Why does DNA have a helical structure



The Deoxyribonucleic acid (short DNS or DNA) (lat.-fr.-gr. made-up word) is a biomolecule that occurs in all living beings and DNA viruses and is the carrier of genetic information. It contains, among other things, the genes that code for ribonucleic acids (RNA, in German also RNS) and proteins that are necessary for the biological development of an organism and the metabolism in the cell. In common parlance, deoxyribonucleic acid is mainly used with the English abbreviation DNA (deoxyribonucleic acid) designated; the parallel existing German abbreviation DNS however, it is used less often and is loud Duden "Obsolete".[1]

In the normal state, the DNA is organized in the form of a double helix (see animation on the right). From a chemical point of view, it is a nucleic acid, a long chain molecule (polymer) made up of individual pieces, so-called nucleotides. Each Nucleotide consists of a phosphate residue, a sugar and one of four organic bases with the abbreviations A, T, G and C. Within the protein-coding genes, the sequence of the bases determines the sequence of the amino acids of the respective protein: in the genetic code three bases each for a particular amino acid.

In the cells of plants, animals and fungi, the so-called eukaryotes, the majority of the DNA in the cell nucleus is organized as chromosomes, while in bacteria and archaea (the prokaryotes) the DNA in the cell sap, the Cytoplasm, distributed. Some cell organelles in eukaryotes, namely mitochondria and chloroplasts, also contain DNA. Some viruses, called RNA viruses, do not have DNA. Here the genetic information is inherited through the molecule RNA, which is related to DNA.

Discovery story

In 1869, the Swiss doctor Friedrich Miescher discovered an extract of pus, a substance that comes from the cell nuclei of the lymphocytes Nucleus called. Back then, Miescher was working in Felix Hoppe-Seyler's laboratory in Tübingen Castle.[2] It was not until 1919, 50 years later, that Phoebus Levene identified the components of DNA (base, sugar and phosphate residue).[3] Levene proposed a chain-like structure of DNA in which the nucleotides are joined together by the phosphate residues and repeat themselves continuously. In 1937, William Astbury published X-ray diffraction patterns for the first time, which indicated a repetitive structure of DNA.[4]

In 1943 Oswald Avery (see description of the experiment) discovered that a non-pathogenic strain of Pneumococcus-Bacteria could acquire pathogenic properties when brought into contact with dead Pneumococcus bacteria of the pathogenic form. Avery identified DNA as the substance that contained the information for this transformation.[5] Avery received support in his interpretation in 1952, when Alfred Hershey and Martha Chase demonstrated that DNA contains the genetic information of the T2 phage.[6]

The structural structure of DNA was first discussed in 1953 by the American James Watson and the British Francis Crick in their famous article Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid described[7]. Watson came to England in 1951 after completing his doctorate at Indiana University in the United States a year earlier. Although he had received a scholarship in molecular biology, he was increasingly concerned with the question of human genome. Crick was unsuccessfully doing his doctorate on the crystal structure of the hemoglobin molecule at Cambridge when he met Watson in 1951. At that time, a bitter race for the structure of DNA had already broken out, in which Linus Pauling at the California Institute of Technology was also participating. Watson and Crick had actually been assigned to other projects and had little expertise in chemistry. They based their considerations on the research of the other scientists. Watson said he did wants to decipher the genome without having to learn chemistry. In a conversation with the renowned chemist Erwin Chargaff, Crick forgot important molecular structures and Watson made inappropriate comments in the same conversation, which illustrated his ignorance in the field of chemistry. Chargaff then called the young colleagues "scientific clowns".

Watson visited in late 1952 Maurice Wilkins at King's College, London, who showed him DNA x-rays of Rosalind Franklin (which happened against Franklin's will). Watson saw immediately that the molecule was a Double-Helix had to act; Franklin himself had suspected the presence of a helix based on the data, but she had no convincing model for the structure to show. Since it was known that the purine and pyrimidine bases form pairs, Watson and Crick succeeded in deriving the complete molecular structure. For example, at the Cavendish Laboratory at Cambridge University, they developed the double helix model of DNA with the base pairs in the middle, which was published in the journal Nature on April 25, 1953.[8] This memorable publication contains the sentence "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material“(It has not escaped our attention that the special pairings that we take for granted immediately suggest a possible mechanism of reproduction for the genetic material.)

