1. DNA Structure, Replication, and Manipulation
Chapter 6
DNA Structure, Replication, and Manipulation

2. Genome Size
The genetic complement of a cell or virus constitutes its genome.
In eukaryotes, this term is commonly used to refer to one complete haploid set of chromosomes, such as that found in a sperm or egg.
The C-value is the DNA content of the haploid genome
The units of length of nucleic acids in which genome sizes are expressed :
• kilobase (kb) 103 base pairs
• megabase (Mb) 106 base pairs

3. Genome Size Viral genomes are typically in the range 100–1000 kb:
Bacteriophage MS2, one of the smallest viruses, has only four genes in a single stranded RNA molecule of about 4000 nucleotides (4kb)
Bacterial genomes are larger, typically in the range 1–10 Mb:
The chromosome of Escherichia coli is a circular DNA molecule of 4600 kb.

4. Genome Size Eukaryotic genomes are typically in the range 100–1000 Mb:
The genome of a fruit fly, Drosophila melanogaster is 180 Mb
Among eukaryotes, genome size often differs tremendously, even among closely related species

5. The C-value Paradox
Genome size among species of protozoa differ by 5800-fold, among arthropods by 250-fold, fish 350-fold, algae 5000-fold, and angiosperms 1000-fold.
The C-value paradox: Among eukaryotes, there is no consistent relationship between the C-value and the metabolic, developmental, or behavioral complexity of the organism
The reason for the discrepancy is that in higher organisms, much of the DNA has functions other than coding for the amino acid sequence of proteins

6. DNA: Chemical Composition
DNA is a linear polymer of four deoxyribonucleotides
Nucleotides composed of 2'- deoxyribose (a five-carbon sugar), phosphoric acid, and the four nitrogen-containing bases denoted A, T, G, and C
Figure 6.3: A typical nucleotide showing the three major components

7. DNA: Chemical Composition
Two of the bases, A and G, have a double-ring structure; these are called purines
The other two bases,T and C, have a single-ring structure; these are called pyrimidines
Figure 6.2: Chemical structures of adenine, thymine, guanine, and cytosine

8. DNA Structure
The nucleotides are joined to form a polynucleotide chain, in which the phosphate attached to the 5' carbon of one sugar is linked to the hydroxyl group attached to the 3' carbon of the next sugar in line
The chemical bonds by which the sugar components of adjacent nucleotides are linked through the phosphate groups are called phosphodiester bonds

9. Figure 6.4: Three nucleotides at the 5’-end of a single polynucleotide strand

10. DNA Structure
The duplex molecule of DNA consists of two polynucleotide chains twisted around one another to form a right-handed helix in which the bases form hydrogen bonds.
Adenine pairs with thymine; guanine with cytosine
A hydrogen bond is a weak bond
The stacking of the base pairs on top of one another also contribute to holding the strands together
The paired bases are planar, parallel to one another, and perpendicular to the long axis of the double helix.

11. DNA Structure
The backbone of each strand consists of deoxyribose sugars alternating with phosphate groups that link 5' carbon of one sugar to the 3' carbon of the next sugar in line
The two polynucleotide strands of the double helix run in opposite directions
The paired strands are said to be antiparallel
Figure 6.7: DNA molecule showing the antiparallel
orientation of the complementary strands

12. DNA: Watson-Crick Model
3-D structure of the DNA molecule:
Double helix forms major and minor grooves
Diameter of the helix = 20 Angstroms
Each turn of the helix = 10 bases = 34 Angstroms

13. Figure 6.5A: Illustration of DNA helix
Figure 6.5B: Computer
model of DNA helix
Part B Courtesy of Antony M. Dean, University of Minnesota

14. Figure 6.8: Watson–Crick model of DNA replication
Hydrogen bonds between DNA bases break to allow strand separation
Each DNA strand is a template for the synthesis of a new strand
Template (parental) strand determines the sequence of bases in the new strand (daughter): complementary base pairing rules
Figure 6.8: Watson–Crick model of DNA replication

