because they provide binding sites for proteins that help activate or deactivate the process of transcription. They can also provide protection for the coding regions. For instance, telomeres consist of repetitive sequences that protect the genetic information on each DNA molecule from being damaged during cell division.


A partnership was just announced between two California firms, Codexis CDXS and Molecular Assemblies, focused on a radical new way of writing DNA. The partnership comes at a booming time for the synthetic biology industry, which seeks to use DNA to create everything from COVID-19 antibodies to new options for high-density data storage.

DNA synthesis is already a hot market. Twist Bioscience, a gene maker, has seen its stock almost triple since its IPO in late 2018. In the same year, Integrated DNA Technologies was acquired by Danaher for a rumored $1.8 billion. All of this recent success, however, is based on a decades-old method for printing DNA that insiders admit is quite limited.

Today’s DNA makers still create their products using chemistry. To form a new double helix, the individual letters of DNA — nicknamed A, T, C and G — are linked together using a process called phosphoramidite synthesis. Though the process has been refined over the years, it still requires harsh solvents that limit the quality of the final product. These solvents also become noxious waste.

A quick glance at biology proves that there is clearly a better way. Your own cells make DNA around the clock, and they do so without harsh chemicals. The DNA copies they produce are millions of times longer and considerably more accurate than what any business can currently obtain through chemical synthesis. This power to create massive amounts of high-quality DNA enables the complexity of life, and if harnessed would transform global manufacturing by opening the floodgates to synthetic biology innovations in the pharmaceutical, textile, agriculture and advanced materials sectors.

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For years, biotechnologists have yearned to make DNA the same way that biology does — with enzymes. These nano-scale machines, which are the products of genes, specialize in corralling smaller chemicals around them. One type of enzyme in particular, called a polymerase, has an unparalleled ability to stitch DNA letters into long chains.

Businesses like San Diego-based Molecular Assemblies have been adapting polymerase enzymes to create custom DNA molecules. They hold 24 patents on the matter, and say they already have the potential to produce DNA chains that are up to 50 times longer than the competition. They have even begun applying their technology to the challenge of DNA data storage.

Codexis, based in the Bay Area, specializes in improving enzymes for industrial use. As I have written about before, they apply advanced computer software to come up with improved enzymes that can aid in the creation of an astonishing array of products, including cannabinoids, bioplastics, biofuels, and even pharmaceutical drugs.

Under the new agreement, Codexis will purchase $1 million in stock from Molecular Assemblies. This is a clear win for both companies: The core business of Molecular Assemblies is based on enzymes, and in Codexis they gain a partner who specializes in enzyme engineering. Codexis benefits as well, as they get a stake in the lucrative and burgeoning field of enzymatic DNA synthesis.

Ultimately, moves like these also benefit the entire synthetic biology industry. DNA made by enzymes would be a boon to any company — big or small — who wishes to take part in the 21st-century effort to build a better, greener and more efficient economy with biology.

For an inside scoop on enzymatic DNA synthesis and what it means for the entire biotechnology . [+] industry, I talked with Molecular Assemblies CEO Michael Kamdar and Codexis CEO John Nicols about making the technology a commercial success.

For the inside scoop, watch my interview with Molecular Assemblies’ CEO Michael Kamdar and Codexis CEO John Nicols about the impact of enzymatic DNA synthesis, and what this deal means to the industry.

Follow me on Twitter at @johncumbers and @synbiobeta. Subscribe to my weekly newsletters in synthetic biology. Thank you to Ian Haydon for additional research and reporting in this article. I’m the founder of SynBioBeta, and some of the companies that I write about—including Molecular Assemblies and Codexis—are sponsors of the SynBioBeta conference and weekly digest. Here’s the full list of SynBioBeta sponsors. I am also an operating partner at DCVC, which has invested in Molecular Assemblies.


7.1: DNA Structure

  • Contributed by E. V. Wong
  • Axolotl Academica Publishing (Biology) at Axolotl Academica Publishing

As you can see in Figure1, the nucleotides only vary slightly, and only in the nitrogenous base. In the case of DNA, those bases are adenine, guanine, cytosine, and thymine. Note the similarity of the shapes of adenine and guanine, and also the similarity between cytosine and thymine. A and G are classified as purines, while C and T are classified as pyrimidines. As long as we&rsquore naming things, notice &ldquodeoxyribose&rdquo and &ldquoribose&rdquo. As the name implies, deoxyribose is just a ribose without an oxygen. More specifically, where there is a hydroxyl group attached to the 2-carbon of ribose, there is only a hydrogen attached to the 2-carbon of deoxyribose. That is the only difference between the two sugars.

