NUCLEIC ACIDS STRUCTURE

LECT-3
 L2- Nucleic Acids Structure

Learning objectives: In this lecture you will learn

1. Structure of nucleic acids

A. Components of nucleic acid
B. Chargaff’s rule
C. Double stranded structure of DNA
D. Measuring length of DNA
E. Hairpin structures
2. Melting temperature (Tm) of DNA and it’s usefulness

Q?

Textbook ref: See Chapter 10

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Structure of DNA
Components of nucleic acids
Phosphate + Sugar + Purines + Pyrimidines

DNA 2, Deoxy-ribose Adenine Thymine

Guanine Cytosine

Ribose Adenine Uracil

RNA
Guanine Cytosine

Nucleic acids are made of three components;

(1) Sugar (S)- Ribose in RNA or Deoxy-ribose in DNA
(2) Phosphate (P) that joins sugar molecules to make a chain
(3) Bases (B) adenine, guanine, cytosine and thymine (in DNA) or
Uracil (in RNA) that are attached to the sugar molecule
S-P-S-P-S-P-S-P-S
A chain of nucleic acid
B B B B (3)
Structure of DNA
Differences between DNA and RNA
DNA contains deoxy-ribose sugar instead of ribose that is in RNA
The nucleotide base uracil is present in RNA but not in DNA while
thymine is present in DNA but not in RNA.
Generally DNA is double stranded while RNA is single stranded.

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Components of Nucleic Acids
Nitrogenous bases

Purines are made of two

carbon-nitrogen rings while
Purine pyrimidines have only one
carbon-nitrogen ring.
bases
Adenine (A) Guanine (G) A base attaches to the 1`
carbon of sugar (ribose or
deoxyribose) to make a
nucleoside.

Purines and pyrimidines

attach to sugars through N9
and N1 respectively.
Cytosine (C) Thymine (T) Uracil (U)
Pyrimidine bases
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 Components of Nucleic Acids

Sugars

Nucleic acids have a pentose sugar (sugar with 5-carbons)

HO 5` OH
O
4` 1` The sugar in RNA (Ribo Nucleic Acid) is Ribose while in
3` 2` DNA (Deoxy-ribo Nucleic Acid) it is Deoxy-ribose.

OH OH These two sugars differ from each other by an OH group at

Ribose the 2` carbon.

HO OH
O

OH

2, Deoxyribose

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Structure of a nucleotide
 A base is attached to a sugar
molecule in a nucleoside
O
 When phosphates are attached
at the 5` carbon of the sugar in
Phosphate H3C
NH
a nucleoside, it is then called a
base nucleotide.
O O O
HO P O P O P O N O
O
OH OH OH
Deoxyribose
OH

Nucleoside
Nucleoside monophosphate (dNMP)
Nucleoside diphosphate (dNDP)
Nucleoside triphosphate (dNTP)

Nucleoside = Sugar + base

Nucleotide = Nucleoside + phosphate
(mono, di or tri for 1, 2 or 3 phosphates, respectively)
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Chargaff’s rules
The total amount of purine nucleotides always equals to the total amount of
pyrimidine nucleotides i.e. A+G=C+T
The amount of G equals to the amount of C and the amount of A equals to the
amount of T i.e. A=T and G=C
This information was vital to understand (a) the specific base pairing ‘A’
with ‘T’ and ‘G’ with ‘C’ and (b) the double stranded structure of DNA.

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DNA polynucleotide strands

Nucleic acids are nucleotide polymers.

Nucleotides join through a phosphate that joins 5` hydroxyl
of one with the 3` hydroxyl of the other molecule.
A polymer chain has a polarity with 5` at one end and 3` at the
other end.

Three important carbons of sugars involved in connecting

different molecules together
 1`-joins a base

 3` and 5` join different sugars through phosphate

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DNA polynucleotide strands

DNA consists of two complementary

and antiparallel nucleotide strands that
form a double helix
Two strands of DNA run antiparallel to
each other, one is called the 5` - 3`
strand and the other 3`-5` strand
On average
 there are 10.4 bases per helical turn,
 length of one turn is 3.4 nm.
Two strands are held together by
hydrogen bonds between bases.

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 Types of DNA sequences in Eukaryotes
1. Unique sequences
2. Moderately repetitive sequences Almost half of the human genome
is composed of repetitive
3. Highly repetitive sequences sequences
1. Unique sequences
Presently only once or only a few times, usually protein encoding regions
2. Moderately repetitive sequences
Usually 150-300 bp sequences repeated many thousand times.
Examples include rRNA and tRNA genes.
Tandem repeats
Interspersed repeats
SINEs (Short Interspersed Elements)-usually <500 bp long and >105 copies
Example: Alu elements, ~300 bp, >million copies, comprised of 11 % of the human genome
LINEs (Long Interspersed Elements) usually > 5kb long and >104 copies
Example: LINE1 500,000 copies comprised of 17 % of the human genome
3. Highly repetitive sequences
These sequences are 10 bp or less in length
Repeated in tandems in hundreds of thousands to millions of copies
Clustered in certain regions, around centromeres and telomeres
Also called as satellite DNA (11)
 Special Structure Can Form in DNA and RNA

