A narrative review assignment on Principle of DNA structure, replication and how it affects plant breeding Submitted to: Assoc. Professor Tigist Abebe (PhD) Bahir dar university College of agriculture and environmental sciences Department: Plant Sciences Program: Plant Breeding and Genetics, Bahir Dar Ethiopia

1. Presentation type: Narrative review
Name: Gedifew Gebrie
Bahir dar university
College of agriculture and environmental sciences
Department: Plant Sciences
Program: Plant Breeding and Genetics (PhD)
24-Feb, 2023
Principle of DNA structure, replication
and how it affects plant breeding

2. Outlines
1. Introduction
2. Structure of DNA
3. DNA replication
4. Significance of DNA in plant breeding
5. Conclusion

3. Objective
Creating a readable cumulative synthesis of the best
resources available in the literature regarding to DNA
structure, replication and its significance in plant
breeding.

4. 1. Introduction
DNA is a biological molecule, responsible for carrying and
transmitting genetic information vertically from generation to
generation and horizontally across species barriers (Bencko
and Sima, 2018).
It is a polymer of nucleotides containing:
o Deoxyribose (5-carbon sugar)
o Phosphate group, and
o 4 nitrogen-containing bases (A, G, T and C)

5. 1. Introduction (Cont.)
 Based on its location and function DNA can be classified as:
o Nuclear DNA
o Mitochondrial DNA
o Ribosomal DNA and
o Chloroplast DNA

6. 2. The structure of DNA
DNA is composed of two complementary polynucleotide
chains running in opposite directions:
oThe polynucleotide chains coil around each other to form
a double helical structure and are connected by hydrogen
bonds between the base pairs and each composed of:
• Phosphate group
• Pentose sugar, and
• 4 Nitrogen-containing bases

7. 2. The structure of DNA (cont.)
•The 1st C to the nitrogenous
base by N-glycosidic linkage.
•The 3rd C to phosphate group
by phospho-diester bond.
•Sugar + phosphate = solid
backbone of polynucleotide
•Sugar + phosphate + N-base
= polynucleotide chain.
Figure: Components of a Polynucleotide Chain

8. 2. The structure of DNA (Cont.)
 A = Nucleotide: An organic molecule containing a
nitrogenous base, pentose sugar and phosphate.
 B = Base Pairs: Two nitrogen-containing bases that
pair together to form the structure of DNA.
 C = Weak hydrogen bond: holds the two strands
of DNA together.
 Phosphate group: allows the bases to produce
proteins and be passed on to new cells.
 D = Sugar-Phosphate back bone: Provides
structural support to the molecule.
 A deoxy-ribose sugar.
Figure 1: A double helix structure of DNA (Credited from: Encyclopedia Bratinica.Inc)
B B
A
C
D

9. 2. The structure of DNA (Cont.)
Figure 2: The structure of four nitrogen containing bases of DNA molecule
 The nitrogen-containing bases are grouped as Purines (double
ringed bases) and Pyrimidines (single ringed bases).

10. 2. The structure of DNA (Cont.)
The weak hydrogen bonds enable replication and transfer of
genetic information from parents to offspring.
The double helical structure of DNA physically protects the
nucleotides from being exposed to chemical modification due
to environmental influences (Baranello et al., 2018).
The sugar-phosphate backbone forms the structural
framework of the DNA molecule (Sinden, 1994).

11. 2. The structure of DNA (Cont.)
The sequence of bases along the DNA’s backbone encodes
biological information, such as instructions for making a
protein or RNA molecule (NHGRI, 2022).
Depending on the environment and number of base pairs per
turn, DNA can be found in several forms (Planat et al, 2022):
o A-DNA
o B-DNA: the most commonly known and widely studied
o Z-DNA

12. 2. The structure of DNA (Cont.)
Characteristics B-Form A-Form Z-Form
Helix sense Right Handed Right Handed Left Handed
Base pairs per turn 10 11 12
Helix width 2nm 2.3nm 1.8nm
Conformation of the
Deo-xyribose sugar
C2' endo
conformation
C3' endo
conformation
C3' endo
conformation
Sources:
•https://bio.libretexts.org/Bookshelves/Genetics/Book%3A_Working_with_Molecular_Genetics
•https://www.google.com/search?q=Comparisons+of+B-form%2C+A-form+and+Z+DNA
Table 1. Comparisons of B-form, A-form and Z DNA forms

13. 2. The structure of DNA (Cont.)
Figure 3: Different proposed structural forms of DNA with x-ray analysis of DNA crystals
Source:
https://geneticeducatio
n.co.in/dna-
deoxyribonucleic-acid-
definition-structure-
function-evidence-and-
types/

14. 2.1. Research over view on structure of DNA
 1869, Friedrich Miescher
o The first crude purification of DNA with its properties and
composition showing that it is fundamentally differed from
proteins (Dahm, 2005) while investigating ‘nuclein’.
 Between 1885 and 1901, Albrecht Kossel
o Identified ‘nuclein’ as a nucleic acid and confirmed that it is
composed of 5 nitrogenous bases: A, C, G, and T which is
replaced by U in RNA (Albrecht, 2023; Britannica, 2022).

