History of the spatial model
The famous spatial structure model of DNA was proposed in 1953 by the American biologist James Watson and the British researcher Francis Crick. Their discovery did not come out of nowhere: the scientists built upon a rich body of data obtained by their colleagues. A key role was played by the results of X-ray diffraction analysis conducted by biophysicist Maurice Wilkins and X-ray crystallographer Rosalind Franklin.
The proposed concept of the double helix was a true breakthrough in molecular biology. For the first time, it provided a clear chemical explanation for the most important biological properties of nucleic acids: the ability to encode genetic information and the process of replication (doubling).
Main principles of double helix organization
The structure is based on two polynucleotide chains. The Watson-Crick model describes the classical $\beta$-form of the molecule, which is characterized by the following principles:
- Coiling. Both chains are wound into a double helix around a single central axis.
- Direction of turns. The helix is right-handed. When viewed along the central axis of the molecule, the turns of the chains follow strictly clockwise.
- Antiparallelism. The polynucleotide strands run in opposite directions. This means that the 5' end of one chain is mirrored opposite the 3' end of the second chain.
- Orientation of nucleotides. Each individual nucleotide lies in a plane that is strictly perpendicular to the central axis of the helix.
- Presence of grooves. In the three-dimensional structure of the coiled molecule, two distinct depressions stand out: the major and minor grooves.
Complementarity and hydrogen bonds
The two antiparallel chains are securely fastened together by hydrogen bonds. These bonds do not form randomly, but strictly between nitrogenous bases belonging to different chains. Base interaction has the highest specificity and obeys the principle of complementarity.
Physicochemical bases of pairing:
- A=T pairs (adenine and thymine) form exactly two hydrogen bonds between each other.
- G≡C pairs (guanine and cytosine) bond more strongly—via three hydrogen bonds.
Due to strict complementarity, the nucleotide sequence in one chain uniquely determines the sequence in the second. This property ensures the template function of DNA: during helix unwinding, each single chain acts as a ready-made template upon which a new, fully complementary chain is synthesized.
Metric parameters of the molecule
The double helix has strict, invariable geometric characteristics. Studying the structure made it possible to derive the following metric parameters:
- Distance between adjacent nucleotides: 0.34 nm.
- One full turn of the helix: equals 3.4 nm. Exactly 10 nucleotides fit within one turn.
- Diameter of the molecule: stably equals 2 nm along its entire length.
An interesting consequence of chemical structure: DNA regions that are rich in A=T pairs are significantly easier to separate (the denaturation process). Since two hydrogen bonds are easier to break than three, it is these A=T-rich regions that in most cases serve as replication origins (origins of replication).
Briefly: answers to topical questions
What chemical bonds connect nucleotides within a single DNA polynucleotide chain?
Nucleotides within a single DNA polynucleotide chain are connected via covalent phosphodiester bonds. These bonds form the sugar-phosphate backbone (framework) of the polynucleotide chain, consisting of alternating deoxyribose and phosphate residues, which is located on the outside of the double helix.
Backbone formation mechanism:
- Phosphodiester bond — the phosphate group at the carbon atom in the $5'$ position of one ring connects to the carbon atom in the $3'$ position of the next pentose ring.
Due to this mechanism, the chain acquires polarity: the $5'$ end has a free phosphate group, and the $3'$ end terminates with a free hydroxyl ($3'$-OH) group.
Which DNA nitrogenous bases are classified as purines and which as pyrimidines?
Nitrogenous bases in the DNA molecule are represented by heterocyclic compounds and are divided into purines and pyrimidines.
- Purine bases — have a two-ring structure (a six-membered and a five-membered ring). In DNA, these include adenine (A) and guanine (G).
- Pyrimidine bases — have a chemical structure consisting of a single six-membered ring. In the DNA molecule, these include cytosine (C) and thymine (T).
Pyrimidine bases also include uracil (U), but it is found only in RNA, whereas thymine is its methylated analog and is characteristic of DNA.
Class and exam questions
What does the antiparallelism of DNA strands mean?
This is the principle of spatial organization in which two polynucleotide strands run in opposite directions. As a result, the 5'-end of one strand always corresponds to the 3'-end of the other.
Which way is the helix wound?
The classical beta form of the molecule is right-handed. When viewed along its axis, the turns of the chain occur clockwise.
Why are origins of replication often enriched with A=T pairs?
Adenine-thymine pairs are held together by only two hydrogen bonds (whereas guanine-cytosine pairs are held by three). Regions with a predominance of A=T are more weakly bound and easier to denature (unwind), which is necessary to initiate replication.
How many nucleotides does one turn of the helix contain?
One full turn of the helix has a length of 3.4 nm and contains exactly 10 nucleotides. The distance between adjacent nucleotides is 0.34 nm.
What else to study on this topic
- Template function and mechanisms of DNA replication
- The process of denaturation and separation of polynucleotide chains
- The role of major and minor grooves in DNA functioning
- Methods of X-ray diffraction analysis of nucleic acids
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