• Hairpin structure:
In single strands of nucleotides, when sequences of nucleotides on the
same strand are inverted complements, a hairpin structure will be formed
(Fig 10.17a)
 Special Structure Can Form in DNA and RNA

• Stem:
When the complementary sequences are contiguous, the hairpin has a
stem but no loop (Fig 10.17b)
 Special Structure Can Form in DNA and RNA

• RNA molecules may contain numerous hairpins, allowing them to fold up into
complex structures(Fig 10.17c)
Genomes can be differentiated by their Tm values
Nucleic acids can be measured quantitatively using a spectrophotometer.
The same amount of ssDNA molecule absorbs more at 260nm than a dsDNA molecule.
Heating of a DNA molecule destroys hydrogen bonds between bases converting it into
single-stranded form. As the double-stranded DNA denatures, A260nm increases until
the whole DNA converts into the single-stranded form.
The melting temperature, Tm, is defined as the temperature at which half of the double-
stranded DNA molecules are denatured into single strands.

% denaturation
of DNA
Absorbance (260 nm)

100

50

Tm 0
Temperature (oC)

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Genomes can be differentiated by their Tm values

GC pairs are held together by 3 hydrogen

GC content bonds that require more energy for melting.
Absorbance (260 nm)

40% 50% 60% Tm increases by an increase in GC

concentration.
This example has three DNA
molecules A, B and C with GC contents of
40, 50 and 60%, respectively.
The vertical lines from each curve indicate
the Tm for each DNA.
Temperature (oC)
The figure shows that the Tm increases with
an increase in the GC contents of DNA

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Revision questions
Find the name of these nucleic acid components from the list
HO 5` OH
OH O
HO 4` 1`
O
3` 2`

OH OH
OH

A- 2, Deoxyribose
B- Ribose
C- Guanine (G)
D- Thymine (T)

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Find the name of these nucleic acid components from the list

HO 5` OH
O
4` 1`
3` 2`

OH OH

A Ribose
B Adenine
C Cytosine

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1. In DNA, the two strands run antiparallel. What does it mean?

2. What are the 5` and 3` ends of a nucleic acid sequence?

3. A single tetranucleotide contains the base sequence 5'-AACG-3'.

A) Can you distinguish whether this is DNA or RNA?

B) If this were DNA, what would be the base sequence and polarity
of the complementary strand?

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Find the 5` and the 3` ends of the following DNA with an explanation

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Name the following structure (hint: the base is thymine) and circle
1. the sugar and label it 1
2. the base and label it 2
3. a phosphate and label it 3
4. the nucleoside and label it 4
5. the nucleotide and label it 5
O

H3C
NH

O O O
HO P O P O P O N O
O
OH OH OH

OH

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Which of the following is the best representation of nucleotide
chains, where S = sugar, P= phosphate, and B = nitrogen base (A,
G, C, T, or U)?

A S S S D P P P
P P S S
B B B B

B P P P E S B P
B B P S B
S S

C S S S
B B
P P
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1. List three differences between DNA and RNA.

2. The genetic materials of an RNA virus, a DNA virus, and a wombat were analyzed by a
very disorganized laboratory technician, who lost the identification tags to the samples.
Identify the source of the nucleic acid for each sample, giving a reason for each choice.

Sample Adenine Cytosine Guanine Thymine Uracil

(a) 28.0 22.0 22.0 0.0 28.0
(b) 21.0 29.0 29.0 21.0 0.0
(c) 27.0 24.0 23.0 0.0 26.0
3. An unknown virus had 23 % cytosine residues. Can you work out the chemical
composition (A, T, G, C contents) of it’s nucleic acid, if it is a
a. ds DNA?
b. ds RNA?
c. ss DNA?
d. ss RNA?

4. A double stranded DNA contains 50 T and 120 G nucleotides. What is the total nucleotide
number in this DNA fragment? What is the length of DNA in bp?

5. Define Tm. The following are melting temperatures for six DNA molecules A, B, C, D, E
and F: 75 0C, 710C, 680C, 84 0C, 62 0C and 55 0C, respectively. Arrange these DNAs in
increasing amount of G-C pairs.

6. Define: tandem and interspersed repeats, SINEs, LINEs, satellite DNA

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Extended answer question
Answer both parts
a. An unknown virus had 23 % cytosine residues. Can you work out the chemical
composition (A, T, G, C contents) of it’s nucleic acid, if it is a
a. ds DNA?
b. ds RNA?
c. ss DNA?
d. ss RNA?
b. Name the following structure (hint: the base is thymine) and circle
 the sugar and label it 1
 the base and label it 2
 a phosphate and label it 3
 the nucleoside and label it 4
 the nucleotide and label it 5
O

H3C
NH

O O O
HO P O P O P O N O
O
OH OH OH

OH

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