The Power of Molecular

Biological Techniques

Mark E. Sobel, MD, PhD

Executive Officer
American Society for Investigative Pathology
[email protected]
www.asip.org
 Overview

I. Introduction to Molecular Pathology

II. DNA, Restriction Enzymes,

Hybridization, PCR

III. Introduction to the Genome

IV. Applications to Molecular Medicine:

SNPs and Chips
 TEST YOUR SCIENCE LITERACY
Adapted from Dave Barry, Miami Herald

Explain in your own words, what is DNA?

1. DNA is deoxyribonucleicantidisestablishmentarianism, a
complex string of syllables found inside your body in tiny
genes called chromosomes.

2. The information in your DNA determines your unique

biological characteristics, such as eye color, Social
Security number, and age. There is surprisingly little
difference between DNA in humans, Democrats, and
Republicans.
Highly Sensitive and Specific
by “Orders of Magnitude”

from Powers of Ten, by Charles and Ray Eames

 BIOLOGY: THE STUDY OF LIFE

1. WHOLE ORGANISMS
2. ORGANS
3. TISSUES
4. CELLS
5. INTRACELLULAR ORGANELLES
6. CHEMICAL COMPONENTS
 CHEMICAL COMPONENTS OF LIFE

1. PROTEINS
2. LIPIDS
3. NUCLEIC ACIDS:
• DNA
• RNA
 MOLECULAR BIOLOGY TECHNIQUES

Molecular biology techniques

utilize DNA, RNA, and enzymes
that interact with nucleic acids to
understand biology at a molecular
level.
 MOLECULAR PATHOLOGY

Molecular Pathology is a subspecialty

of pathology that utilizes molecular
biology techniques to:
•Detect normal and disease states
(diagnosis)
•Predict disease progression
(prognosis)
 SUBSPECIALTIES OF
MOLECULAR PATHOLOGY
•INHERITED DISEASES (GENETICS)
– Cystic fibrosis
– Sickle cell anemia
– Predispositions to cancer
•INFECTIOUS DISEASES
– Bacteria
– Viruses
– Fungi
 SUBSPECIALTIES OF
MOLECULAR PATHOLOGY

•HEMATOPATHOLOGY
– Leukemias
– Lymphomas
•SOLID TUMORS
– Breast cancer
– Colon cancer
– Brain cancer
 SUBSPECIALTIES OF
MOLECULAR PATHOLOGY

•FORENSICS

•IDENTITY TESTING
– HLA
– parentage
 NUCLEIC ACIDS
• Genetic material of all known organisms
• DNA: deoxyribonucleic acid
• RNA: ribonucleic acid (e.g., some viruses)
• Consist of chemically linked sequences of nucleotides
• Nitrogenous base
• Pentose- 5-carbon sugar (ribose or deoxyribose)
• Phosphate group
• The sequence of bases provides the genetic information
 Bases

• Two types of bases

• Purines are fused five- and six-membered rings
• Adenine A DNA RNA
• Guanine G DNA RNA
• Pyrimidines are six-membered rings
• Cytosine C DNA RNA
• Thymine T DNA
• Uracil U RNA
 Base-pairing

• Hydrogen bonds are relatively weak bonds

compared to covalent bonds
• Hydrogen bonds can form between a pyrimidine
and a purine

• Watson-Crick base-pairing rules

•A T
•G C
 Hydrogen Bonds
H H
H
H C O
H N H
C N
Thymine C C
C C
H C N Adenine
H N
N C
N C
C N
O
H

H N
H
C N H
Cytosine C O
C
H C N C C
Guanine
H N
N C N C
O N
C

N
H H
 DNA: Helix
3’

5’ 5’

3’

In general, DNA is double-stranded.

