• All the information that is needed for the formation, function and

activity of a living system are ultimately specified by its genome.

A genome is an organism’s complete set of DNA,

including all of its genes. In humans, a copy of the
entire genome—more than 3 billion DNA base
pairs—is contained in all cells that have a nucleus.
• Genes to proteins and beyond….

Transcription Translation
DNA RNA Protein
• DNA: DeoxyriboNucleic Acid

• RNA: RiboNucleic Acid

• The nature of this “information flow” is dependent on the successful

decoding of the genetic material. As we will see, the mechanisms
used to make this work with high fidelity are laid in the structure of
nucleic acids.

We still don’t understand the function of large portion of the genome…

 Some nomenclature
• Size of DNA is expressed as base pairs (bp) or kilobase
pairs (kb).
• A short single-stranded polymer of nucleotide is called
oligonucleotide.
• Nucleotides are polymerized by enzymes called
polymerases.
• The phosphodiester bond between nucleotides can be
broken by nuclease.
• An exonuclease removes a residue from the end of a
nucleotide chain while endonuclease cleaves at some other
point along the chain.
 Nucleic Acids are polymers of nucleotides

• The term “nucleic acid” refers to both DNA and RNA.

• Nucleic acids are polymers of nucleotides.
• Each nucleotide is composed of a sugar (ribose or
deoxyribose), a phosphate, and a base.

Glycosidic bond

ADP: diphosphate
AMP: monophosphate
 • RNA and DNA differ in the sugar component
and one of the bases

(In RNA) (In DNA)

• Note the numbering of the ribose ring.

 Bases in Nucleic Acids
(Purines and Pyrimidines)

Only in RNA Only in DNA

DNA is a polymer of nucleotides
• Nucleic acids are chains of nucleotides held
together by phosphodiester bonds that bridge
the 3’ and 5’ positions of adjacent ribose units.
Each nucleotide is called a residue in the DNA
polymer.
• The end residue of a DNA polymer whose C5’
position is not connected to another nucleotide
is called the 5’ end, while the end whose C3’
position is not connected to another nucleotide
is called the 3’ end.
• By convention, the base sequence of DNA is
read from the 5’ end to the 3’ end and specified
by the identity of the bases. This is also
referred as the primary structure of DNA.
• Sugars linked by phosphates form a common
backbone that plays a structural role while the
bases point away from the backbone.
• This is also referred as the primary structure of DNA.
X-ray crystallography determination of DNA structure
 Double Helical Structure of DNA 5’ 3’

• DNA contains two polynucleotide strands. The bases from

the two strands pair with each other through hydrogen
bonding, they are called the Watson-Crick base pairs. The
base pairs are: A-T and G-C. This allows faithful
information transfer.
• The two polynucleotide chains wind around each other
(antiparallel) to form a right handed double helix.
5’ 3’

A-T

G-C
Double Helical Structure of DNA

• DNA forms a periodic helical structure with

two strands running antiparallel against each
other.

• The diameter of a B form double helix is ~

20Å, the length per rise is ~ 34Å (10 bp).

• The sugar-phosphate backbone of the DNA

double helix runs along the peripheral and
minimizes the charge repulsion.

• The double helical structure of DNA allows

successive base pairing, which are essentially
planar. The base pair plane is perpendicular
to the helix axis.
 Double Helical Structure of DNA
• The specific H bonds between A-T
and G-C pairs are critical for the
double helical structure of DNA.
• The sugar-phosphate backbone
engages in polar interactions with water.

• The base pairs of DNA stack on top of

each other in the center of the helix, so
the core of the helix is solid.

• The van der Waals interactions

between the stacked base stabilizes
the DNA double helix.

• In addition, the double helix is stabilized by the

hydrophobic effect of burying the bases inside
the double helix.
 Major and minor grooves of DNA
The major and minor grooves are lined by sequence-specific H-bond groups.

• DNA in the B form has a major groove and a

minor groove.
• The presence of the grooves allows access to
the hydrogen-bonding capabilities of the
exposed bases.
• The hydrogen bonding capability provides a
means of sequence-specific interactions
between DNA and other molecules in
replication and transcription.
 The double helix can adopt different forms
In the cell, the most commonly
seen form of DNA double helix
is called the B form or the
Watson-Crick helix.

The double helix can also exist

in an A form, which is shorter
and wider than the B form with
the bases at an angle rather
than perpendicular to the helix
axis.

The A form is seen in RNA

double helices and in RNA-
DNA hybrid helices, structures
observed in transcription and
information processing.
 RNA can adopt elaborate structures
• RNA is single-stranded and thus has greater conformational freedom than
DNA.
• RNA molecules can adopt intricate three-dimensional structures that
allow them to express information stored in DNA. Three or more bases
form hydrogen bonds to stabilize these structures.
 RNA can adopt elaborate structures

• RNA is also capable of base-pairing with DNA-RNA hybrid helix

a complementary single strand DNA to
produce an RNA-DNA hybrid double
helix.

