Archive for the ‘Nucleic Acids’ Category


Today I would be writing about a very unusual form of DNA, that is, H-DNA.

The H-DNA is a triple helix. This particularly unusual form of DNA is found in vitro or possibly during recombination and DNA repair. It forms by pairing and interwinding of 3 strands of DNA. Two of the three strands contain pyrimidines and the third contains purines. The three strands show a special base pairing known as Hoogsteen base pairing. Some sequences that can form H-DNA are found within regions involved in the regulation of a number of genes in eukaryotes.

You can read the following article about the H-DNA:

Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells.


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Z-DNA was discovered in vitro under high salt conditions. It is know to exist in the interband regions of the giant salivary gland chromosomes of Drosophila and in the transcriptionally active macronucleus of the ciliated protozoan Stylonchia mytilus. The properties of Z-form DNA are listed below:

1) It is a left-handed helix and the helical diameter is 18Å.

2) There are 12 base pairs per turn in the Z-DNA. Because of the maximum number of base pairs per turn found in this form, the Z-DNA has the least twisted structure.

3) It has a zig-zag sugar phosphate backbone.

4) It has a rise of 0.38 nm per base pair.

5) The Z-form DNA occurs in polymers that have a sequence of alternating purines and pyrimidines (especially Gs and Cs). The alternating polymers could be poly d(GC) or poly d(AC).

6) Instead of having both major and minor grooves, the Z-DNA has only a single groove.

Scientists have raised antibodies specific to Z-DNA (E M Lafer, R P Valle, A Möller, A Nordheim, P H Schur, A Rich, and B D Stollar. J Clin Invest. 1983 February; 71(2): 314–321). The antibodies have helped in the detection of Z-DNA under different cellular conditions (M Robert-Nicoud, D J Arndt-Jovin, D A Zarling, and T M Jovin. EMBO J. 1984 April; 3(4): 721–731).

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A-form DNA

The A-DNA is favoured in many solutions that are relatively of water. The properties of A-DNA are:

1) Right-handed helix

2) Helix rise per base pair is 0.23 nm

3) The number of base pairs per helical turn is 11.

4) A-form DNA is shorter and has a greater helical diameter than the B-DNA. The helical diameter of A-DNA is 23 angstrom or 26 angstrom.

5) The rotation per base pair is 34.7°.

6) RNA-DNA and RNA-RNA helices also exist in this form.

7) The A-form is probably very close to the conformation of double stranded regions of RNA, where the presence of the 2′-OH group prevents the adoption of the B-form.

The major groove of A-DNA is less accessible and bases are tilted with regard to the helical axis. The A-DNA is sometimes formed during DNA crystallization because the reagents used to promote DNA crystallization tend to dehydrate it. This leads to a tendency for many DNAs to crystallize in the A-form.

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One of the properties of the DNA is that it shows confirmational flexibility, and could exist in alternative structural forms. The Watson-Crick structure is the B-form DNA, or B-DNA. The B from is the most stable structure for a random sequence DNA molecule under physiological conditions and is therefore “the standard point of reference in any study of the properties of DNA” (Lehninger Principle of Biochemistry, Nelson and Cox, 2000, pp. 338). The B-DNA predominates in the cell. There are two other structural variants of DNA that have been well characterized in crystal structures. They are the A-DNA and Z-DNA. There is another alternative form of DNA known as the H-DNA. These DNA variants differ in their helical sense, diameter, base pairs per helical turn, helix rise per base pair, base tilt normal to the helix axis, sugar pucker conformation, and glycosyl bond conformation.

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DNA structure

The double helical model of DNA structure was given by Watson and Crick.

DNA molecule is helical with two periodicities along its long axis, a primary one of 0.34 nm and a secondary one of 3.4 nm. The most predominant form of DNA present in the cell is B-form. It is a right-handed double helix and runs in the clockwise direction. The two strands of DNA run in antiparallel direction. The two strands in a DNA double helix are joined by hydrogen bonding (H-bonding) between bases. Adenine pairs with thyminne, and guanine pairs with cytosine. Adenine pairs with thymine with two H-bonds, whereas guanine forms 3 H-bonds with cytosine. This is known as complementary base pairing or Watson-Crick base pairing. The base pairs contribute to the thermodynamic stability of the double helix in two ways:

a) H-bonding between bases releases energy.

b) Hydrophobic base-stacking. The interactions between electron systems of stacked base pairs contribute to the stability of the helix.

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DNA: Its properties

Some of the properties of the DNA are listed below:

1) Double helical

2) Acidic in nature

3) Shows antiparallelity

4) Shows confirmational flexibility (alternative structures) and bending

5) Binds with basic histone proteins

6) Absorbs UV light at 260 nm (heterocyclic rings of nucleotides absorb in the UV region)

7) Undergoes reversible strand separation; many DNA molecules are circular; local unwinding of DNA induces supercoiling

Supercoiling occurs during replication, transcription and binding of many proteins. Supercoiling is recognized and regulated by enzymes called topoisomerases.

There were 3 important aspects that led to the elucidation of the structure of DNA double helix. These are:

1) X-ray diffraction data

2) Density of DNA

3) Chargaff ‘s rule

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To qualify as the genetic material, DNA has to fulfil two key requirements:

1) Genotype function or Replication: The genetic material must have the capability to store genetic information, and transmit this information faithfully from parents to offspring, generation after generation. This indicates that the genetic material should have the ability to replicate itself and make its copies.

2) Phenotype function or Gene Expression: The genetic material must control the development of phenotype of the organism. It means that it should control the growth and differentiation of the organism from the single-celled zygote to the mature adult.

There are three landmark experiments, which showed that DNA is the genetic material.

1) Griffith’s Experiment (1928)

2)  Avery, MacLeod and McCraty’s Experiment (1944): They showed that if highly purified DNA from Type IIIS pneumococci was present with TypeIIR pneumococci, some of the pneumococci were transformed to Type IIIS.

3)  Hershey-Chase Experiment (1952): The basis for the experiment: DNA contains phosphorus but no sulfur; whereas proteins contain sulfur but no phosphorus. The experiment is also referred to as the Waring blender experiment. Alfred D. Hershey won the Noble Prize in Physiology or Medicine in 1969.

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