Double-stranded (ds) DNA takes the
form of a right handed helix with
approximately 10 base pairs per turn of
the helix.
 Complementarity

• In the DNA double helix, purines and pyrimidines

face each other
• The two polynucleotide chains in the double helix
are connected by hydrogen bonds between the
bases
• Watson-Crick base-pairing rules
•A T
•G C
• GC base pairs (bps)have more energy than AT bps
• Since one strand of DNA is complementary to the
other, genetic material can be accurately
reproduced; each strand serves as the template
for the synthesis of the other
 Antiparallel Chains

5’p OH 3’

3’OH p5’

Two strands of the DNA double helix are

antiparallel and complementary to each
other
 Gene

•A gene is a unit of inheritance

•Carries the information for a:
-polypeptide
-structural RNA molecule

flank flank

5’ promoter Structural gene 3’

upstream downstream
 Nucleases

5’ Exonuclease 3’ Exonuclease

Endonuclease
 Restriction enzymes

• Specific endonucleases
• Recognize specific short sequences of DNA and
cleave the DNA at or near the recognition
sequence
• Recognition sequences: usually 4 or 6 bases but
there are some that are 5, 8, or longer
• Recognition sequences are palindromes
• Palindrome: sequence of DNA that is the same
when one strand is read from left to right or the
other strand is read from right to left– consists of
adjacent inverted repeats
 Restriction enzymes (cont’d)

• Example of a palindrome:
GAATTC
CTTAAG
• Restriction enzymes are isolated from bacteria
• Derive names from the bacteria
• Genus- first letter capitalized
• Species- second and third letters (small case)
• Additional letters from “strains”
• Roman numeral designates different enzymes from the
same bacterial strain, in numerical order of discovery
• Example: EcoRI
– E Escherichia
– Co coli
– R R strain
– I first enzyme discovered from Escherichia coli R
 Hybridization

• Nucleic acid hybridization is the formation of a

duplex between two complementary sequences
• Intermolecular hybridization: between two
polynucleotide chains which have complementary
bases
– DNA-DNA
– DNA-RNA
– RNA-RNA
• Annealing is another term used to describe the
hybridization of two complementary molecules
 Denaturation - Renaturation

Denaturation Renaturation

Double- Single- Initial Renatured

stranded stranded Base DNA
DNA DNA pairing
 Probes

• Probe is a nucleic acid that

– can be labeled with a marker which allows
identification and quantitation
– will hybridize to another nucleic acid on the basis of
base complementarity
• Types of labels
– Radioactive (32P, 35S, 14C, 3H)
– Fluorescent
• FISH: fluorescent in situ hybridization
– chromosomes
– Biotinylated (avidin-streptavidin)
 Solid Support Hybridization

• Solid support hybridization: DNA or RNA is

immobilized on an inert support so that self-annealing
is prevented
• Bound sequences are available for hybridization with
an added nucleic acid (probe).
• Filter hybridization is the most common application:
– Southern Blots
– Dot/Slot Blots
– Northern Blots
• In-silica hybridization (glass slides)
– in situ hybridization (tissue)
– Chromosomal (FISH)
– Microarrays
 Southern Blots

• Southern blotting is a procedure for transferring

denatured DNA from an agarose gel to a solid
support filter where it can be hybridized with a
complementary nucleic acid probe
• The DNA is separated by size so that specific
fragments can be identified
• Procedure:
– Restriction digest to make different sized fragments
– Agarose gel electrophoresis to separate by size
– Since only single strands bind to the filter, the DNA
must be denatured.
– Denaturation to permit binding to the filter (NaOH)
– Transfer to filter paper (capillary flow)
– Hybridization to probe
– Visualization of probe
Southern Blot

Restriction enzyme

DNA of
various sizes

Electrophorese on agarose gel

gel

Denature - transfer to
filter paper.

blot
Denature- transfer to
filter paper.

blot

Hybridize to probe

Visualize
Southern Blot
 Dot/Slot Blots

• DNA or RNA is bound directly to a solid support

filter
• No size separation
• Ideal for multiple samples and quantitative
measurements
• Important to establish specificity of conditions
Slot Blot
A Focus of Development: Automation
User-Friendly, Faster, and Cost-Effective