“For their discoveries about the molecular structure of nucleic acids and their importance for the transmission of information in living matter”, Watson and Crick received the 1962 Nobel Prize for Medicine together with Maurice Wilkins.[9]Rosalind Franklin, whose X-ray diffraction diagrams had contributed significantly to the decoding of the DNA structure, had already died at this point and could therefore no longer be nominated.

For further historical information on deciphering the inheritance processes see “History of the Cell Nucleus” as well as “History of Chromosomes” and “Chromosome Theory of Inheritance”.

Structure and organization

building blocks

The deoxyribonucleic acid is a long chain molecule (polymer) made up of many building blocks, which are called deoxyribonucleotides or short Nucleotides is called. Each nucleotide has three components: phosphoric acid or phosphate, the sugar deoxyribose and a heterocyclic nucleobase or base for short. The deoxyribose and phosphoric acid subunits are the same for each nucleotide. They form the backbone of the molecule. Units made up of base and sugar (without phosphate) are called nucleosides.

The Phosphate residueswhich are hydrophilic due to their negative charge, give the DNA an overall negative charge. It is they who chemically turn DNA into acid.

In the base can it be a purine, namely adenine (A.) or guanine (G), or a pyrimidine, namely thymine (T) or cytosine (C.), act. Since the four different nucleotides only differ in their base, the abbreviations A, G, T and C are also used for the corresponding nucleotides.

The five carbon atoms one Deoxyribose are from 1 '(pron One line) numbered to 5 '. The base is attached to the 1 'end of this sugar. The phosphate residue hangs at the 5 'end. Strictly speaking, deoxyribose is 2-deoxyribose, the name comes from the fact that, compared to a ribose molecule, there is no alcoholic OH group at the 2 'position (or it has been replaced by a hydrogen).

At the 3'-position there is an OH group which links the deoxyribose via a so-called phosphodiester bond with the phosphate group of the next nucleotide to the 5'-carbon atom of the associated sugar (see figure). As a result, everyone owns so-called Single strand, two different ends: a 5 'end and a 3' end. DNA polymerases, which carry out the synthesis of DNA strands in the living world, can only add new nucleotides to the OH group at the 3 'end, but not at the 5' end. The single strand always grows from 5 'to 3' (see also DNA replication below). A nucleoside triphosphate (with three phosphate residues) is delivered as a new component, from which two phosphates are split off in the form of pyrophosphate. The remaining phosphate residue of the newly added nucleotide is connected to the OH group at the 3 'end of the last nucleotide present in the strand with elimination of water. The sequence of bases in the strand codes the genetic information.

The double helix

DNA usually occurs as a helical double helix in a conformation called "B-DNA". Two of the single strands just described are attached to one another, specifically in opposite directions: at each end of the double helix, one of the two single strands has its 3 'end, the other its 5' end. Due to the juxtaposition, there are always two specific bases facing each other in the middle of the double helix, they are "paired". The cohesion of the double helix is ​​stabilized through hydrogen bonds between the paired bases and through hydrophobic interactions between successive bases.

Adenine and thymine are always paired, which form two hydrogen bonds, or cytosine with guanine, which are linked to one another via three hydrogen bonds. A bridge is formed between the molecular positions 1 = 1 and 6 = 6, with guanine-cytosine pairings additionally between 2 = 2. Since the same bases are always paired, the sequence of the bases in one strand can be used to derive those of the other strand, which are sequences complementary. (See also: base pair.) The proportion of guanine and cytosine relative to adenine and thymine in a DNA double strand provides information about the stability of the links between the two complementary single strands: Guanine-cytosine pairings with their three hydrogen bonds each cause a stronger linkage two single strands than between adenine and thymine, since their complementary pairings only occur through two hydrogen bonds.