• The cell contains mRNA, tRNA and

ribosomal RNA and siRNA, ShRNA……
• RNA as enzymes
 Protein-nucleic acids interaction

Structure of p63 DNA Binding

Domain in Complex with a 22
Base Pair A/T Rich Response
Element

• Transcription factor p63, a p53

family member, plays a role in
epithelial cell development, cell
cycle arrest, apoptosis, and
carcinogenesis
The double helix facilitates accurate
transmission of hereditary information.
• DNA must be replicated to transmit
information to the new generation: the
separated strands direct the synthesis of
a complimentary strands.

• High degree of fidelity in DNA replication

is essential for accurate transmission of
biological information. The error rate of
DNA polymerase is 1 per 106 bases. The
cell also has multiple repair mechanisms
to further ensure fidelity during
replication.

• DNA replication is also highly processive,

1000 bp/s
 DNA replication
E.Coli DNA polymerase

35Å

sliding clamp
 DNA à Protein

• Genetic information in DNA must be transcribed to mRNA to

express its genes in the ribosome.

G-C and A-U

RNA polymerase
• Transcription (the production of
an RNA transcript) is the first
process in the readout of
information encoded in DNA

• In translation, the
sequence of nucleotides
in an mRNA molecule
provides the information
for the synthesis of a
protein at the ribosome.
 Genetic Codes
• Amino acids are encoded by groups of three residues in
DNA (codon) starting from a fixed point.
• The genetic code is the relationship between the
sequence of bases in DNA (or its RNA transcripts) and
the sequence of amino acids in proteins
1. Three nucleotides encode an amino acid
2. The code is non-overlapping: AGT CGG TCA
3. The code has no punctuation
4. The genetic code is degenerate. Most amino acids
are encoded by more than one codon. Degeneracy
minimizes the deleterious effects of mutations
DNA molecules are tightly
packaged inside the cell
• Gene: a unique sequence of
nucleotides that encode either a
protein or an RNA molecule. A
gene may include nontranscribed
or nontranslated sequences,
some of which have regulatory
functions.

• Only 1% of human genome is

used for coding proteins.
Scientists believe 80% of the
noncoding genome regulates the
coding regions.

• There is still a lot we don’t know

about human genome.
 Genes and Disease
• A mutated gene can cause disease, Deletion, insertion and mutation.
• Almost 2,000 genes have been linked to human disease.
• Single-nucleotide polymorphism (SNP) can be used as genetic markers for various
disease.
• Human population has ~ 1 SNP every 300 bases; (3,200,000 kb)
• SNPs are only proxies for disease

A deletion in CFTR occurring in 70% of CF patients

Lung tissue

Cystic fibrosis transmembrane

conductance regulator (CFTR)
 DNA absorb at 260 nm

• DNA molecules absorb light at

260 nm.

• Single-stranded DNA has

higher absorbance than
double- stranded DNA.
 The Double-Strand Helix can be Reversibly Melted
melting
• At high temperature, the base pairs
unstack and the hydrogen bonds annealing
break. This eventually leads to
separation of the two strand:
denaturation.

• Melting Temperature (Tm): the

temperature at which half the
helical structure is lost.

• Denatured DNA will renature when

temperature is lowered slowly.

• G-C pair disruption requires more

energy than A-T pair.

Helix-coil transition is cooperative: early structural changes promote later ones, and
“melting” of the helical structure occurs over a small temperature range;
 PCR
• DAN amplification by polymerase Starting
chain reaction (PCR). template

• Template: contains the DNA

sequence of interest
• Primer: short single stranded DNA
molecules that contains part of the
target sequence
• dNTPs: A, T, G, C nucleotides
• Polymerase: the enzyme that
catalyzes the phosphodiester bond
formation.
With 1 starting template, after 30
cycles of PCR
230 = 1,073,741,824 ~ 1.1 x109

• Amplifying a certain fragment of DNA.

• Introduce mutations
 DNA sequencing
• ddNTP

• DNA to be sequenced
• dNTPs
• DNA polymerase
• Primer
• Fluorescent ddNTP
• Different ddNTP has
different colors
 • Electrophoretogram of
fluorescent DNA
fragments, DNA
molecules are separated
by size

• Sequence of
DNA
 Creation of a recombinant DNA molecule

• Restriction enzymes
(endonucleases) cut DNA
at specific sequences

EcoR1
Cloning a DNA fragment into a plasmid vector
Site directed
mutagenesis
 Manipulating DNA

• Cloned genes yield valuable products

• Genetically modified organisms have practical applications

• Bacteria that can convert solar energy to fuels.
• Transgenic plants
• Animal models for human disease