15. Figure 6.9: Predictions of semiconservative DNA replication
In 1958 M. Meselson and F. Stahl showed that DNA replication is semiconservative:
The parental strands remain intact and serves as a template for a new strand
Figure 6.9: Predictions of semiconservative DNA replication

16. Circular DNA Replication
Autoradiogram of the intact replicating circular chromosome of E. coli shows that
DNA synthesis is bidirectional
Replication starts from a single site called origin of replication (OR)
The region in which parental strands are separating and new strands are being synthesized is called a replication fork

17. Figure 6.12: The distinction between unidirectional and bidirectional DNA replication

18. Rolling Circle Replication
Some circular DNA molecules of a number of bacterial and eukaryotic viruses, replicate by a different mode called rolling-circle replication.
One DNA strand is cut by a nuclease to produce a
3'-OH extended by DNA polymerase.
The newly replicated strand is displaced from the template strand as DNA synthesis continues.
Displaced strand is template for complementary DNA strand.

19. Figure 6.13: Rolling-circle replication

20. Replication of Linear DNA
The linear DNA duplex in a eukaryotic chromosome also replicates bidirectionally
Replication is initiated at many sites along the DNA
Multiple initiation is a means of reducing the total replication time

21. Figure 6.14: Replicating DNA of D. melanogaster

22. Replication of Linear DNA
In eukaryotic cell, origins of replication are about 40,000 bp apart, which allows each chromosome to be replicated in 15 to 30 minutes.
Because chromosomes do not replicate simultaneously, complete replication of all chromosomes in eukaryotes usually takes from 5 to 10 hours.

23. DNA Synthesis
One strand of the newly made DNA, leading strand, is synthesized continuously.
The other, lagging strand is made in small precursor fragments = Okazaki fragments
The size of Okazaki fragments is 1000–2000 base pairs in prokaryotic cells and 100–200 base pairs in eukaryotic cells.

24. Figure 6.22: Short fragments in the replication fork

25. DNA vs. RNA DNA sugar = deoxyribose RNA sugar = ribose
RNA contains the pyrimidine uracil (U) in place of thymine (T)
DNA is double-stranded
RNA is single-strand
Short RNA fragment serves as a primer to initiate DNA synthesis at origins of replication

26. DNA Replication: Proteins
Gyrase = topoisomerase II introduces a double-stranded break ahead of the replication fork and swivels the cleaved ends to relieve the stress of helix unwinding
Helicase unwinds DNA at replication fork to separate the parental strands
Single-strand binding protein (SSB) stabilizes single strands of DNA at replication fork

27. DNA Replication: Proteins
Multienzyme complex called primosome initiates strand synthesis by forming RNA primer
The enzyme DNA polymerase forms the phosphodiester bond between adjacent nucleotides in a new DNA acid chain in 5' to 3' direction
DNA polymerase has a proofreading function that corrects errors in replication

28. DNA Replication: Proteins
The final stitching together of the lagging strand must require:
Removal of the RNA primer
Replacement with a DNA sequence
Joining adjacent DNA fragments
Primer removal and replacement in E. coli is accomplished by a special DNA polymerase (Pol I) that removes one ribonucleotide at a time

29. DNA Replication: Proteins
In eukaryotes, the primer RNA is removed as an intact unit by a protein called RPA (replication protein A)
DNA ligase catalyzes the formation of the final bond connecting the two precursor

30. Figure 6.15: Role of proteins in DNA replication

31. Nucleic Acid Hybridization
DNA denaturation: Two DNA strands can be separated by heat without breaking phosphodiester bonds
DNA renaturation = hybridization: Two single strands that are complementary or nearly complementary in sequence can come together to form a different double helix
Single strands of DNA can also hybridize complementary sequences of RNA

32. Figure 6.24: Nucleic acid hybridization

33. Restriction Enzymes
Restriction enzymes cleave duplex DNA at particular nucleotide sequences
The nucleotide sequence recognized for cleavage by a restriction enzyme is called the restriction site of the enzyme
In virtually all cases, the restriction site of a restriction enzyme reads the same on both strands
A DNA sequence with this type of symmetry is called a palindrome