In randomly constructing a single strand of nucleic acid in vitro, there are no particular rules regarding the ordering of the nucleotides with respect to their bases. The identities of their nitrogenous bases are irrelevant because the nucleotides are attached by phosphodiester bonds through the phosphate group and the pentose. It is therefore often referred to as the sugar-phosphate backbone. If we break down the word &ldquophosphodiester&rdquo, we see that it quite handily describes the connection: the sugars are connected by two ester bonds ( &mdashO&mdash) with a phosphorous in between. One of the ideas that often confuses students is the directionality of this bond, and therefore, of nucleic acids in general. For example, when we talk about DNA polymerase, the enzyme that catalyzes the addition of nucleotides in living cells, we say that it works in a 5-prime (5&rsquo) to 3-prime (3&rsquo) direction. This may seem like arcane molecular-biologist-speak, but it is actually very simple. Take another look at two of the nucleotides joined together by the phosphodiester bond (Figure (PageIndex<1>), bottom left). An adenine nucleotide is joined to a cytosine nucleotide. The phosphodiester bond will always link the 5-carbon of one deoxyribose (or ribose in RNA) to the 3-carbon of the next sugar. This also means that on one end of a chain of linked nucleotides, there will be a free 5&rsquo phosphate (-PO4) group, and on the other end, a free 3&rsquo hydroxyl (-OH). These define the directionality of a strand of DNA or RNA.

Figure (PageIndex<1>). DNA. Deoxyribonucleic acid is a polymer chain of nucleotides connected by 5&rsquo to 3&rsquo phosphodiester bonds. DNA normally exists as a two antiparallel complementary strands held together by hydrogen bonds between adenines (A) and thymines (T), and between guanines (G) and cytosines (C).

DNA is normally found as a double-stranded molecule in the cell whereas RNA is mostly single-stranded. It is important to understand though, that under the appropriate conditions, DNA could be made single-stranded, and RNA can be double-stranded. In fact, the molecules are so similar that it is even possible to create double-stranded hybrid molecules with one strand of DNA and one of RNA. Interestingly, RNA-RNA double helices and RNA-DNA double helices are actually slightly more stable than the more conventional DNA-DNA double helix.

The basis of the double-stranded nature of DNA, and in fact the basis of nucleic acids as the medium for storage and transfer of genetic information, is base-pairing. Base-pairing refers to the formation of hydrogen bonds between adenines and thymines, and between guanines and cytosines. These pairs are significantly more stable than any association formed with the other possible bases. Furthermore, when these base-pair associations form in the context of two strands of nucleic acids, their spacing is also uniform and highly stable. You may recall that hydrogen bonds are relatively weak bonds. However, in the context of DNA, the hydrogen bonding is what makes DNA extremely stable and therefore well suited as a long-term storage medium for genetic information. Since even in simple prokaryotes, DNA double helices are at least thousands of nucleotides long, this means that there are several thousand hydrogen bonds holding the two strands together. Although any individual nucleotide-to-nucleotide hydrogen bonding interaction could easily be temporarily disrupted by a slight increase in temperature, or a miniscule change in the ionic strength of the solution, a full double-helix of DNA requires very high temperatures (generally over 90 o C) to completely denature the double helix into individual strands.

Because there is an exact one-to-one pairing of nucleotides, it turns out that the two strands are essentially backup copies of each other - a safety net in the event that nucleotides are lost from one strand. In fact, even if parts of both strands are damaged, as long as the other strand is intact in the area of damage, then the essential information is still there in the complementary sequence of the opposite strand and can be written into place. Keep in mind though, that while one strand of DNA can thus act as a &ldquobackup&rdquo of the other, the two strands are not identical - they are complementary. An interesting consequence of this system of complementary and antiparallel strands is that the two strands can each carry unique information.

