The following seven points will highlight the seven important criteria generally used for the classification of DNA.
The seven criteria which are generally used for the classification of DNA include: (1) Number of base pairs per turn (2) Coiling pattern (3) Location (4) Structure (5) Nucleotide sequences (6) Coding and Non-coding DNA and (7) Number of strands.
(1) Number of base pairs per turn,
(2) Coiling pattern,
(3) Location,
(4) Structure,
(5) Nucleotide sequences,
(6) Coding and Non-coding DNA and
(7) Number of strands.
A brief classification of DNA on the basis of these criteria is presented below: (Fig. 6.11)
Criteria # 1. Number of Nucleotide Base Per Turn:
Depending upon the nucleotide base per turn of the helix, pitch of the helix, tilt of the base pair and humidity of the sample, the DNA can be observed in four different forms, namely A, B, C and D.
A brief description of each form is given below:
B-DNA (Common form of DNA):
This form is the same as proposed by Watson and Crick and is the most common form. The B-form X-ray diffraction is observed when humidity is 92% and salt concentration is high. This is a right handed double helical structure. The pitch is 3. 4 nm and there are 10 base pairs per turn of the helix.
A-DNA:
This form is found when humidity of the sample is 75%. This has pitch of 2.8nm and 11 base pairs per turn of helix. The base pairs are almost perpendicular in B-DNA, whereas base pairs are titled in A-DNA. As a result, the depth of the deep grooves is increased and that of shallow grooves is reduced.
C-DNA:
The C-form of DNA is observed when humidity of DNA fibre is below 66%. This form of DNA has pitch of 3.1nm and 9.3 base pairs per turn of the helix. The base pair has negative tilt (-7.8).
D-DNA:
This is the rare form. This form has 8 base pairs per turn of the helix and the tilt is negative but higher than C form (-16.7). The B-DNA is the most stable form. It can change to another form depending upon humidity and salt concentration of the sample.
Criteria # 2. Coiling Pattern:
On the basis of coiling pattern of the helix, DNA is of two types, viz., right handed and left handed.
These are briefly described below:
Right Handed DNA:
Most of the DNA molecules are right handed, means the coiling of the helix is in the right direction. The right handed coiling is also known as positive coiling. All the four forms of DNA, viz., A, B, C and D are right handed.
Left Handed DNA:
The Z-DNA has left handed double helical structure. Since sugar and phosphate linkages follow a zigzag pattern in this DNA, it is also called as Z-DNA. This DNA is considered to be associated with gene regulation. This has a pitch of 4.5 nm and 12 base pairs per turn of helix.
Criteria # 3. Location:
Based on the location in the cell, DNA is of three types, viz., chromosomal DNA, cytoplasmic DNA and promiscuous DNA.
These are briefly described below:
Chromosomal DNA:
Mostly the DNA is found in the chromosomes. Such DNA is called chromosomal DNA or nuclear DNA in case of eukaryotes. The chromosomes are composed of DNA, histones and RNA. Thus, major amount of DNA is found in association with chromosomes.
Cytoplasmic DNA:
Some amount of DNA is also found in the cytoplasm especially in mitochondria and chloroplasts. Such DNA is referred to as cytoplasmic DNA, which plays an important role in the cytoplasmic inheritance. Cytoplasmic DNA has circular structure.
Promiscuous DNA:
Some DNA segments with common base sequence are found in chloroplasts, mitochondria and nucleus. This suggests that some DNA sequences move from one organelle to other. Such DNA is referred to as promiscuous DNA. The first case of movement of DNA from chloroplasts to mitochondria was reported in maize. Later on, such movement of DNA was reported in yeast and sea urchin. Now movements of DNA have been reported in several crop plants such as spinach, mungbean, maize and peas.
Criteria # 4. Structure:
On the basis of structure, DNA is of two types, viz., linear and circular as discussed below:
Linear DNA:
The DNA which has a thread like structure with both the ends free, is known as linear DNA. Such DNA is found in eukaryotes.
Circular DNA:
The DNA which has ring or circular shape structure is called circular DNA. The DNA molecules of bacteria and viruses are circular. It may be a covalently enclosed circle consisting of two unbroken complementary strands or it may be a nicked circle. When it is nicked circle, it may have one or more nicks (cuts) in one or both strands. The DNA of mitochondria and chloroplasts is also circular.
Criteria # 5. Repetition of Nucleotide Base Sequences:
On the basis of copies of nucleotide sequences, the chromosomal DNA is of two types, viz.,
(1) Repetitive DNA,
(2) Unique DNA and
(3) Palindromic DNA.
These are described below:
Repetitive DNA:
Most of the non-coding DNA having multiple repeats of the same nucleotides or base sequences are known as repetitive DNA. There may be many thousands of these copies present tandemly repeated (follow one another directly) and called as satellite DNA, when multiple copies found scattered in the genome is called as dispersed repetitive DNA (e.g., Alu elements in human). On the basis of the length of repeating sequence satellite DNA is of two types i.e. mini-satellites (variable number tandem repeats, VNTRs) and microsatellites (simple tandem repeats, STRs).
Repetitive DNA is found almost in all eukaryotes (except yeast) but almost negligible (0.3%) in prokaryotes. Such DNA is found near the centromere in the chromosome. The percentage of repetitive DNA varies from species to species. In many cases, the repeating sequences have different base composition from the remaining DNA. In such case, separation of repetitive DNA is very easy by way of ultra centrifugation.
Palindromic DNA:
A palindrome is a sentence that reads the same in forward and backward direction. As for example: ‘AND MADAM DNA’. Palindromic sequence of nucleotides is sometimes found in DNA. Such a DNA sequence is called palindromic DNA. This term was first used by Thomas et. al. (1973).
Criteria # 6. Coding and Non-coding DNA:
(i) Non-coding DNA:
Greater part of DNA in eukaryotic cells does not code for RNAs. This “extra” or non-coding DNA seems to have no function. The non-coding DNA has many base sequences repeated several times. The repeated sequences are collectively called repetitive DNA.
Some repetitive DNA sequences are not found at fixed sites in the DNA of different individuals of the same species. Such “mobile” DNA segments are often referred to as “jumping genes”. A jumping gene can make a copy of itself but the copy becomes incorporated in another part of the genome. The original gene remains in place and does not “jump”. Bacteria have very little non-coding DNA.
(ii) Coding DNA:
The coding DNA sequences (i.e., genes) lie in between non-functional DNA sequences. It is further of two types —
(a) Protein coding DNA:
It contains most of the genetic information. It codes for all the proteins other than histones.
(b) DNA coding for rRNA, tRNA and histones:
The DNA sequences that code for rRNA, tRNA and histones are repeated because these substances are needed in large amounts in the cells.
Criteria # 7. Number of Strands:
Based on the number of strands, DNA is of two types, viz., double-stranded DNA and single- stranded DNA as discussed below:
Double-stranded DNA:
The DNA which has spirally arranged double strands is known as double-stranded DNA. In most of the organisms including plants, animals and bacteria, DNA is double-stranded. Such DNA may be either linear or circular.
Single-stranded DNA:
The DNA with one helix is known as single stranded DNA. Such DNA has been reported in bacteriophage φ x 174.