This electronic microarray is an example of "Lab-on-a-Chip"

technology. It is an electrophoresis device that produces
results up to 1000 times faster than conventional techniques
while using much less sample.
 High Resolution Banding and FISH

Control Signals

Region-Specific Signal

The chromosome banding technique performed 20 years ago missed the

small deletion. High resolution banding developed more recently can
elucidate the abnormality. Fluorescence in situ Hybridization (FISH) is a
powerful technique in that it can reveal submicroscopic abnormalities even
in non-dividing cells.
 Polymerase chain reaction

• PCR is the in vitro enzymatic

synthesis and amplification of
specific DNA sequences
• Can amplify one molecule of
DNA into billions of copies in a
few hours
 Applications of PCR

• Detection of chromosomal translocations

– Amplification across a translocation sequence
• Chromosome painting
• Detection of residual disease
• Infectious disease
• Forensics
• HLA typing
• Detection of Loss of Suppressor Genes
– Loss of Heterozygosity (LOH)
 Genome Literacy

• Genome: The entire DNA of an organism

– Humans
• diploid (chromosome pairs)
• 6 x 109 bp per diploid genome
• Haploid genome is one set of chromosomes
• Chromosome: structure found within a cell
nucleus consisting of a continuous length of ds
DNA
– Humans
• 22 pairs of autosomal chromosomes
• 2 sex chromosomes
 Human Genome Project

• 40,000 genes
• Speaking a language of molecular
fingerprints
• Gene expression is another language of
complexity
 Genome Mapping Terms

• Locus: a position on a chromosome

• Allele: alternate form of DNA at a
specific locus on the chromosome
– Each individual inherits two copies of
DNA
• Maternal
• Paternal
– Homozygous alleles: the two copies
are identical
– Heterozygous alleles: the two copies
are different
Restriction fragment length polymorphism

• RFLP is a polymorphic allele identified by the

presence or absence of a specific restriction
endonuclease recognition site:
– GAATTC versus GATTTC
• RFLP is usually identified by digestion of genomic
DNA with specific restriction enzymes followed by
Southern blotting
• Regions of DNA with polymorphisms:
– Introns
– Flanking sequences
– Exons
 Genetic Variation

• Most genes have small sequence differences between individuals

– Occur every 1350 bp on average
• Some of these polymorphisms may affect:
– How well the protein works
– How the protein interacts with another protein or substrate
• The different gene forms containing polymorphisms are called
alleles
 Mutation detection

• Sequence DNA
• Hybridization Methods
– Blotting
– Chips
• Restriction enzyme polymorphisms:
– GAATTC versus GATTTC
• SNPs (single nucleotide polymorphisms)
 SNPs

• Single nucleotide polymorphisms

• Distinction from mutations
 ASO

Allele Specific Oligonucleotides

ATGTGGCCATGTGGC

ATGCGGCCATGTGGC

ASOs can be used to detect SNPs

(single nucleotide polymorphisms)
 More About SNPs

• SNPs in exons are called coding SNPs

• SNPs in introns or regulatory regions may affect
transcription, translation, RNA stability, RNA
splicing
 Pharmacogenomics
• Cytochrome P450
• Uptake and metabolsim of drugs
• Seizure disorders
• Psychiatric disorders
• Cancer therapy
 Resources

• www.amptestdirectory.org is an online directory of

laboratories that perform molecular techniques.

• www.genetests.org has an illustrated glossary and good

explanations of genetic testing.

• http://www.ornl.gov/sci/techresources/Human_Genome/education/
has links to many educational resources and images.

• http://www.dnalc.org/resources/resources.html has an
animated DNA primer targeted at the level of a “bright
teenager.” It is a part of the website of the Dolan DNA
Learning Center of Cold Spring Harbor Laboratory.
 FISH

r = 0.91

log10 (ratio), T3-3

aRA

Microarrays 

Laser microscope Tissue arrays
genome