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MOLECULAR
STRUCTURE OF DNA
Submitted to,
Dr. Arya P. Mohan
Assistant professor
Dept of Botany
St Teresa’s college
Submitted by,
Silpa Selvaraj
Roll no: 13
I M.Sc. Botany
St Teresa’s college
Overview
• DNA triplex.
• DNA quadruplex.
• I motif.
• Topoisomerases.
2
Non canonical structures of DNA
⮚Watson and Crick described the double helical structure of DNA in
1953.
⮚Double stranded DNA – B DNA.
⮚Non canonical DNA structures – DNA triplex and DNA
quadruplex.
⮚These non canonical structures are rare and are sometimes seen in
the cell.
3
Triplex DNA
• Triple stranded DNA.
• The third strand of DNA is formed at the major groove
of the DNA.
• Less stable structure.
❖Conditions for the formation of the third strand ;
▪ Low pH.
▪ Purine (A, G) ie, T-A-T , C-G-C
4
5
C = Watson & Crick base pairing.
⮚Triplex DNA forms due to the occurrence of additional hydrogen
bonds between the bases, especially during low pH.
⮚A=T, G
⮚Additional hydrogen bonds = Hoogsteen hydrogen bonds.
⮚At the major groove of the DNA, the third strand is seen which is
attached with the help of Hoogsteen hydrogen bonds.
⮚Thymine can form two Hoogsteen hydrogen bonds with the adenine
of A=T basepair to form T=A=T.
T, C =pyrimidine
A, G = purine
⮚Cytosine can also form two hydrogen bonds with guanine of G-C
base pair to form C-G-C.
⮚Triple helical structure is less stable than double helix.
⮚Due to negatively charged backbone strands in the triplex DNA, it
results in an increased electrostatic repulsion.
6
7
Triplex
DNA
• A and G have the ability to form
hydrogen bonds.
• Adenine – at C7, nitrogen is present –
forms H bond.
• At C6, NH2 – forms H bond.
• Guanine, at C7 , nitrogen present – forms
H bond.
• At C6, oxygen present – forms H bond.
8
T-A-T
C-G-C
DNA quadruplex
⮚Four stranded DNA.
⮚Less stable structure.
⮚Guanine is essential for the formation of quadruplex DNA.
⮚Guanine – ability to make maximum bonds.
⮚It can make up to 4 bonds – tetrameric bonds.
⮚The structure made using tetrameric bonds is called G-quartet (quadruplex
structure).
⮚This structure is found on the telomere.
⮚Large amount of guanine is present in the telomere and it forms the
tetrameric structure in a single plane.
9
Molecular structure of quadruplex DNA
10
Guanine
K +
• i-motif DNA = intercalated motif DNA.
• First discovered by Maurice Gueron in 1993.
• Cytosine rich four stranded DNA structure.
• This structure was originally found only in vitro, usually
at a slightly acidic pH – recently discovered in the nuclei
of human cells.
• It consists of two parallel-stranded duplexes intercalated
in an antiparallel orientation and held together by hemi-
protonated cytosine-cytosine+ (C:C+) base pairs
• Dr. Mahdi Zeraati mentioned that these complexes are
constantly forming and dissociating due to their
constantly changing temperatures.
11
An artist's impression of the i-motif
DNA structure inside cells, along with
the antibody-based tool used to detect
it. Image Credit: Chris Hammang /
Shutterstock
i motif
12
• Although the exact function of these structures is unknown, the
transient nature of these molecules give insight regarding their
biological functions.
• It is said that they are found primarily in the G1 phase and in the
promoter regions.
• Most of them are stable at slightly acidic Ph (4.2 – 5.2).
• Experiments are in progress to determine their role in
nanotechnology as biosensors and nanomachines.
DNA Supercoiling
• Unwinding of the helix during DNA replication results
in supercoiling of the DNA ahead of the replication fork.
• This supercoiling increases with the progression of the replication
fork.
• If the supercoiling is not relieved, it will physically prevent the
movement of helicase.
• Two types of DNA supercoiling processes are positive supercoiling
(clockwise manner) and negative supercoiling (Anticlockwise).
• Only the dsDNA supports supercoiling.
13
14
Topoisomerases
• Topoisomerases are the enzymes that can alter the topology of the
DNA.
• It was first found by J.C. Wang in the 1970s while working
on Escherichia coli. It was the type I topoisomerase.