Bi-directional gene pairs are two genes on opposite strands of DNA, but sharing a promoter, which lies in between them. Since DNA can only be made in one direction, 5&rsquo to 3&rsquo, this bi-directional promoter, often a CpG island (see next chapter), thus sends the RNA polymerase for each gene in opposite physical directions. This has been shown for a number of genes involved in cancers (breast, ovarian), and is a mechanism for coordinating the expression of networks of gene products.

The strands of a DNA double-helix are antiparallel. This means that if we looked at a double-helix of DNA from left to right, one strand would be constructed in the 5&rsquo to 3&rsquo direction, while the complementary strand is constructed in the 3&rsquo to 5&rsquo direction. This is important to the function of enzymes that create and repair DNA, as we will be discussing soon. In Figure (PageIndex<1>), the left strand is 5&rsquo to 3&rsquo from top to bottom, and the other is 5&rsquo to 3&rsquo from bottom to top.

From a physical standpoint, DNA molecules are negatively charged (all those phosphates), and normally a double-helix with a right-handed twist. In this normal (also called the &ldquoB&rdquo conformation) state, one full twist of the molecule encompasses 11 base pairs, with 0.34 nm between each nucleotide base. Each of the nitrogenous bases are planar, and when paired with the complementary base, forms a at planar &ldquorung&rdquo on the &ldquoladder&rdquo of DNA. These are perpendicular to the longitudinal axis of the DNA. Most of the free-floating DNA in a cell, and most DNA in any aqueous solution of near-physiological osmolarity and pH, is found in this B conformation. However, other conformations have been found, usually under very specific environmental circumstances. A compressed conformation, A-DNA, was observed as an artifact of in vitro crystallization, with slightly more bases per turn, shorter turn length, and base-pairs that are not perpendicular to the longitudinal axis. Another, Z-DNA, appears to form transiently in GC-rich stretches of DNA in which, interestingly, the DNA twists the opposite direction.

Figure (PageIndex<2>). Three conformations of DNA. B-DNA is most common, A-DNA is likely an artifact of crystallization in vitro, and Z-DNA may form transiently in parts of the chromosome.

It has been suggested that both the A and Z forms of DNA are, in fact, physiologically relevant. There is evidence to suggest that the A form may occur in RNA-DNA hybrid double helices as well as when DNA is complexed to some enzymes. The Z conformation may occur in response to methylation of the DNA. Furthermore, the &ldquonormal&rdquo B-DNA conformation is something of a idealized structure based on being fully hydrated, as is certainly very likely inside a cell. However, that hydration state is constantly changing, albeit minutely, so the DNA conformation will often vary slightly from the B-conformation parameters in Figure (PageIndex<2>).

In prokaryotes, the DNA is found in the cytoplasm (rather obvious since there is no other choice in those simple organisms), while in eukaryotes, the DNA is found inside the nucleus. Despite the differences in their locations, the level of protection from external forces, and most of all, their sizes, both prokaryotic and eukaryotic DNA is packaged with proteins that help to organize and stabilize the overall chromosome structure. Relatively little is understood with regard to prokaryotic chromosomal packaging although there are structural similarities between some of the proteins found in prokaryotic and eukaryotic chromosomes. Therefore, most introductory cell biology courses stick to eukaryotic chromosomal packaging.

Figure (PageIndex<3>). DNA packaging. (A) A naked strand of DNA is approximately 2 nm in diameter. (B) Histones, which are octameric proteins depicted here as a roughly cylindrical protein, have positive charges distributed on the outer surface to interact with the negatively-charged DNA backbone. (C) Even the organization afforded by histone binding can leave an unmanageable tangle of DNA, especially with longer eukaryotic genomes, and therefore the histone-bound DNA is packaged into the &ldquo30-nm strand&rdquo. This is held together, in part, by histone interactions. (D) The 30-nm fibers are looped into 700-nm fibers, which are themselves formed into the typical eukaryotic chromosome (E).