Since a purine is always combined with a pyrimidine, the distance between the strands is the same everywhere, resulting in a regular structure. The whole helix is ​​about 2 nanometers (nm) in diameter and continues to wind 0.34 nm with each sugar molecule. The planes of the sugar molecules are at an angle of 36 ° to each other and a complete rotation is therefore achieved after 10 bases (360 °) and 3.4 nm. DNA molecules can grow very large. For example, the largest human chromosome contains 247 million base pairs[10] in a continuous DNA thread 8.4 centimeters long.

When the two single strands are wound around each other, there are gaps on the side so that the bases are directly on the surface. Of these Furrows there are two that wrap around the double helix (see images and animation at the beginning of the article). The "large furrow" is 2.2 nm wide, the "small furrow" only 1.2 nm[11]. Accordingly, the bases in the large furrow are more accessible. Proteins that bind to the DNA in a sequence-specific manner, e.g. B. transcription factors, therefore mostly bind to the great furrow [12]. Some DNA dyes, such as B. DAPI attach to a furrow.

The accumulated binding energy of the hydrogen bonds between the two single strands holds them together. There are no covalent bonds here, so the DNA double helix does not consist of one molecule, but of two. This allows the two strands to be temporarily separated in biological processes.

In addition to the B-DNA just described, there is also an “A-form” as well as a left-handed so-called “Z-DNA” that was first examined by Alexander Rich and his colleagues at MIT in 1979. This occurs especially in G-C-rich sections. A crystal structure was only reported in 2005, which shows Z-DNA directly in connection with B-DNA and thus provides indications of a biological activity of Z-DNA[13]. The following table and the illustration next to it show the differences between the three forms in direct comparison.

 

Structural feature A-DNA B-DNA Z-DNA
helical sense of rotation right right Left
diameter ~ 2.6 nm ~ 2.0 nm ~ 1.8 nm
Base pairs per helical turn 11.6 10.0 12 (6 dimers)
Helical turn per base pair (twist) 31° 36° 60 ° (per dimer)
Pitch (increase per turn) 3.4 nm 3.4 nm 4.4 nm
Increase per base 0.29 nm 0.34 nm 0.74 nm (per dimer)
Inclination angle of the base pairs to the axis 20°
Big furrow tight and deep wide and deep flat
Small furrow wide and flat tight and deep tight and deep
Sugar conformation C3'-endo C2'-endoPyrimidines: C2'-endo
Purines: C3'-endo
Glycosidic bond anti anti Pyrimidines: anti
Purines: syn

The stacks of the base pairs (base stacking) are not exactly parallel to each other like books, but form wedges that incline the helix in one direction or the other. The largest wedge is formed by adenosines, which are paired with thymidines on the other strand. As a result, a series of AT pairs form an arc in the helix. If such series follow one another at short intervals, the DNA molecule assumes a curved or curved structure, which is stable. This is also called sequence-induced diffraction, since the diffraction can also be caused by proteins (the so-called protein-induced diffraction). Sequence-induced diffraction is often found at important locations in the genome.

Chromatin and chromosomes

 

Main article: Chromatin and chromosome

The DNA in the eukaryotic cell is organized in the form of chromatin threads, called chromosomes, which are located in the cell nucleus. A single chromosome contains a long, continuous double strand of DNA. Since such a DNA thread can be several centimeters long, but a cell nucleus is only a few micrometers in diameter, the DNA must also be compressed or “packed”. In eukaryotes, this happens with so-called chromatin proteins, of which the basic histones deserve special mention. They form the nucleosomes around which the DNA is wrapped at the lowest level of packaging. During nuclear division (mitosis), each chromosome is condensed into a compact form. This makes them visible with a light microscope even at low magnification.