15. 2.1. Research over view on structure of DNA (Cont.)
 In 1882, Walther Flemming
o Realized that chromosomes have to double before they can
divide (Luna, 2019; Maderspacher, 2008).
 In 1951, Roslind Franklin
o Identify the DNA’s helical form of X-ray diffraction photographs
using X-ray crystallography (Cramer, 2020).
 In 1953, James D. Watson and Francis Crick
oDemonstrated the molecular structure of DNA and described DNA
as a double helix (Hernandez, 2020).

16. 2.1. Research over view on structure of DNA (Cont.)
 In 1953, James D. Watson and Francis Crick…
o Stated that each antiparallel long helical strand contains a chain
of repeating units called nucleotides (Von, 2004).
oEach nucleotide composed of a five carbon sugar, a phosphate
group, and a nitrogen containing bases (Hernandez, 2020).
oConfirmed that the nucleotides are arranged on the inside of
each strand (Franjic, 2022).
oStated that two strands are joined together by hydrogen bonds
between the base pairs, provides stability to the helix (𝐀𝐓, 𝐂G).

17. 2.1. Research over view on structure of DNA (Cont.)
Credited from:
•https://collection.scien
cemuseumgroup.org.uk
/objects/co146411/crick
-and-watsons-dna-
molecular-model
•https://www.thedrinks
business.com/2017/02/
on-this-day-1953-
discovering-dna
Figure 4: Watson and Crick with their DNA model

18. 2.1. Research over view on structure of DNA (Cont.)
Figure 5: Detailed page of the Watson-Crick structure of DNA and its double helix
Credited from:
https://mammothmemory.net/biology/
dna-genetics-and-inheritance/dna-
base-pairing/dna-double-helix.html

19. 3. DNA Replication
DNA replication is the process of producing two identical copies
of new DNA molecules from one original double stranded DNA.
oEach strand of the original DNA serves as a template for the
production of complementary strand (Simion, 2018).
oOccurs in all living organisms and allows genetic inheritance
(Chaudhry and Khaddour, 2021) through the help of several
enzymes (Kahn-Academy, 2022).

20. Table 2. List of enzymes and protein complexes and their roles in
DNA replication
PCNA –Proliferating (increasing) cell nuclear antigen.
Over winding)

21. 3. DNA Replication (Cont.)
Figure 6: Mechanisms of DNA replication with the action of different enzymes and Proteins

22. 3. DNA Replication (Cont.)
With the discovery of structure of DNA using the Watson-Crick
model, three basic modes of DNA replication was proposed as
(Javed, 2008):
A. Semi-conservative
B. Conservative, and
C. Dispersive modes of replication

23. 3. DNA Replication (Cont.)
A. Conservative mode of DNA replication:
oThe original DNA strands stay associated with each other, while
the new DNA strands form a new double-helix (Wong, 2021).
oThe parent DNA is conserved, and a single daughter double helix
is produced (Portin, 2014).
B. Dispersive replication:
oResults in two DNA molecules which are hybrids of parental and
daughter DNA (Kahn-Academy, 2022).

24. 3. DNA Replication (Cont.)
C. Semi-conservative replication:
o Universally accepted mode of DNA replication .
oThe two single strands separate and each acts as a template for
the synthesis of a new strand of DNA (Amin, 2019).
oEach new copy of the double-stranded DNA contains one original
strand and one newly replicated strand (Gair & Molnar, 2015).

25. 3. DNA Replication (Cont.)
Figure 7: The three Proposed Models of DNA Replication

26. 3.1. DNA replication in prokaryotic and eukaryotic cells
Commonly:
oIt occurs before nuclear division through semiconservative
patterns, in a 5' to 3' direction with similar stages (Taylor, 2023).
oDNA polymerase coordinates the synthesis of new DNA strands.
oIt is initiated using a short RNA primer (Mokobi, 2022).
oThe primer binds to the 3' end of the strand as the starting point
for replication and generated by DNA primase (Bailey, 2019).