Naked DNA, whether prokaryotic or eukaryotic, is an extremely thin strand of material, roughly 11 nm in diameter. However, given the size of eukaryotic genomes, if the DNA was stored that way inside the nucleus, it would become unmanageably tangled. Picture a bucket into which you have tossed a hundred meters of yarn without any attempt whatsoever to organize it by coiling it or bunching it. Now consider whether you would be able to reach into that bucket pull on one strand, and expect to pull up only one strand, or if instead you are likely to pull up at least a small tangle of yarn. The cell does essentially what you would do with the yarn to keep it organized: it is packaged neatly into smaller, manageable skeins. In the case of DNA, each chromosome is looped around a histone complex to form the first order of chromosomal organization: the nucleosome.

Figure (PageIndex<4>). The nucleosome is composed of slightly over two turns of DNA around a histone core containing two copies each of H2A, H2B, H3, and H4 histones. The H1 histone is not part of the core unit and functions in coor- dinating interaction between nucleosomes.

The 30-nm fiber is held together by two sets of interactions. First, the linker histone, H1, brings the nucleosomes together into an approximate 30-nm structure. This structure is then stabilized by disulfide bonds that form between the H2A histone of one nucleosome and the H4 histone of its neighbor.

Histones are a family of basic (positively-charged) proteins. They all function primarily in organizing DNA, and the nucleosome is formed when DNA wraps (a little over 2 times) around a core of eight histones - two each of H2A, H2B, H3, and H4. The number and position of the positive charges (mostly from lysines and arginines) are crucial to their ability to tightly bind DNA, which as previously pointed out, is very negatively charged. That &ldquoopposites attract&rdquo idea is not just a dating tip from the advice columns.

Figure from RCSB Protein Data Bank (http://www.rcsb.org).

Upon examination of the 3D structure of the histone core complex, we see that while relatively uncharged protein interaction domains hold the histones together in the center, the positively charged residues are found around the outside of the complex, available to interact with the negatively charged phosphates of DNA.

In a later chapter, we will discuss how enzymes read the DNA to transcribe its information onto smaller, more manageable pieces of RNA. For now, we only need to be aware that at any given time, much of the DNA is packaged tightly away, while some parts of the DNA are not. Because the parts that are available for use can vary depending on what is happening to/in the cell at any given time, the packaging of DNA must be dynamic. There must be a mechanism to quickly loosen the binding of DNA to histones when that DNA is needed for gene expression, and to tighten the binding when it is not. As it turns out, this process involves acetylation and deacetylation of the histones.

Figure (PageIndex<6>). (A) Deacetylated histone allows interaction between the negatively charged phosphates of the DNA and the positively charged lysines of the histone. (B) When the histone is acetylated, not only is the positive charge on the lysine lost, the acetyl group also imparts a negative charge, repelling the DNA phosphates.

Histone Acetyltransferases (HATs) are enzymes that place an acetyl group on a lysine of a histone protein. The acetyl groups are negatively charged, and the acetylation not only adds a negatively charged group, it also removes the positive charge from the lysine. This has the effect of not only neutralizing a point of attraction between the protein and the DNA, but even slightly repelling it (with like charges). On the other side of the mechanism, Histone Deactylases (HDACs) are enzymes that remove the acetylation, and thereby restore the interaction between histone protein and DNA. Since these are such important enzymes, it stands to reason that they are not allowed to operate willy-nilly on any available histone, and in fact, they are often found in a complex with other proteins that control and coordinate their activation with other processes such as activation of transcription.


What does double helix mean in biology?

A "filled-in" helix &ndash for example, a "spiral" (helical) ramp &ndash is called a helicoid. Helices are important in biology, as the DNA molecule is formed as two intertwined helices, and many proteins have helical substructures, known as alpha helices. The word helix comes from the Greek word ?&lambda&iota&xi, "twisted, curved".

what does the double helix tell us about DNA? A double helix resembles a twisted ladder. Each 'upright' pole of the ladder is formed from a backbone of alternating sugar and phosphate groups. Each DNA base ? (adenine, cytosine, guanine, thymine) is attached to the backbone and these bases form the rungs.

Beside above, what does it mean to call the DNA double helix antiparallel?

Antiparallel: A term applied to two molecules that are side by side but run in opposite directions. The two strands of DNA are antiparallel. The head of one strand is always laid against the tail of the other strand of DNA.

What is a helix in medical terms?

Medical Definition of helix 1 : the incurved rim of the external ear. 2 : a curve traced on a cylinder by the rotation of a point crossing its right sections at a constant oblique angle broadly : spiral sense 2 &mdash see alpha-helix, double helix.


