This document provides information about DNA structure and types. It begins with a timeline of important discoveries in DNA research. It then discusses the primary and secondary structures of DNA, including the double helix model proposed by Watson and Crick. It describes Chargaff's rules and the complementary base pairing of A-T and G-C. Finally, it summarizes the different forms of DNA like A, B, and Z-DNA and discusses mitochondrial DNA and unusual DNA sequences.

1. Past Inquiries
1.Why do children sometimes
resemble their parents?

2. Past Inquiries
2.What process do people use to
test if they're the biological
parents?

3. Dad + Mom = ?

4. Based on the pictures of
the parents, describe what
their child will look like.

9. DNA
STRUCTURE

10. LESSON OBJECTIVES
1.Conduct DNA denaturation using
tomatoes; and
2.Understand the structure of DNA.

11. DNA
Denaturation

12. Conduct an experiment
entitled DNA denaturation by
following the procedure
shown in the video.

13. • History
• Introduction
• Complementary Base
pairing

14. TIMELINE
Friedrich Miescher : identified the “nuclein” by isolating a
molecule from a cell nucleus that would later become known as DNA
Albrecht Kossel, who is credited with naming DNA, identified nuclein as a nucleic acid. He also
isolated those five nitrogen bases : adenine (A), cytosine (C), guanine (G), thymine
(T) and uracil (U)
Avery, McCleod & McCarty- Transforming principle is DNA. i.e carrier of genetic
information.
Erwin Chargaff :Chargaff ’s Rules, proved that guanine = cytosine , as well as adenine= thymine .
Sum of Purine is equal to sum of Pyrimidine
Roslind Franklin’s work in X-ray crystallography, started taking X-ray diffraction photographs
of DNA. Images showed the helical form, which was confirmed by Watson and Crick nearly
two years later.
J Watson and F Crick :published on DNA’s double helix structure that twists to form
the ladder-like structure
1869
1881
1944
1950
1951
1953

15. • DNA is a polymer of
deoxyribonucleoside
monophosphates covalently
linked by 3′→5′– phosphodiester
bonds
• Found in chromosomes,
mitochondria and
chloroplasts
DNA: Deoxyribonucleic
Acid

16. • Genetic Information (Genetic Blue
Print):
DNA contains the genetic instructions
necessary for the development, growth,
functioning, and reproduction of all
known living organisms.
SAMPLE FUNCTIONS OF DNA

17. 2. Protein Synthesis:
DNA provides the instructions for
protein synthesis through a process
called gene expression. Genes,
segments of DNA, are transcribed into
RNA, which is then translated into
proteins.
SAMPLE FUNCTIONS OF DNA

18. The Primary
structure of
DNA is
Sequence

19. The secondary structure of DNA is the double
helix

20. • DNA double helical structure coils round Histones.
• DNA bound to histones forms NUCLEOSOMES
(10nm FIBRES)
• Nucleosomes contain 146 nucleotides

22. DNA STRUCTURE: Watson &
Crick
Double helix
• In 1953 Watson and
Crick postulated a three
dimensional model of
DNA structure
⚬ which consists of two
helical DNA chains
￭ wound around the
same axis to form
a right handed double
helix

23. Double helix
• Each strand has :
• The hydrophilic
backbones of alternating
deoxyribose and
phosphate groups on the
outside of the double helix
⚬ facing the
surrounding water
DNA STRUCTURE: Watson &
Crick

24. DNA STRUCTURE: Erwin Chargaff
• Most important clue to the structure of DNA
came from the work of Erwin Chargaff and
his colleagues in the late 1940s.
• The base composition of DNA generally
varies from one species to another.

25. DNA STRUCTURE: Erwin Chargaff
• In all cellular DNAs, the number of adenosine
residues is equal to the number of thymidine
residues (that is, A=T), and the number of
guanosine residues is equal to the number
of cytidine residues (G=C).
• GCAT
• A+G = T+ C.