• It can also be called DNA topoisomerase as it only acts on DNA
strands.
• They act by transiently by cutting one or both the strands of the
DNA.
• This transient break allows the DNA to be untangled or unwound
and at the end of these processes, the DNA backbone is resealed.
15
16
TOPOISOMERASES
TYPE I TYPE II
TOPOISOMERASE I TOPOISOMERASE III TOPOISOMERASE II
TOPOISOMERASE II α TOPOISOMERASE II β
In prokaryotes,
topoisomerase II is called as
DNA gyrase
TOPOISOMERASE I - MECHANISM
17
18
19
Topoisomerase II binds to the DNA.
Creates a double strand break.
Passes uncut DNA through the gap.
Reseals the break.
20
TOPOISOMERASE II - MECHANISM
Inhibitors of topoisomerase
▪ Two classes of bacterial topoisomerase inhibitors have been
developed as antibiotics.
▪ Class I – Coumarins – including Novobiocin and Coumermycin A1.
▪ They are derived from Streptomyces species.
▪ They inhibit the ATP binding of the bacterial type II topoisomerases.
▪ Class II – Quinolone antibiotics – inhibitors of DNA gyrase.
21
▪ Fluoroquinolones, ciprofloxacin Etc
▪ The quinolones act by blocking the last step of the topoisomerase
reaction.
▪ Camptothecin – isolated from Chinese ornamental tree – inhibitor of
eukaryotic type I topoisomerases.
▪ All of these drugs act by trapping the topoisomerase-DNA complex
such that they inhibit the religation process.
22
References
1. Avinash & Upadhyay, K. (2005). Basic molecular biology. Himalaya
Publishing House. Nagpur.
2. Karp, G. (2010). Cell biology. Cardiff University. Wales, UK.
3. Kumar, H.D. (2000). Molecular biology. Vikas Publishing House Pvt
Ltd. New Delhi.
4. Lehringer, (2017). Principles of biochemistry. W H Freeman &
company.
5. Rastogi, S.C. (2002). Cell biology. New Age International Publishers.
23
Thank you
24

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molecular structure of DNA: quadruplex ,DNA triplex, DNA i motif, DNA supercoiling, topoisomerases

  • 1. MOLECULAR STRUCTURE OF DNA Submitted to, Dr. Arya P. Mohan Assistant professor Dept of Botany St Teresa’s college Submitted by, Silpa Selvaraj Roll no: 13 I M.Sc. Botany St Teresa’s college
  • 2. Overview • DNA triplex. • DNA quadruplex. • I motif. • Topoisomerases. 2
  • 3. Non canonical structures of DNA ⮚Watson and Crick described the double helical structure of DNA in 1953. ⮚Double stranded DNA – B DNA. ⮚Non canonical DNA structures – DNA triplex and DNA quadruplex. ⮚These non canonical structures are rare and are sometimes seen in the cell. 3
  • 4. Triplex DNA • Triple stranded DNA. • The third strand of DNA is formed at the major groove of the DNA. • Less stable structure. ❖Conditions for the formation of the third strand ; ▪ Low pH. ▪ Purine (A, G) ie, T-A-T , C-G-C 4
  • 5. 5 C = Watson & Crick base pairing. ⮚Triplex DNA forms due to the occurrence of additional hydrogen bonds between the bases, especially during low pH. ⮚A=T, G ⮚Additional hydrogen bonds = Hoogsteen hydrogen bonds. ⮚At the major groove of the DNA, the third strand is seen which is attached with the help of Hoogsteen hydrogen bonds. ⮚Thymine can form two Hoogsteen hydrogen bonds with the adenine of A=T basepair to form T=A=T. T, C =pyrimidine A, G = purine
  • 6. ⮚Cytosine can also form two hydrogen bonds with guanine of G-C base pair to form C-G-C. ⮚Triple helical structure is less stable than double helix. ⮚Due to negatively charged backbone strands in the triplex DNA, it results in an increased electrostatic repulsion. 6
  • 8. • A and G have the ability to form hydrogen bonds. • Adenine – at C7, nitrogen is present – forms H bond. • At C6, NH2 – forms H bond. • Guanine, at C7 , nitrogen present – forms H bond. • At C6, oxygen present – forms H bond. 8 T-A-T C-G-C
  • 9. DNA quadruplex ⮚Four stranded DNA. ⮚Less stable structure. ⮚Guanine is essential for the formation of quadruplex DNA. ⮚Guanine – ability to make maximum bonds. ⮚It can make up to 4 bonds – tetrameric bonds. ⮚The structure made using tetrameric bonds is called G-quartet (quadruplex structure). ⮚This structure is found on the telomere. ⮚Large amount of guanine is present in the telomere and it forms the tetrameric structure in a single plane. 9
