RECOMBINANT DNA 202

Dr Danisile Tembe, SLS Room 05-105, Tel: 031 260 7586, Email: TembeD@ukzn.ac.za
 What is DNA?
➢ A polynucleotide with a specific sequence of deoxyribonucleotide
units covalently joined through 3’-5’ –phosphodiester bonds.
 Structure and properties of nucleotide

➢ A DNA nucleotide is composed of three components:

a) Sugar deoxyribose

b) Phosphate group

c) Nitrogenous

➢ DNA is composed of 4 different nucleotides which differ in

their nitrogenous bases:

• There are four different bases: Adenine, Thymine,

Guanine & Cytosine
 Structure of bases

➢ The nitrogenous bases A & G each have two

linked rings and are called Purines
➢ Thymine and Cytosine each have a single ring
and they are called Pyrimidines
 Structure of sugar
Attachment site for
phosphate group

Attachment site
for base
https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/

➢ DNA contains the sugar deoxyribose while RNA contains ribose

 Structure of Sugar
➢ The structural units of DNAs are called deoxyribonucleotides or deoxyribonucleoside while RNAs are called
ribonucleotides or ribonucleoiside

Deoxyribonucleotides and Ribonucleotides

BASE NUCLEOSIDE NUCLEOTIDE SHORT
ADENINE Deoxyadenosine (DNA) Deoxyadenosine (DNA) dAMP (DNA)
Adenosine (RNA) Adenosine-5’-phosphate (RNA) AMP (RNA)
GUANINE Deoxyguanosine (DNA) Deoxyguanosine (DNA) dGMP (DNA)
Guanosine (RNA) Guanosine-5’-phosphate (RNA) GMP (RNA)
THYMINE Deoxythymidine (DNA) Deoxythymidine (DNA) dTMP (DNA
only)

CYTOSINE DEOXYCYTIDINE Deoxycytidine (DNA) dCMP (DNA)

Cytidine (RNA) Cytidine-5’-phosphate (RNA) CMP (RNA)
URACIL Uridine URIDINE-5’-PHOSPHATE UMP(RNA
only)
 Phosphodiester Bonds Joins Nucleotides in Nucleic Acids
5’ Terminus

➢ A bond that covalently connect/joins the nucleotides units in

DNA and RNA is called Phosphodiester bond
5’
➢ A short nucleic acid containing 50 or fewer nucleotides is called
oligonucleotides

➢ A longer nucleic acid containing more nucleotides is called

polynucleotide

• Each polynucleotide has a 3 prime end and a five prime

end. These are abbreviated to the terms 3’ and 5’ end. Phosphodiester
3’

3’ Terminus
 Polarity – naming the ends of a polynucleotide

This is a 5’ end
The carbon closest to
the end is a 5’ carbon

How do you tell what kind of end you are looking at?

Look at the sugar closest to that end - if the carbon

closest to that end is a 5’ carbon, then that is the 5’
end. If, however, it is a 3’ carbon, then that is the 3’
end.

This is a 3’ end
The carbon closest to
the end is a 3’ carbon

http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm
 DNA Is A Double Helix
➢ DNA consist of two complementary strands of
nucleotides twisted together to form a double
helix
➢ The two strands in DNA are oriented in the
opposite direction and the helix is antiparallel
➢ The two strands of DNA are joined by the
hydrogen bonds
DNA Is A Double Helix
 DNA Is A Double Helix

➢ The twist of the helix forms two unequal surfaces

• Called major grooves and minor grooves
• Major groves forms where the backbones are far
apart and minor grooves occurs where the
backbones are close together
• This is where most interactions with proteins or
other nucleic acids occur

Lehninger principles of Biochemistry, Fifth Edition, 2008. @W.H. Freeman and Company
 Three Forms of DNA Helical structures
➢ There are 3 helical forms of DNA

• A form: Is favored in many solutions that are relatively devoid of water

• B form: Is the most stable structure and commonly occurring form

• Z form: no clear function

Form A B Z
Helix direction Right handed right left

Base prs/turn 11 10.5 12

Overall morphology Short Longer Elongated &

wide thinner Thinner/slender
Form A B Z
Helix direction Right handed right left

Base prs/turn 10.9 10 12

Overall morphology Short Longer Elongated

wide thinner thinner

diameter 2.2 nm 2 nm 1.8 nm

Base configuration anti anti Alternate

Anti/syn
 Double Helical DNA Can be Denatured
➢ DNA denaturation: process where a double stranded DNA is separated
into 2 single strands
• For example, in a well isolated solution, double stranded DNA are
high viscous at 7.0 pH and room temperature, when such solution is
exposed to extremes of pH or temperature above 80 ֯C, its viscosity
degrease indicating that double helical DNA undergone a physical
change
• Due to denaturation or melting of the double helical strand
➢ Disruption of both hydrogen bonding between paired bases on opposite
strands & base stacking causes the double helix to unwind
• Forming two single strands that are completely separate from each
other
 Central dogma
➢ The flow of genetic information from DNA to RNA to protein
 Central dogma
➢ At least three types of RNA are needed:
1. Ribosomal RNA (rRNA): catalyzes translation

2. Messenger RNA (mRNA): carries genetic message from the DNA

3. Transfer RNA (tRNA): deliver correct amino acid to ribosome during translation

➢ Other functional RNAs:

• microRNAs (miRNA): used to silence the unwanted gene

• Short interfering RNAs (siRNA): responsible for degrading mRNA- stopping it from producing
synthesis of proteins
 Central dogma video

https://www.youtube.com/watch?v=KIvBn6gfRgY