This presentation consists of basic understanding of DNA structure

1. DNA STRUCTURE:
STRUCTURE OF –A,-B,-Z, -P DNA AND
TRIPLEX DNA
Done By: Angela Grace Abraham

2. INTRODUCTION
o DNA- Discovered by Francis Crick and James Watson in 1953-
Nobel Prize
o DNA- combination of nitrogenous bases, sugar molecules and
phosphate groups that are linked by different bonds in a series of
sequences.
o The DNA structure defines the basic genetic makeup of our body.
• Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are four
types of nitrogen bases.
• These base pairs are essential for the DNA’s double helix
structure, which resembles a twisted ladder.

3. o The two strands of DNA run in opposite directions.
o These strands are held together by the hydrogen bond that is present
between the two complementary bases.
o The strands are helically twisted, where each strand forms a right-
handed coil, and ten nucleotides make up a single turn.
o The pitch of each helix is 3.4 nm.
o Hence, the distance between two consecutive base pairs (i.e.,
hydrogen-bonded bases of the opposite strands) is 0.34 nm.
Chargaff’s Rule:
Nitrogenous bases in the DNA was present in equal quantities. The
amount of A is equal to T, whereas the amount of C is equal to G.

4. STRUCTURE AND TYPES OF DNA
Why is DNA a helix?
Helix comes from the stacking of the individual bases on top of
one another. Both the sugar and phosphate which constitute the
backbone are quite soluble in water.
However, the DNA bases which are in the middle of the helix
are relatively hydrophobic and insoluble. Reason for a helix in
DNA is primarily due to the hydrophobic stacking interactions of
the bases.
• -A form
• -B form
• -Z form
• -P form
• Triplex DNA

5. -B DNA
• The double helix that most people are familiar with the right-sided figure.
• Strands are held together by H bonding between the bases (in anti-
conformation).The two strands of the duplex are antiparallel and
plectonemically coiled.
• The nucleotides arrayed in a 5' to 3' orientation on one strand align with
complementary nucleotides in the 3' to 5' orientation of the opposite
strand.
• B-form is the most common form, stable form, present in most DNA at
neutral pH and physiological salt concentrations.
• The two helices are wound in such a way so as to produce to interchain
spacing or groove.These grooves provide surface with which protein,
chemicals, drugs can interact

6. -A DNA
• It was discovered by Rosalind Franklin, who also named the A and B forms.
• She showed that DNA is driven into the A form when under dehydrating
conditions.
• It is right handed helix, displaced away from the central axis and closer to
major groove, ribbon like helix with more open cylindrical core in A- form.
• Such conditions are commonly used to form crystals, and many DNA crystal
structures are in the A form.
• The same helical conformation occurs in double-stranded RNAs, and in
DNA-RNA hybrid double helices.
• The A-DNA helix is a bit wider than B-DNA

7. • A-DNA helix being less stable than the B-DNA conformation. A-DNA is also more rigid
than B-DNA, again because the off-centre stacking of the bases makes them less flexible.
• An A-helix is the common form due to the extra OH group on the ribose sugar, which
cannot fit easily into the tight space allotted to it in B-DNA.
• The A conformation is favoured in triplex DNA.
• A transition from B-DNA to A-DNA has been postulated to occur during transcription,
where the RNA–DNA hybrid would be more stable in the A-conformation.

8. -Z DNA
• The backbone of the left-handed helix takes on a zigzag appearance and is more
elongated. Z-DNA is a transient form of DNA, only occasionally existing in response
to certain types of biological activity.
• It can form when the DNA is in an alternating purine- pyrimidine sequence such as
GCGCGCG and C nucleotides are in different conformations, leading to the zig-zag
pattern
• There are 12 base pairs per helical turn
• The purine adopts a syn conformation while the pyrimidine is in the anti conformation.
• The major groove is barely apparent but minor groove is deepen yet narrow
• Does exist in vivo though not abundantly. Certain proteins bind very strongly to Z-DNA,
suggesting that Z-DNA plays an important biological role in protection against
viral disease

9. COMPARISON OF DIFFERENT HELICAL PARAMETERS

10. -P DNA
• This new structure has a helical periodicity of 2.6 bp/turn and an extension
≈75% longer than B-DNA.
• Molecular modeling indicates that the phosphate backbones lie inside this
helical structure whereas the bases are exposed on the outside.
• This surprising structure, which we term P-DNA, thus shares features of the DNA
that resembles a structure for interwound single-stranded DNA.
• The expelled bases are relatively free to rotate. Depending on the sequence
modeled, both stacking and hydrogen bonding between adjacent bases can
occur, and certain purines were seen to move to syn conformations to favor such
interactions.
• Structures which were reached after passing though a completely unwound
state, strongly resembled their right-handed analogues.

11. TRIPLEX DNA
• A DNA triplex is formed when pyrimidine or purine bases occupy
the major groove of the DNA double Helix forming Hoogsteen pairs
with purines of the Watson-Crick basepairs.
• Intermolecular triplexes are formed between triplex forming
oligonucleotides (TFO) and target sequences on duplex DNA.
• Intramolecular triplexes are the major elements of H-DNAs, unusual
DNA structures, which are formed in homopurine-homopyrimidine
regions of supercoiled DNAs.
• Since there are 3 strands present, many phosphates groups and
higher negative charge are along it. This increases the
electrostatic repulsion. Therefore seen only in certain rare cases like
gene regulation, as promoter etc

12. REFERENCES
• NIH- National Human Genome Research Institute
• Discovery of DNA Structure and Function: Watson and Crick
By: Leslie A. Pray, Ph.D. © 2008 Nature Education
• Stretched and overwound DNA forms a Pauling-like structure with exposed bases J.
F. Allemand, D. Bensimon, R. Lavery, and V. Croquette
• DNA Structure: A-, B- and Z-DNA Helix Families David W Ussery, Danish Technical University, Lyngby
• DNA structure and types- Anurag Gupta/ SlideShare
• https://www.genome.gov/deoxyribonucleicacid

13. THANK YOU!!