26. BASE PAIRING
• Purines -
adenine (A)
and guanine (G)
• Pyrimidines -
cytosine
(C) and thymine (T)
• The two strands
are
complementary
• DNA double helix is
held
together by 2 forces
• H-bonding between
complementary base
pairs
• van
der
interactions
stacked
bases
Waals
between

27. Major groove :
• Sequence-specific interactions
⚬ provide access for the binding of regulatory proteins
￭ Maintained by hydrogen bonds, ionic interactions and van der Waals
forces.
Minor groove
• Offers the highest sequence specificity binding between a small molecule and DNA
⚬ To disrupt the specific gene expression
￭ Certain anticancer drugs, such adactinomycin (actinomycin D), exert their
cytotoxic effect by intercalating into the narrow groove of the DNA double
helix, thus interfering with DNA synthesis
• Compared to minor
groove
binding,
interactions between small molecules and
the DNA major groove have not been
extensively explored.

28. DIFFERENT 3-DIMENSIONAL FORMS OF
DNA
• DNA is a remarkably flexible.
⚬ Considerable rotation is possible around several types of bonds
⚬ Thermal fluctuation can produce bending, stretching and unpairing
(melting) of the strands.
The structural variations reflect 3 things:
⚬ Different possible conformations of deoxyribose
⚬ Rotation about the contiguous bonds that make up
the phospho- deoxyribose backbone
⚬ Free rotation about C-1’-N glycosyl bond

29. VARIOUS TYPES OF
DNA
• At least 6 different forms of DNA (A-E, Z) have been found
out.
⚬ Amongst these, A,B,Z are predominant.
• The Watson-Crick structure is also referred to as B form
DNA, or B DNA.
⚬ Most stable structure for a random-sequence DNA molecule
under physiological conditions
￭ Therefore the standard point of reference in any study of the
properties of DNA.

30. A-
DNA
• X-ray diffraction studies of less-hydrated DNA fibers revealed a A
form DNA
• When the relative humidity of B-form DNA falls to less than
75%,
o the B-form undergoes a reversible transition into the A-form of DNA
• It is also a right-handed helix
⚬ Helix is wider ,
⚬ Number of base pairs per helical turn is 11
⚬ The plane of the base pairs is tilted about 20° with respect to the
helix axis.
• In A-DNA, C-3’ lies out of the plane (a conformation referred
to as C-3’endo) formed by the
other four atoms of the ring

31. Z-
DNA
• Z-DNA is a left handed helix containing 12 base pairs per turn.
• To form the left-handed helix in Z-DNA
o the purine residues flip to the synconformation, alternating with pyrimidines in
the anti conformation.
owhenthe sequence of
nucleotides purine/pyrimidine
stretches- form, Z-DNA
• is also favored at high ionic concentrations
consists of
alternating
• DNA with a zigzag configuration along the sugar phosphate
backbone.
o hence named Z-DNA
• The major groove is barely apparent in Z-DNA, and the minor groove
is narrow and deep.
• The Z-DNA tracts may play a role (as yet undefined) in regulating
the
expression of some genes or in genetic
recombination.

32. • Blue: sugar phosphate
backbone
• Yellow: for pyrimidines
(thymine and cytosine)
• brown for
purines (adenine and
guanine)

33. COMPARISON OF DIFFERENT FORMS OF DNA
Ref: Lehninger Principles of Biochemistry

35. • Observed at some conditions such as
relatively low humidity and the presence of
certain ions, such as Li+ or Mg2+
• Not very stable and Not very common.
• Right handed helice
• Has 9 base pairs per turn of spiral
• Has diameter of 19A°,smaller than that
of A-&B- DNA.
• The tilt of base is 7.8°

36. • Extremely rare variant with only 8base pairs per helical
turn .
• This forms of DNA found in some DNA molecules devoid
of guanine.
• Axial rise of 3.03A°per base pairs .
• Tilt of 16.7° from axis of helix

37. • E-DNA - extended &eccentric double helix
⚬ Cytosine methylation of or bromination of DNA
sequence d(GGCGCC)₂
• E-DNA has a long helical axis rise and base
perpendicular to the helical axis.
• Deep major groove and shallow minor groove.
• E-DNA allowed to crystallize for a period time
longer, the methylated sequence forms
standard A-DNA.

38. • E-DNA is the intermediate in the transition to A-
DNA.
• E-DNA is the intermediate in the
crystallographic pathway from B-DNA to A-DNA

40. • Mitochondria also have a small amount of their own DNA.
⚬ mitochondrial DNA
• In humans, mitochondrial DNA spans about 16,569 DNA
building blocks (base pairs)
• Mitochondrial DNA contains 37 genes,
⚬ Thirteen of these genes
￭ Provide instructions for making enzymes involved in oxidative
phosphorylation.
⚬ The remaining genes
￭ Provide instructions for making molecules called transfer RNA
(tRNA) and ribosomal RNA (rRNA), which are chemical cousins of
DNA.