Bacterial and Viral DNA

In prokaryotic cells, the DNA is not a linear thread with a beginning and an end, but a circular molecule - the 5 'end is therefore connected to the 3' end of the DNA strand. These circularly closed DNA molecules are called bacterial chromosomes or plasmids, depending on the length of the sequence. In bacteria, they are not located in a cell nucleus, but are freely present in the plasma. The prokaryote DNA is wound up with the help of enzymes (e.g. topoisomerases and gyrases) into simple “supercoils” that can be imagined as a twisted telephone cord. By turning the helices around themselves, the space required for the genetic information is reduced. In the bacteria, topoisomerases ensure that by constantly cutting and reconnecting the DNA, the twisted double strand is untwisted at a desired point (prerequisite for transcription and replication). Viruses contain either DNA or RNA as genetic information, depending on their type. In both the DNA viruses and the RNA viruses, the nucleic acid is protected by a protein shell.

Chemical and physical properties of the DNA double helix

further articles: GC content and Agarose gel electrophoresis

At neutral pH, DNA is a negatively charged molecule, with the negative charges sitting on the phosphates in the backbone of the strands. Although two of the three acidic OH groups of the phosphates are esterified with the neighboring deoxyriboses, the third is still present and emits a proton at a neutral pH value, which causes the negative charge. This property is used in agarose gel electrophoresis to separate different DNA strands according to their length.

Another important property of a DNA strand is the so-called melting point. In contrast to the normal usage of the word, which characterizes the transition from the solid to the liquid phase, the denotes Melting point of DNA the temperature at which the binding forces between the two individual strands are overcome and these separate from each other. This is also called the denature designated. The exact temperature of the melting point Tm depends on the density and strength of the hydrogen bonds in the helix: Since A-T base pairs only form two, G-C pairs form three hydrogen bonds, GC-rich sections have a higher melting temperature. The ratio of these base pairings to one another is referred to as the GC content. The strength of the bonds varies with the concentration of ions in the solution, so that this also has an influence.For a na+-Concentration of 0.2 M, the melting temperature in ° C can be calculated using the following formula:

Tm= 69.3 + 0.41 × (GC content in percent)[14].

With a GC content of 50%, the result is Tm = 89.8 ° C, with a pure AT DNA the result would be T.m = 69.3 ° C, with a pure GC DNA Tm = 110.3 ° C. The formula does not apply to short DNA fragments of around 5-20 base pairs, so-called oligonucleotides or oligos for short, as they separate at lower temperatures. Also hydrophobic interactions and van der Waals forces between the bases lying on top of each other in the double strand (together stacking forces(German for about stacking forces) influence the melting point, so that with such short pieces of DNA it also depends on the length. In buffers with a little salt (

Tm = 4 (G + C) +2 (A + T)[15]

the number of nucleotides being used for the letters. For example, 10 G-C and 8 A-T pairings result in a Tm of 4 x 10 + 2 x 8 = 56 ° C. By reducing the ion concentration or using a solvent that reduces the strength of the hydrogen bond between the individual strands, such as. B. formamide, the melting temperature can be reduced considerably. Conversely, under controlled conditions, the melting point of a DNA can be used to determine its GC content. Since single-stranded DNA absorbs about 40% more UV light than double-stranded DNA, the transition temperature can be easily determined in a photometer.

When the temperature of the solution returns below Tm falls, the individual strands can attach to each other again. This process is called Renaturation or Hybridization designated. The interplay between denaturation and renaturation is used in many biotechnological processes, for example in the polymerase chain reaction (PCR), in Southern blots and in situ hybridization.

Cross-shaped DNA on palindromes

A palindrome is a sequence of nucleotides in which the two complementary strands can be read from the right as well as from the left. Under natural conditions (with high torsional stress in the DNA) or artificially in a test tube, this linear helix can develop as a cruciform, in which two branches protrude from the linear helix. The branches each represent a helix, but at least three nucleotides remain unpaired at the end of a branch. In the transition from the cross shape to the linear helix, the base pairing is retained because of the flexibility of the phosphodiester sugar backbone. The spontaneous agglomeration of complementary bases to form so-called stem-loop structures is also often observed with single-stranded DNA or RNA.

Genetic information content and transcription

 

Main article: Gen as Genetic code and Transcription (biology)

DNA molecules play an important role as information carriers and “docking points” for enzymes that are responsible for transcription. Furthermore, the information of certain DNA segments, as it is present in operative units such as the operon, is important for regulatory processes within the cell.