34. Restriction Enzymes
Many restriction enzymes all cleave their restriction site asymmetrically—at a different site on the two DNA strands
They create sticky ends = each end of the cleaved site has a single-stranded overhang that is complementary in base sequence to the other end
Some restriction enzymes cleave symmetrically— at the same site in both strands
They yield DNA fragments that have blunt ends

35. Restriction Enzymes
Because of the sequence specificity, a particular restriction enzyme produces a unique set of restriction fragments for a particular DNA molecule.
Another enzyme will produce a different set of restriction fragments from the same DNA molecule.
A map showing the unique sites of cutting of a particular DNA molecule by restriction enzyme is called a restriction map

36. Figure 6. 26: A. A. EcoRI enzyme; B
Figure 6.26: A. A. EcoRI enzyme; B. Electrophoresis gel of BamHI and EcoRI; C. BamHI enzyme

37. Southern Blot Analysis
DNA fragments on a gel can often be visualized by staining with ethidium bromide, a dye that binds DNA
Particular DNA fragments can be isolated by cutting out the small region of the gel that contains the fragment and removing the DNA from the gel.
Specific DNA fragments are identified by hybridization with a probe = a radioactive fragment of DNA or RNA
Southern blot analysis is used to detect very small amounts of DNA or to identify a particular DNA band by DNA-DNA or DNA-RNA hybridization

38. Southern Blot Analysis
Steps in Southern blot procedure:
DNA is digested by restriction enzymes
DNA fragments are separated by gel electrophoresis
DNA is transferred from gel to hybridization filter = blot procedure
DNA denatured to produce single-stranded DNA

39. Southern Blot Analysis
Filter is mixed with radiolabeled single-stranded DNA or RNA probe at high temperatures that permit hybridization = formation of hydrogen bonds between complementary base pairs
DNA bands hybridized to a probe are detected by x-ray film exposure

40. Figure 6.27: Southern blot

41. Polymerase Chain Reaction
Polymerase chain reaction (PCR) makes possible the amplification of a particular DNA fragment
Oligonucleotide primers that are complementary to the ends of the target sequence are used in repeated rounds of denaturation, annealing, and DNA replication
The number of copies of the target sequence doubles in each round of replication, eventually overwhelming any other sequences that may be present

42. Polymerase Chain Reaction
Special DNA polymerase is used in PCR = Taq polymerase isolated from bacterial thermophiles that can withstand high temperature used in procedure
PCR accomplishes the rapid production of large amounts of target DNA that can then be identified and analyzed

43. Figure 6.28: Polymerase chain reaction (PCR) for amplification

44. DNA Sequence Analysis
DNA sequence analysis determines the order of bases in DNA
The dideoxy sequencing method employs DNA synthesis in the presence of small amounts of fluorescently labeled nucleotides that contain the sugar dideoxyribose instead of deoxyribose
Figure 6.29: Structures of normal deoxyribose
and the dideoxyribose sugar used in DNA sequencing.

45. DNA Sequencing: Dideoxy Method
Modified sugars cause chain termination because it lacks the 3'-OH group, which is essential for attachment of the next nucleotide in a growing DNA strand
The products of DNA synthesis are then separated by electrophoresis. In principle, the sequence can be read directly from the gel.
Figure 6.30: Dideoxy method of DNA sequencing

46. DNA Sequencing: Dideoxy Method
Each band on the gel is one base longer than the previous band
Each didyoxynucleotide is labeled by different fluorescent dye
G, black; A, green; T, red; C, purple
As each band comes off the bottom of the gel, the fluorescent dye that it contains is excited by laser light, and the color of the fluorescence is read automatically by a photocell and recorded in a computer

47. Figure 6.31: Fluorescence pattern obtained from a DNA sequencing gel

48. DNA Sequencing
Massively parallel sequencing yields billions of base pairs per day.

49. Figure 6.32: A method for massively parallel DNA sequencing that captures and amplifies DNA template strands on tiny beads