27. Table 3: Main differences b/n prokaryotic and eukaryotic DNA
replication
Prokaryotic Replication Eukaryotic Replication
Takes place in the cytoplasm of the cell Occurs in the nucleus of cell
It is a continuous process. occurs in the S-phase of cell cycle.
Each DNA molecule has a single place of
origin
A single DNA molecule has several sites of
origin
The replication origin has more nucleotides Each replication origin has less nucleotides
Bidirectional, and only two replication forks
are created
In multiple replication bubbles, many
replication forks develop
There is just one replicon There are approximately 50,000 replicons
The Okazaki fragments are huge and longer The Okazaki fragments are tiny and shorter
Faster Slower
Sources:
• https://byjus.com/biology/difference-between-prokaryotic-and-eukaryotic-replication/
• https://unacademy.com/content/neet-ug/difference-between/prokaryotic-and-eukaryotic-replication/

28. 3.2. Eukaryotic DNA Replication
Eukaryotic DNA replication is more complex than prokaryotes’
due to differences in:
o DNA sizes
o Its unique linear DNA end structures called telomeres
• The telomeres protect the chromosome ends from
DNA degradation, recombination, and DNA end fusions
(Pfeiffer and Lingner, 2013)

29. 3.2. Eukaryotic DNA Replication (Cont.)
o Its distinctive DNA packaging, involves complexes with histones
(Bhagavan and Chung-Eun, 2015).
• The histones regulate the structural organization of the DNA
by compressing it within the nucleus to form chromatin.
• The chromatin provides a platform for regulating gene
transcription (Sudhir and Leman, 2020).
Eukaryotic DNA replication involves three different replication
processes (Moreno and Gambus, 2020). :
• Initiation, Elongation, and Termination

30. Initiation
 The starting action of DNA replication which involves:
o Recognition of the replication origins
o Assembly of the pre-replication complexes
o Activation of replicative DNA helicase, and
o Loading of pre-replicative enzymes by origin recognition
protein complex (ORC) (Ekundayo and Bleichert, 2019).
o The pre-replicative enzyme activates the unwinding events of
DNA double helix (Pray, 2008).

31. Initiation (Cont.)
The DNA helicase facilitates the unwinding of DNA double
helix strands in the 5’ to 3’ direction (Malone et al., 2022).
Exposes each of the two strands to be used as a template for
replication.
o The main events at the initiation stage of DNA replication,
called as the stage of DNA replication fork formation (Dovey,
2022).

32. Initiation (Cont.)
o Forms the classical bi-directional Y-shaped replication forks:
• One strand is oriented in the 3' to 5' direction (leading
strand) while the other is oriented in the 5' to 3' (lagging
strand).
• The 5' end has a phosphate (P) group attached, while
the 3' end has a hydroxyl (OH) group attached.

33. Initiation (Cont.)
Figure 8: Initiation stage of eukaryotic DNA replication at the early G1-phase of cell division
Credited from: Fundamentals of Cell Biology/Chapter 14-DNA Replication (https://alg.manifoldapp.org)
 The origin recognition complex (ORC) is a
protein complex binds to DNA at
replication origin sites and serves as a
scaffold (support ) for the assembly of
other key initiation factors.
 A pre-replication complex (pre-RC) is a
protein complex that forms at the origin of
replication during the initiation of DNA
replication (ORC, Cdc6 (cell division cycle
6), CDT1 (chromatin licensing and DNA
replication factor 1), and the helicase.)

34. Beginning of DNA Replication
The DNA primase synthesizes the RNA primer (RNA polymerase).
The RNA primer acts as a ‘kick-starter’ for DNA polymerase,
creating and expanding new DNA strands (Dovey, 2022).
o The RNA primer "walks" along the original DNA strand, in
the 3' to 5' direction and forms a new strand as the starting
point for replication.
o The DNA polymerase confirms that if the original strand
reads A-G-C-T, the new strand will read T-C-G-A.

35. DNA polymerase catalyzes the
process of replication by adding
nucleotides one by one to the
growing DNA strand,
incorporating only those that are
complementary to the template.
Figure 9: Addition of free nucleotides during DNA synthesis by DNA polymerase
Beginning of DNA Replication (Cont.)

36. Elongation
 The process of expanding the newly formed DNA strands.
 The DNA polymerase removes the RNA primer, which is then
replaced with DNA nucleotides.
 A continuous sugar-phosphate backbone generates for the lagging
strand causing its elongation.
 The Elongation stage of DNA replication ends:
oWhen no more DNA template strand left to replicate and two
replication forks meet and subsequently terminate (Dovey, 2022).

37. Elongation (Cont.)
Figure 10: DNA replication at Elongation stage

38. Termination
Stage of DNA replication at which the DNA synthesis is
completed, which involves (Rudolph et al., 2019):
oThe disassembly of a protein complex called ‘replisome’
through a process of gap filling between the leading strand at
one fork and the lagging strand of the other fork.
• Involves several enzymatic activities, such as helicase,
primase and DNA polymerase
oMeeting and fusing of two oppositely running replication forks
(Deegan et al., 2019).

