Molecular Techniques for

Identifying Unknown
Organisms
Improved DNA technologies for
defining site communities and
sources of biological contamination.
 Methods for Site Analysis
• Molecular Analysis – PCR, DGGE, RFLP, Sequencing,
Restriction Enzyme Assay.

• Microbiological Analysis – Culture, Selective Media,

Plate Counts, Microscopic Examination.

• Biochemical Analysis – Elisa, Protein Assay,

Biomarker Analysis.

• Chemical Analysis – GC/MS, LC, Toxicology Assay,

Chemical Profiling.
Polymerase Chain Reaction

• Amplification of specific DNA

sequences.
• 1-2 copies of a gene into millions of
copies.
• Sequence Analysis and Species
Identification.
 DGGE - Denaturing Gradient
Gel Electrophoresis

• Separates DNA fragments based on

sequence composition.
• Isolation of species based on DNA
sequence not culturing.
• Profiling of microbial communities and
their development over time.
RFLP and Restriction Analysis

• RFLP – Random Fragment Length

Polymorphisms.
– Uses differences in gene length and gene copy
number to differentiate subspecies.

• Restriction Enzyme Assay.

– Uses enzymes to cut DNA into small fragments
which can then be used to profile a species or
subspecies.
ELISA – Enzyme Linked
Immunosorbent Assay

• Uses antibodies linked with enzymes to

detect specific proteins and biomarkers.
• Colorimetric change is used to detect and
quantify target.
• Can also detect specific segments of
DNA based on secondary structure.
 Source Tracking

• Comparing chemical and biological

profiles between sample site and
potential sources.
• Using target compounds/species to
source track.
• DNA fingerprinting/profiling to show
match between sample site and source.