'Lost' Letters Reveal Twists in Discovery of Double Helix

Rediscovered letters and postcards highlight the fierce competition among scientists who discovered DNA's famous double-helix structure and unraveled the genetic code.

Francis Crick and James D. Watson shared a 1962 Nobel Prize with Maurice Wilkins for their work on revealing the structure of the DNA molecule that encodes instructions for the development and function of living beings. But formerly lost letters kept by Crick add more color to the well-known rivalries between Wilkins and the Crick-Watson duo.

"The [letters] give us much more flavor and examples illuminating the characters and the relations between them," said study researcher Alexander Gann, editorial director at Cold Spring Harbor Laboratory Press in New York. "They're consistent with what we already believed, but they add important details."

A fourth researcher credited with initial DNA work, Rosalind Franklin, died of cancer in 1958 and was never nominated for a Nobel Prize. She and her male colleagues did not get along despite their professional collaboration, as seen in some rather blunt messages contained within the new material.

"I hope the smoke of witchcraft will soon be getting out of our eyes," Wilkins wrote to Crick and Watson in 1953, as Franklin prepared to leave Wilkins' lab for Birbeck College in London.

Nine boxes of Crick's material turned up mixed in with the correspondence of a colleague, Sydney Brenner, who had donated his personal documents to Cold Spring Harbor Laboratory Library in New York. Researchers knew that much of Crick's earlier correspondence had been lost, but no one suspected it would emerge in Brenner's files.

The rediscovered material contains several nuggets about the race between rival labs to develop a DNA model in the early 1950s. Wilkins and Franklin worked at King&rsquos College London, while Crick and Watson did their research at the Cavendish Lab of Cambridge University.

Watson and Crick built an incorrect triple-helix model of DNA in 1951, after Watson saw a lecture by Franklin where she showed crystallographic X-ray images she had taken of DNA. The overconfident Watson had failed to take notes, and so he underestimated the amount of water in the DNA structure.

That led to a temporary agreement that Watson and Crick should not pursue a model of DNA for the time being, because the duo had merely used data from the rival King's College lab. Wilkins and Crick exchanged newly uncovered letters that show Wilkins alternating between a formal, typed letter about the agreement and a handwritten note expressing more personal anguish over the situation.

Yet Crick and Watson still managed to come off as confident in a rediscovered letter to Wilkins, and even include a verbal jab.

Rather than end the letter by praising Wilkins for now having a clear chance to solve the DNA structure, they crossed it out and wrote: "…So cheer up and take it from us that even if we kicked you in the pants it was between friends. We hope our burglary will at least produce a united front in your group!"

The exchange emphasizes the different attitudes among the scientists, Gann explained.

"Watson and Crick are jovial and cavalier, even though they've just been humiliated," Gann told Livescience. "But Wilkins was always anxious and tortured about different things."

'Rosy' the scientist

The rediscovered Crick material, which includes correspondence, photographs, postcards, preprints, reprints, meeting programs, notes and newspaper cuttings, also gives new details on the relationship between Rosalind Franklin and her male colleagues.

Well-known tensions reigned early on. An early misunderstanding poisoned the relationship between Wilkins and Franklin, and Watson's rather chauvinist attitude toward Franklin at the time included complaints that she failed to wear lipstick or pretty herself up like other women.

Franklin's male peers also persisted in calling her "Rosy" or "Rosie," a nickname she disliked immensely.

Still, her work with X-ray crystallography created a certain "Photograph 51," which allowed Crick and Watson to realize that DNA has a double-helix structure. Without Franklin knowing, Wilkins showed her photograph to Crick and Watson in 1953.

Wilkins later complained to Crick and Watson in a rediscovered letter: "To think that Rosie had all the 3D data for 9 months & wouldn&rsquot fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ."

The rival labs eventually agreed to publish several papers together on the DNA structure in the journal Nature.

A twist of discovery

Many have argued that Franklin deserved Nobel recognition, because her experimental work revealed the double-helix structure that helped Crick and Watson build their DNA model. Even Watson suggested much later that Franklin and Wilkins should have shared a Nobel Prize in chemistry for their contributions.