39. oResolving of daughter DNA molecules through de-catenation
(unlinking) of the sister chromatids.
oFormation of two separate and complete double-stranded
DNA molecules.
oRemoval of RNA primers and replacement by a new DNA
strand by DNA polymerase I.
oSealing the grooves due to removal of RNA primers by an
enzyme called DNA ligase joining the cuts in the DNA.
Termination (Cont.)

40. Replisome = Protein complex , carries out
DNA replication. Contains several enzymatic
activities, such as helicase, primase and DNA
polymerase
Where: CMGs (CDC45–MCM–GINS) are
types of helicase enzymes
Credited from: Moreno and Gambus, 2020
(https://www.researchgate.net/publication/34188855
9_Mechanisms_of_eukaryotic_replisome_disassem
bly/figures)
Figure 11: Mechanism of DNA replication termination

41. 4. The Significance of DNA in Plant breeding
Plant breeding is the science of changing the genes and traits of
plants (Swarup, 2021).
oProducing desired traits improving the quality of crops.
As the primary medium for storage of biological information,
DNA:
o Helps plant breeders in understanding cell function (Miller et al., 2021).
o Identified as the key source for crop development (Kern, 2015).

42. 4. The Significance of DNA in Plant breeding (Cont.)
oSaves time and other resources to identify the plants with the
desired trait (Baenziger et al., 2017)
• Example: Genome modification, gene editing, DNA sequencing, etc.
oProvides understandings in designing new breeding strategies or
improving the existed approaches of crop improvement (Verma et
al., 2020):
• Example: DNA repair and recombination technologies to increase resistance
of crop plants to different biotic and abiotic stresses.

43. 4. The Significance of DNA in Plant breeding (Cont.)
The double-helical structure of DNA helps in explaining the
heritability of genetic information (Sinden, 1994), that:
oIt is considered as the primary unit of heredity and brings slight
changes to the diversity of plants (Nature Education, 2014).
oIt expresses the phenotype of plants with replication (O’Donnell
et al., 2013).
oDNA has a great role in crop improvement program with a
transfer of desired traits.

44. 4. The Significance of DNA in Plant breeding (Cont.)
The precise knowledge of genome structure and function:
oProvides information on plant biology which enhances the
techniques of crop production (Ovesna et al., 2002).
oLeads to a better understanding of the genetic basis of
superior genotypes and development of new cultivars with
improved agronomic traits (Swarup, 2021).
oCan be applied to cultivar identification and crop genetic
improvement (Banerjee, 2022).

45. 4. The Significance of DNA in Plant breeding (Cont.)
o Help plant breeders in genetic resource characterization and
utilization through:
• Genetic diversity and quantitative trait loci (QTL) analysis
to develop new cultivars with improved agronomic traits.
to improve the nutritional quality of foods (Swarup, 2021).
facilitates development of new lines (Bhandari et al., 2017).
• Different techniques of plant biotechnology, and
• Genetic engineering (Hodkinson, 2007).

46. 4. The Significance of DNA in Plant breeding (Cont.)
 With the progress made in molecular plant breeding, genetics,
genomic selection and genome editing:
o Understanding of molecular markers has been increased and
DNA provides deeper understandings into crop’s diversity
(Nadeem et al., 2018).
o The DNA markers simplify characterization of genetic
resources, selection of parents and screening of the best
progeny (Ovesna and Poláková, 2002).

47. 5. Conclusion
DNA as a biological molecule carries the genetic information in
the linear sequence of nucleotides that can be passed from one
generation to another generation.
o It is essential for inheritance, synthesis of proteins and
providing instructions for life and its processes.
DNA is present in the form of a double-stranded helical structure
formed from two complementary strands of nucleotides.
o The strands held together by hydrogen bonds between the base pairs:
Cytosine-to-Guanine and Adenine-to-Thymine (𝐂G; 𝐀𝐓).

48. 5. Conclusion (Cont.)
DNA replication is facilitated by different enzymes and protein
complexes where each original strands of its double helix
serves as a template for a new DNA strand, which:
oInvolves priming of the template strand by RNA primer
and assembly of the newly formed DNA strands.
oOccurs continuously in prokaryotes where as it occurs
only during the S-phase of cell cycle in eukaryotes.

49. 5. Conclusion (Cont.)
DNA can be useful in identifying, isolating, and extracting the
required gene to be replicated in successive generations of plants.
Through altering the natural genetic information of crops by
adding, changing or removing the nucleotide sequences of their
DNA, it is possible to modify the specific natural traits or
introduce new desirable traits of plants.

50. 5. Conclusion (Cont.)
The concepts of DNA replication and structure is basic for
understanding the molecular bases of plants:
o to design new breeding strategies for different improvement
programs regarding to the identified constraints of production.

51. The End
Thanks for your attention!!
Feb, 2023
Bahir Dar, Ethiopia