Structure and Function of

Nucleic Acid (3 classes)

Anupam Bandyopadhyay
IIT-Ropar
Nucleic Acid
Class-1
 DNA as genetic material
1928 Griffith’s Experiment Horizontal Gene Transfer ( Transformation)
1940 What is life? By Schrodinger (all living things are governed by simple physical
Laws as those encountered in daily life, thermodynamics and Newton’s law of
motion)
1952 Hershey-Chase ( Direct proof of DNA is genetic material by Phage experiment)
1952 Watson and Crick DNA structure ( X-ray structure)
1953 Urey and Miller ( formation of biomolecule from inorganic AND ORGANIC
molecules)
1958 Meselson and Stahl ( Idea of DNA replication)
 Urey and Miller experiment
https://www.youtube.com/watch?v=hj3Rhf2vlZg

Aggregation and formation Coacervates

of organic molecules and Floating on the ocean
begin life
 Meselson and Stahl
https://www.youtube.com/watch?v=MbxkiEmi5TU

Hypothesis
1. Conservative
2. Semi-conservative
3. Dispersion
 Genome, Gene, Chromosome, Histone,
and DNA
A genome is an organism’s complete set of genetic
instructions. Each genome contains all of the
information needed to build that organism and allow it
to grow and develop.

In biology, a gene is a sequence of nucleotides in DNA or

RNA that codes for a molecule that has a function.
During gene expression, the DNA is first copied into RNA.
The RNA can be directly functional or be the
intermediate template for a protein that performs a
Dissection of a
chromosome
DNA Structure: First Nature paper published by Watson and Crick
DNA Secondary Structure:
Double helix
Simplified model to understand the
H-bond
The double helix is the principal secondary structure of DNA and RNA
Hydrogen bonding between bases is important for the formation of double helices, but its
effect is weakened due to interactions with water.

How do they form double

helix?

Cooperative electronic
polarization
enhances d-helix
The electronic polarization of the bases contributes to
strong stacking interactions between bases

The bases, both purines and pyrimidines, are

flat and planar, so they can stack on top of one
another. In addition, the atoms of the aromatic
rings are very polarizable, and many of the
atoms have a partial charge. These two factors
make the combination of van der Waals and
electrostatic interactions between stacked bases
particularly strong. Th ese effects are known
collectively as base-stacking interactions, and
they provide the dominant contribution to
stabilizing the double-helical conformation of
nucleic acids.
Nucleic Acid
Class-2
DNA Secondary Structure: Double helix Type

Minor groove

Major groove
Major Groove and Minor Groove
There are two common relative orientations of the
base and the Sugar
 The ribose ring has alternate conformations defined by the sugar
pucker
Another important conformational parameter for DNA and RNA is known as the sugar pucker, which
refers to the different out-of-plane distortions in the deoxyribose or ribose rings of nucleosides

In nucleic acids, endo sugar puckers are more common than exo. In DNA, the
sugar pucker can be either C2ʹ endo (in B-form DNA) or C3ʹ endo (in A-form of DNA).
Book: The Molecules of Life
 In RNA, the C2ʹ endo sugar pucker cannot be adopted
because of steric hindrance between the OH group on C2ʹ
and the phosphate group on C3ʹ

The Molecules of Life

Molecular view of the sugar pucker in RNA
and DNA.
Conformational Studies of Nucleic acid

Essential Chemical Biology, Andrew Miller

Taken from Original
paper
Conformational Studies of Nucleic acid

Essential Chemical Biology, Andrew Miller

The standard Watson-Crick model of double-helical DNA is
the B-form
 The major groove of A-form double helices is less
accessible to proteins than that of B-form DNA
In A-form helices, however, the base pairs are tilted away from perpendicular and are
moved away from the center of the helix. As a result, the major groove in the A-form is
deeper and narrower than it is in B-form DNA, while the minor groove is wider and
shallower.

Why is the Nature preferring B-DNA more than A-DNA?

The narrowing and deepening of the major groove in A-form helices means that it is more difficult for proteins to
read out the sequence-specific information at the edges of the bases in A-form helices (that is, α helices cannot
readily enter the narrower major groove of the A-form helix).
The Molecules of Life
The Molecules of Life
Nucleic Acid
Class-3
RNA Secondary Substructur
e
Structure
There can be multiple substructures
of same type in single secondary
structure and if not same they can
be different in size (in terms of no.
of paired and unpaired base).

Any RNA secondary structure will

be combination of these
substructures only.
Example of RNA structure
 Tertiary structure of Nucleic Acid
Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer.
RNA and DNA molecules are capable of diverse functions ranging from molecular
recognition to catalysis. Such functions require a precise three-dimensional tertiary structure.
 Quaternary structure of Nucleic acid
Nucleic acid quaternary structure refers to the interactions between
separate nucleic acid molecules, or between nucleic acid molecules and
proteins.
DNA RN
(Nucleosome) A
 How to represent the DNA and RNA?
The two strands of DNA in a double helix are not identical—they are complementary.
Complementary DNA strands are strands of DNA in a double helix with base
pairing such that each base is located opposite its complementary base.

In specifying the base sequence of a segment of a strand of DNA (or RNA), we list
the bases in sequential order (using their one-letter abbreviations) in the direction from
the 5’ end to the 3’ end of the segment.