41. Mitochondrial DNA Nuclear DNA
Location Mitochondria Cell Nucleus
Copies per somatic cell 100-1,000 2
Structure Circular and closed Linear and open ended
Membrane enclosure
Not enveloped by a
membrane
Enclosed by a nuclear
membrane
Genome size
1 chromosome with 16,569
base pairs
46 chromosomes with 3.3
billion base pairs
Number of genes 37 genes 20,000-25,000 genes
Method of inheritance Maternal Maternal and Paternal
Method of translation
Some codons do not follow
universal codon pattern
Follows universal codon
pattern
Method of transcription Polycistronic Monocistronic

42. SATELLITE DNA
• Originally identified as a subfraction of DNA with a
buoyant density slightly lower than that of genomic DNA
⚬ because of its higher content of AT base pairs.
• Consists of clusters of short, species-specific, nearly
identical sequences that are tandemly repeated hundreds
of thousands of times.
• These clusters lack protein-coding genes
⚬ Found principally near the centromeres of chromosomes.
• Two types
⚬ Microsatellite sequences
￭ 1-6 bp repeat units flanked by conserved sequences
⚬ Minisatellite sequences
￭ 11-60 bp flanked by conserved restriction sites.
• Used for DNA matching or finger printing as first found
out by Jeffreys et al (1985).

43. • Viral DNA (and in some, RNA)
⚬ Some circular, some linear
⚬ Some double stranded, some single stranded
⚬ Very small amount, packed very tightly
⚬ Small size is an advantage
⚬ Viruses use host cell enzymes, need few genes
• Bacterial DNA
⚬ Usually single copy of double stranded
⚬ Usually circular
• Eukaryotic DNA
⚬ Linear, in several pieces

44. UNUSUAL SEQUENCES
/ STRUCTURES OF DNA
• Important for molecular recognition of DNA
by proteins and enzymes
• Bent DNA:
• Bends occur in the DNA helix
wherever four or more adenosine residues appear sequentially
in one strand.
• Cause a collapse of the helix into the
minor groove.
• Six adenosines in a row produce a bend of about 18°.
• Drugs, photochemical damage, mispairing of bases can also
produce

45. • DNA duplex possesses areas where sequence of nucleotides is the
same but opposite in the two strands.
• These sequences are recognized by restriction endonucleases and
are used in genetic engineering.
• It is similar to palindrome words having same words in both
forward and backward direction, e.g., NITIN, MALAYALAM
• When the inverted repeat occurs within each individual strand
of the DNA, the sequence is called a mirror repeat.

46. • Palindromic DNA sequences can form alternative
structures with intrastrand base pairing.
⚬ (a) When only a single DNA (or RNA) strand is involved, the
structure is called a hairpin.
⚬ (b) When both strands of a duplex DNA are involved, it is called a
cruciform.

47. TRIPLEX DNA/
TRIPLE
STRANDED DNA
• Due to additional H-bond between bases particularly
with functional groups arrayed in the major groove.
• The bonds are called as Hoogsteen H-bonds
• The non-Watson-Crick pairing is called Hoogsteen
pairing, after Karst Hoogsteen, who in 1963 first
recognized the potential for these unusual pairings
• Triple helical structure is less stable than double
helix - increased electrostatic repulsion.

48. G-TETRAPLEX / FOUR STRANDED
DNA
• High content of Guanine – form tetrameric structure called G-quartets.
• These structures are planar & are connected by Hoogsteen hydrogen
bonds.
• Eukaryotic chromosomes - Telomeres are rich in guanine - forms G-
tetraplexes.
Ref: Lehninger Principles of Biochemistry

50. • Type of deoxyribonucleic acid, discovered in cell
nuclei in 2018,
⚬ that is found in the nuclei of human cells.
• I-motifs are four-stranded quadruplex
structures formed by cytosine-rich DNA.
⚬ C-rich DNA regions are common in gene regulation
portions of the genome.
(Zeraati et al., Nat Chem, 2018)

51. • Postulated to play a role in gene regulation and
expression in the cell
• I-motifs have potential applications in nano-
technology
and nano-medicine,
⚬ because size is more than 1nm and less than 100nm due to
their unique pH sensitivity
• Have been used as biosensors, nanomachines, and
molecular switches.