  • 10. Molecular structure of quadruplex DNA 10 Guanine K +
  • 11. • i-motif DNA = intercalated motif DNA. • First discovered by Maurice Gueron in 1993. • Cytosine rich four stranded DNA structure. • This structure was originally found only in vitro, usually at a slightly acidic pH – recently discovered in the nuclei of human cells. • It consists of two parallel-stranded duplexes intercalated in an antiparallel orientation and held together by hemi- protonated cytosine-cytosine+ (C:C+) base pairs • Dr. Mahdi Zeraati mentioned that these complexes are constantly forming and dissociating due to their constantly changing temperatures. 11 An artist's impression of the i-motif DNA structure inside cells, along with the antibody-based tool used to detect it. Image Credit: Chris Hammang / Shutterstock i motif
  • 12. 12 • Although the exact function of these structures is unknown, the transient nature of these molecules give insight regarding their biological functions. • It is said that they are found primarily in the G1 phase and in the promoter regions. • Most of them are stable at slightly acidic Ph (4.2 – 5.2). • Experiments are in progress to determine their role in nanotechnology as biosensors and nanomachines.
  • 13. DNA Supercoiling • Unwinding of the helix during DNA replication results in supercoiling of the DNA ahead of the replication fork. • This supercoiling increases with the progression of the replication fork. • If the supercoiling is not relieved, it will physically prevent the movement of helicase. • Two types of DNA supercoiling processes are positive supercoiling (clockwise manner) and negative supercoiling (Anticlockwise). • Only the dsDNA supports supercoiling. 13
  • 14. 14
  • 15. Topoisomerases • Topoisomerases are the enzymes that can alter the topology of the DNA. • It was first found by J.C. Wang in the 1970s while working on Escherichia coli. It was the type I topoisomerase. • It can also be called DNA topoisomerase as it only acts on DNA strands. • They act by transiently by cutting one or both the strands of the DNA. • This transient break allows the DNA to be untangled or unwound and at the end of these processes, the DNA backbone is resealed. 15
  • 16. 16 TOPOISOMERASES TYPE I TYPE II TOPOISOMERASE I TOPOISOMERASE III TOPOISOMERASE II TOPOISOMERASE II α TOPOISOMERASE II β In prokaryotes, topoisomerase II is called as DNA gyrase
  • 17. TOPOISOMERASE I - MECHANISM 17
  • 18. 18
  • 19. 19
  • 20. Topoisomerase II binds to the DNA. Creates a double strand break. Passes uncut DNA through the gap. Reseals the break. 20 TOPOISOMERASE II - MECHANISM
  • 21. Inhibitors of topoisomerase ▪ Two classes of bacterial topoisomerase inhibitors have been developed as antibiotics. ▪ Class I – Coumarins – including Novobiocin and Coumermycin A1. ▪ They are derived from Streptomyces species. ▪ They inhibit the ATP binding of the bacterial type II topoisomerases. ▪ Class II – Quinolone antibiotics – inhibitors of DNA gyrase. 21
  • 22. ▪ Fluoroquinolones, ciprofloxacin Etc ▪ The quinolones act by blocking the last step of the topoisomerase reaction. ▪ Camptothecin – isolated from Chinese ornamental tree – inhibitor of eukaryotic type I topoisomerases. ▪ All of these drugs act by trapping the topoisomerase-DNA complex such that they inhibit the religation process. 22
  • 23. References 1. Avinash & Upadhyay, K. (2005). Basic molecular biology. Himalaya Publishing House. Nagpur. 2. Karp, G. (2010). Cell biology. Cardiff University. Wales, UK. 3. Kumar, H.D. (2000). Molecular biology. Vikas Publishing House Pvt Ltd. New Delhi. 4. Lehringer, (2017). Principles of biochemistry. W H Freeman & company. 5. Rastogi, S.C. (2002). Cell biology. New Age International Publishers. 23