Certain sections of DNA, called genes, code for genetic information that is useful to the organism. Genes contain “blueprints” for proteins or molecules that are involved in protein synthesis or the regulation of the metabolism of a cell. The sequence of the bases determines the genetic information. This base sequence can be determined by sequencing, for. B. can be determined using the Sanger method.

The base sequence (base sequence) of a gene segment of the DNA is initially overwritten by the transcription into the complementary base sequence of a so-called ribonucleic acid molecule (abbreviated RNA, rarely also German RNA). In contrast to DNA, RNA contains the sugar ribose instead of deoxyribose and the base uracil instead of thymine, but the information content is the same. So-called mRNAs are used for protein synthesis, single-stranded RNA molecules that are transported from the nucleus into the cytoplasm, where protein synthesis takes place (please referProtein biosynthesis).

The so-called “one-gene-one-protein hypothesis”, which states that the sequence of a protein molecule is read from a coding section on the DNA, is only valid to a limited extent today: There are regions of DNA that, through the use of different Reading frame encode several proteins in each case during transcription. In addition, different isoforms of a protein can be produced by alternative splicing (subsequent cutting of the mRNA).

DNA replication

 

Main article: replication

The DNA is able to duplicate itself with the help of enzymes. She will after the so-called semiconservative Principle replicated. The double-stranded helix is ​​first created by the enzyme Helicase separated. Each of the two resulting individual strands now serves as a template (template) for the complementary counter-strand to be synthesized, i.e. That is, each of the two daughter molecules of the replicated DNA consists of an old and a complementary, newly synthesized single strand.

The process of DNA synthesis, i.e. H. the binding of the nucleotides to be linked is carried out by enzymes from the group of DNA polymerases completed. A nucleotide to be linked must be present in the triphosphate compound - i.e. as a deoxyribonucleoside triphosphate. The energy required for the binding process is released by splitting off two phosphate parts.

In the area formed by the enzyme helicase Replication fork - two diverging single strands of DNA - initially marked one RNA primers, which is synthesized by the enzyme primase, the starting point of the new DNA synthesis. The DNA polymerase then attaches a nucleotide complementary to the nucleotide of the old DNA single strand to this RNA molecule, and another new matching nucleotide, etc., until the DNA has been completed again to form a double strand. This happens on both open single strands.

Nevertheless, a problem arises here: the linkage of the new nucleotides to a complementary single strand of DNA only runs in the 5 '→ 3' direction, i.e. H. continuously along the old 3 '→ 5' strand (and reading it at the same time) in the direction of the ever-opening replication fork without a break in one step.

The synthesis of the second new strand on the old 5 '→ 3' strand, on the other hand, cannot take place continuously in the direction of the replication fork, but only away from it, also in the 5 '→ 3' direction. The replication fork is only slightly open at the beginning of the replication, which is why only a short piece of new complementary DNA can ever develop on this strand - in the “unsuitable” opposite direction.

Since a DNA polymerase only links approx. 1000 nucleotides here, it is necessary to synthesize the entire complementary strand piece by piece. When the replication fork is a little more open, a new RNA primer is therefore attached again directly to the bifurcation point on the DNA single strand, and the next DNA polymerase begins - moving away from the replication fork - again approx. 1000 nucleotides on the RNA Primer to hang.

The same process is continuously repeated, i.e. In other words, the complementary DNA strand gradually emerges in bits and pieces. When synthesizing the 3 '→ 5' strand, a new RNA primer is therefore required for each DNA synthesis unit. The primer and the associated synthesis unit are referred to as Okazaki fragment. The RNA primers required to start replication are then enzymatically degraded. This creates gaps in the new DNA strand, which are filled with DNA nucleotides by special DNA polymerases.

Finally, the enzyme links Ligase the not yet connected new DNA segments into a single, long, complementary strand.

After the replication was complete, two single strands of DNA were each supplemented to form a double strand in a slightly different manner. Two identical DNA molecules have thus arisen from one DNA molecule.