Franklin, who had all the photographic evidence of DNA's double-helix structure in front of her, had dismissed the idea of a helix. That's because she focused her attention on the clearer data from the A form of DNA, which looks less obviously like a helix than the B form of DNA.

The crucial photograph shown to Crick and Watson had contained the B form of DNA, and so the pair immediately seized upon its helical shape. But a newly rediscovered letter shows that even they might have hesitated for a moment upon seeing the A form of DNA.

"This is the first time I have had an opportunity for a detailed study of the picture of Structure A, and I must say I am glad I didn&rsquot see it earlier, as it would have worried me considerably," Crick told Wilkins in the summer of 1953.

Gann suspects today that Crick and Watson would have gone ahead with their double-helix model and ignored the more ambiguous evidence from the A form of DNA.

"It wasn't anti-helical it just wasn't obviously helical," Gann said in a phone interview.

Publishing what-ifs

Other rediscovered letters include one in 1963 from C.P. Snow, the British physicist who bemoaned the communication gap between science and the humanities in a lecture titled "The Two Cultures." Snow wanted Crick to write something for general audiences about the DNA discovery story.

But Crick declined by noting he would have to consult Watson, Wilkins and everyone else involved. Five years later, Watson published his famous first-person account on his own, titled "The Double Helix."

Similarly, Crick spent six years putting off writing a textbook on molecular biology, despite pleas from a publisher. Watson eventually published a textbook called "Molecular Biology of the Gene," which defined the field of molecular biology and is now in its sixth edition.

Had Crick gone ahead and written his textbook, he might have ended up defining molecular biology in the same way, but in a different style, Gann said.

"Watson's first response when we showed him [the correspondence] was 'Wow, if he had written that I would have never written mine,'" Gann recalled.

Gann and Jan Witkowski, executive director of the Banbury Center in Cold Spring Harbor Laboratory, commented on the new Crick material in the Sept. 30 issue of the journal Nature.


Simple twist of DNA determines fate of placenta

(© stock.adobe.com)

The development of the mammalian placenta depends upon an unusual twist that separates DNA’s classic double helix into a single-stranded form, Yale researchers report July 15 in the journal Nature.

The Yale team also identified the molecular regulator that acts upon this single strand to accelerate or stop placental development, a discovery with implications not only for diseases of pregnancy but also for understanding how cancer tumors proliferate.

“ Placental tissue grows very fast, stimulates blood vessel formation, and invades into neighboring tissues, like a tumor,” said senior author Andrew Xiao, associate professor of genetics and a researcher with the Yale Stem Cell Center. “Unlike a tumor, however, the placenta grows through a precise, coordinated, and well-controlled manner.”

At the earliest stage of fetal development two linked processes begin simultaneously. As the fertilized egg begins developing specialized cells of the new life, another set of cells begins producing blood vessels in the placenta to nourish the growing fetus.

“ In many ways, pregnancy is like a prolonged state of inflammation, as the placenta constantly invades the uterine tissue,” Xiao said.

The DNA of the cells that will make up the growing placenta share an unusual trait — the double helix begins to twist. The resulting torsion causes certain sections of the genome break into a single strand. Although the primary sequences of the DNA are the same between the placenta and embryo, the different structure of the DNA between the two helps determine the fate of the cells.

The Yale team led by Xiao discovered placental growth is then regulated by the sixth base of DNA, N6-methyladenine. This base stabilizes the single-stranded regions of DNA and repels SATB1. SATB1 is protein critical for the organization of chromatin, the material that makes up chromosomes.

Placentas without N6-methyladenine grow uncontrollably while placentas with abnormally high levels of N6-methyladenine develop severe defects that eventually halt embryo development, the researchers found.

The findings could help researchers develop new therapies for conditions such as preeclampsia in pregnancy as well as certain types of cancer characterized by activity from single strands of DNA, the researchers said.

Yale’s Zheng Li, Shuai Zhao, Raman V. Nelakanti, Kaixuan Lin, and Tao P. Wu are co-first authors of the paper.

The research was primarily funded by National Institutes of Health and the Ludwig Family Foundation. A team of researchers led by Haitao Li in Tsinghua University also contributed to this study.


Watch the video: California Jubilee in Lets Twist Again (July 2022).


Comments:

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