5′ A–A–G–C–T–A–G–C–T–T–A–C–T 3′
3′ T–T–C–G–A–T–C–G–A–A–T–G–A 5′
Template
strand

Similarly trend of complementary sequence follows for RNA, where T is

replaced by U
 Polymerase chain reaction (PCR)
PCR, is a technique to make many copies of a specific DNA region in vitro (in a test tube rather than an
organism).
Application: DNA cloning, medical diagnostics, and forensic analysis of DNA

Required material
Taq polymerase
Like DNA replication in an organism, PCR requires a DNA polymerase enzyme that makes new
strands of DNA, using existing strands as templates. The DNA polymerase typically used in PCR is
called Taq polymerase, after the heat-tolerant bacterium from which it was isolated
(Thermus aquaticus).
Primers
Like other DNA polymerases, Taq polymerase can only make DNA if it's given a primer, a short
sequence of nucleotides that provides a starting point for DNA synthesis. In a PCR reaction, the
experimenter determines the region of DNA that will be copied, or amplified, by the primers she or he
chooses.

PCR primers are short pieces of single-stranded DNA, usually around 20 nucleotides in length. Two
primers are used in each PCR reaction, and they are designed so that they flank the target region
(region that should be copied). That is, they are given sequences that will make them bind to opposite
strands of the template DNA, just at the edges of the region to be copied. The primers bind to the
 Polymer Chain Reaction
(PCR)

Required Primer Required Primer

https://www.youtube.
com/
watch?v=JmveVAYKylk
 PCR Machine process

The basic steps are:

1. Denaturation (96°C): Heat the reaction strongly to
separate, or denature, the DNA strands. This provides
single-stranded template for the next step.

2. Annealing (55 - 65°C): Cool the reaction so the primers

can bind to their complementary sequences on the
single-stranded template DNA.

3. Extension (72°C): Raise the reaction temperatures

so Taq polymerase extends the primers, synthesizing
new strands of DNA.
The Polymerase Chain Reaction (PCR) Graph
 Genetic Engineering

Editing gene sequence is the direct manipulation of an

organism's genes using biotechnology

10 successful examples of genetic

modification
1. Mouse-ear cress
2. Western corn rootworm, European corn borer
Or other
3.
organism Bananas
4. Abiotic stress
5. Onions that do not make you cry
6. Golden rice
7. Purple tomatoes
8. Carrots that help prevent osteoporosis
9. Soybean oil for frying
10. Arctic apple
DNA vs RNA
 DNA and Mutations
A mutation is a change in DNA, the hereditary material of life. An organism's DNA affects
how it looks, how it behaves, and its physiology. So a change in an organism's DNA can
cause changes in all aspects of its life.

Mutations are essential to evolution

Mutations to control genes can

transform one body part into another.
Scientists have studied flies
carrying Hox mutations that sprout
legs on their foreheads instead of
antennae!
 Types of mutations
There are many different ways that DNA can be changed, resulting in different types of
mutation. Here is a quick summary of a few of these:
1. Substitution                                                                        
A substitution is a mutation that exchanges one base for another (i.e., a change in a single "chemical
letter" such as switching an A to a G ). Such a substitution could

1. change a codon to one that encodes a different amino acid and cause a small change in the protein
produced. For example, sickle cell anemia is caused by a substitution in the beta-hemoglobin gene, which
alters a single amino acid in the protein produced.
2. change a codon to one that encodes the same amino acid and causes no change in the protein produced.
These are called silent mutations .
3. Change an amino-acid-coding codon to a single "stop" codon and cause an incomplete protein. This can
have serious effects since the incomplete protein probably won't function.

Insertion
Insertions are mutations in which extra base pairs are inserted into a new place in the DNA.

Deletion
Deletions are mutations in which a section of DNA is lost, or deleted.

Frameshift
Since protein-coding DNA is divided into codons three bases long, insertions and deletions can alter a gene
so that its message is no longer correctly parsed. These changes are called frame shifts. For example,
consider the sentence, "The fat cat sat." Each word represents a codon. If we delete the first letter and
parse the sentence in the same way, it doesn't make sense.
In frameshifts, a similar error occurs at the DNA level, causing the codons to be parsed incorrectly. This
usually generates truncated proteins that are as useless as "hef atc ats at" is uninformative.
There are other types of mutations as well, but this short list should give you an idea of the possibilities.
 The causes of mutations
Mutations happen for several reasons.

1. DNA fails to copy accurately

Most of the mutations that we think matter to evolution are "naturally-
occurring." For example, when a cell divides, it makes a copy of its DNA — and
sometimes the copy is not quite perfect. That small difference from the original
DNA sequence is a mutation.

2. External influences can create mutations

Mutations can also be caused by exposure to specific chemicals or radiation. These agents cause
the DNA to break down. This is not necessarily unnatural — even in the most isolated and
pristine environments, DNA breaks down. Nevertheless, when the cell repairs the DNA, it might
not do a perfect job of the repair. So the cell would end up with DNA slightly different than the
original DNA and hence, a mutation.
 A case study of the effects of mutation: Sickle cell
anemia
The mutations that cause sickle cell anemia have been extensively studied and demonstrate
how the effects of mutations can be traced from the DNA level up to the level of the whole
organism. Consider someone carrying only one copy of the gene. She does not have the disease,
but the gene that she carries still affects her, her cells, and her proteins:

1. There are effects at the DNA level

2. There are effects at the protein level

Normal hemoglobin (left) and hemoglobin in sickled red blood cells (right) look different; the
mutation in the DNA slightly changes the shape of the hemoglobin molecule, allowing it to
clump together.

3. There are effects at the cellular level

When red blood cells carrying mutant hemoglobin are deprived of
oxygen, they become "sickle-shaped" instead of the usual round
shape (see picture). This shape can sometimes interrupt blood flow.