Mutations and other DNA damage

Main article: mutation and DNA repair

Mutations of DNA segments - e.g. B. Exchange of bases for others or changes in the base sequence - lead to changes in the genetic make-up, some of which can be fatal for the organism concerned. In rare cases, however, such mutations are also beneficial; they then form the starting point for the change in living beings in the course of evolution. By means of recombination during sexual reproduction, this change in DNA even becomes a decisive factor in evolution: the eukaryotic cell usually has several sets of chromosomes, i.e. H. a DNA double strand is present at least twice. The mutual exchange of parts of these DNA strands, the crossing-over in meiosis, can create new properties.

DNA molecules can be damaged by various influences. UV or γ radiation, alkylation and oxidation can chemically change the DNA bases or lead to strand breakage. These chemical changes may affect the pairing properties of the affected bases. This principle is a major cause of mutations during replication.

Some common DNA damage are:

  • the formation of uracil from cytosine with the spontaneous loss of an amino group through hydrolysis: like thymine, uracil is complementary to adenine.
  • Thymine-thymine dimer damage caused by photochemical reaction of two successive thymine bases in the DNA strand by UV radiation, e.g. B. from sunlight. (This damage is likely a major cause of skin cancer development).
  • the formation of 8-oxo-guanine through oxidation of guanine: 8-oxo-guanine is complementary to both cytosine and adenine. During replication, both bases can be incorporated against 8-oxo-guanine.

Due to their mutagenic properties and their frequent occurrence (estimates are 104-106 new damage per cell and day), DNA damage must be removed from the genome in good time. For this, cells have an efficient DNA repair system. This eliminates damage with the help of the following strategies:

  • Direct damage reversal: An enzyme reverses the chemical change in the DNA base.
  • Base Excision Repair: The faulty base, e.g. B. 8-oxo-guanine, is excised from the genome. The resulting free space is re-synthesized on the basis of the information in the opposite strand.
  • Nucleotide excision repair: A larger part of the strand containing the damage is cut out of the genome. This is re-synthesized on the basis of the information in the opposite strand.
  • Homologous recombination: If both DNA strands are damaged, the genetic information from the second chromosome of the homologous chromosome pair is used for the repair.
  • Replication with special polymerases: DNA polymerase η can e.g. B. replicate error-free via a TT dimer damage. People in whom polymerase η does not work or only to a limited extent often suffer from Xeroderma pigmentosum, a hereditary disease that leads to extreme sensitivity to sunlight.

References

  1. Duden. The German spelling. 22nd edition, Mannheim, 2000
  2. Hubert Mania: A victim of the scientific prejudices of his time. The DNA was discovered as early as 1869 in the Tübingen Renaissance castle. Telepolis. April 17, 2004.
  3. Levene P ,: The structure of yeast nucleic acid. In: J Biol Chem. 40, No. 2, 1919, pp. 415-24
  4. Astbury W ,: Nucleic acid. In: Symp. SOC. Exp. Bbl. 1, No. 66, 1947
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  6. Hershey A, Chase M: Independent functions of viral protein and nucleic acid in growth of bacteriophage. In: J Gen Physiol. 36, No. 1, 1952, pp. 39-56. PMID 12981234
  7. Watson, J.D. & Crick F.H. (1953): Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. In: Nature. Vol. 171, No. 4356, pp. 737-738. PMID 13054692, http://www.nature.com/nature/dna50/watsoncrick.pdf
  8. Katharina Kramer: On the trail of life. GEO compact No. 7 (2006)
  9. Information from the Nobel Foundation about the award ceremony
  10. www.ensembl.org, homo sapiens. Database status as of September 2006. (website in English) [1]
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  12. Pabo C, Sauer R: Protein-DNA recognition. In: Annu Rev Biochem. 53, pp. 293-321. PMID 6236744
  13. Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK: Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. In: Nature. 437, 2005, pp. 1183-1186 PMID 16237447
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  15. C. Stan Tsai: Biomacromolecules. Wiley, Hoboken (New Jersey) 2007, ISBN 978-0-471-71397-5, P. 90.

literature

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Categories: nucleic acid | DNA