52. Nucleic Acids Research, Volume 30, Issue 21, 1 November 2002, Pages 4618–4625, https://doi.org/10.1093/nar/gkf597
The content of this slide may be subject to copyright: please see the slide notes for details.
FIGURE 6. SOME POSSIBLE MODELS OF DUPLEX, I‐MOTIF AND G‐QUADRUPLEX
ASSOCIATION FOR THE HUMAN TELOMERE ...

53. NUCLEIC ACID
CHEMISTRY
• Thechemical transformations that do occur are
generally very low in the absence of an enzyme catalyst.
• Understanding the nucleic acid chemistry gives us:
⚬ Powerful array of technologies that have applications in molecular
biology, medicine & forensic medicine.
• DENATURATION
• Disruption of the hydrogen bonds between paired bases
and of base stacking
⚬ causes unwinding of the double helix to
form two single
strands,
￭ completely separate from each other along the entire length
or part of length

54. DENATURATION
• Causes:
⚬ Extreme pH,
⚬ Temperature above 80 ̊C,
⚬ Chemicals such as formamide and urea
• Hyperchromic effect
⚬ Denaturation of a double stranded nucleic acid produces an increase
in absorption of UV light
￭ Relative to that of a solution with the same concentration of paired
complementary nucleic acid strands
⚬ The transition from double stranded DNA to the single stranded
denatured form can be detected by monitoring UV absorption at
260nm

55. DENATURATION
43
Each species of DNA has a characteristic
denaturation temperature or melting poin
Melting temperatures (Tm) of DNA
molecules with different nucleotide
compositions

56. ANNEALIN
G
• Process by whichseparated complementary
strands form a double helix
• Occurs when the temperature and pH is returned to the
range in which most organisms live
• Rapid one step process
⚬ If double helical segment of a dozen or more residues still
unites the two strands

57. ANNEALING
• If the two strands are completely separated, renaturation
occurs in two steps
• First step:
⚬ Slow, the two strands find each other by random collisons
￭ Form a short segment of complementary double helix
• Second step:
⚬ Faster, the remaining unpaired bases successively
come into register as base pair
￭ The two strands unite to form double helix

58. Fig :Reversible denaturation and
annealing (renaturation) of DNA.
Ref: Lehninger Principles of Biochemistry

59. ORGANIZATION OF DNA
• A segment of DNA molecule that contains the
information required for the synthesis of a functional
biological product (RNA or protein) is called gene
• A cell has many thousands of genes and so the DNA
molecules are very large
• Large DNA molecules must be packaged in such a way
that they can fit inside the cell and still be functional

60. ORGANIZATION OF DNA
• Nuclear DNA in eukaryotes is found in chromatin associated with
histones and non histone proteins

61. ORGANIZATION OF DNA
• DNA (negatively charged) loops twice around the histone octamer to
form nucleosomes (series of nucleosomes: beads on a string)
• Histone H1 is associated with the linker DNA
found between nucleosomes to help package them into a
solenoid like structure
• Further condensation occurs to eventually form the chromosome.

62. ORGANIZATION OF DNA
Polynucleosomes(nucleofilaments)

63. REFERENCE
S
• Lehninger Principle of Biochemistry 4th edition
• Robert k. Murray, D.K.Granner ,P.A.Mayes & Victor W.Rodwell Harpers
illustrated biochemistry 26th edition
• Lubert Stryer, Jeremy M. Berg , John L. Tymoczko Biochemistry, 4th
edition
• Lippincott’s Illustrated Reviews: Biochemistry, 4th Edition
• https://www.lunadna.com/blog/history-of-dna/
• http://www.biologydiscussion.com/dna/dna-types-structure-and- function-
of-dna/1301
• http://www.differencebetween.net/science/difference-between-
mitochondrial-dna-and-nuclear-dna/
• https://bio.libretexts.org/Bookshelves/Genetics/Book%3A_Working_with
_Molecular_Genetics_(Hardison)/Unit_I%3A_Genes%2C_Nucleic_Acids
%2C_Genomes_and_Chromosomes/2%3A_Structures_of_Nucleic_Acids/
2.5%3A_B-Form%2C_A-Form%2C_and_Z-Form_of_DNA
• https://www.ncbi.nlm.nih.gov/pubmed/10966645
• https://academic.oup.com/nar/article/30/21/4618/1105212