HERBAL DRUG TECHNOLOGY

PLANT DNA
FINGERPRINTING

Dr. Oeke Yunita, S.Si., M.Si., Apt.

Pharmaceutical Biology,
Faculty of Pharmacy, University of Surabaya
INDONESIA
oeke.ynita@gmail.com
Genetic structure of rDNA (ribosomal DNA) Repeat

IGS = intergenic spacer; includes the promoter region for RNA Pol I complex
ITS = internal transcribed spacers

5’ ETS ITS1 ITS2 IGS 3’

18S 26S 18S

5.8S

In angiosperms, rDNA are organized in long tandem repeats, with

each containing a single transcribed region spanning the 18S, 5.8S,
and 26S rDNA, ITS1 and ITS2, and IGS. Although the 18S, 5.8S, and
26S rDNA are highly conserved, the ITS regions are variable in
different genus, species, even populations. Thus, the diversity of the
ITS region is widely used as a molecular marker for species
authentication and polygenetic analysis.
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• DNA fingerprinting is a useful tool in plant genetics
to meet recent challenges:
– Cultivar identification
– Maintenance of breeding lines
– Protecting breeders’ rights
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QUALITY ASSURANCE PROTOCOL
FOR HERBAL MEDICINE PRODUCT

CORRECT IDENTIFICATION
• small amount of
dried/powdered sample
provided;
• ambiguous taxonomy due to
confusion between Latin
nomenclature and local
terminology;
• adulteration of rare,
expensive medicinal plants
with easily available local
plants. - AUTHENTICATION

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 COMPARISON OF DIFFERENT AUTHENTICATION METHODS

Zhao, et al., 2007. QC of Chinese Herbal Medicines, Journal of Food and Drug Analysis, Vol. 15,
No. 4, 337-346 5
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APPLICATION OF MOLECULAR MARKER
(Khushwaha et al., Arch. Appl. Sci. Res., 2(1): 225-229

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 DNA markers used for HERBAL DRUG
identification

• DNA sequencing marker：

Show the difference of aim gene directly，information is accurate
and universal
1. chloroplast DNA (cpDNA)：evolves relatively slowly, moderate to
detect the genetic variation and relationship of high levels, such as intra–
family, family and upward family level. matK、atpB、rps1b、rbcL、
ndhD、trnK、trnF、trnT,
2. mitochondria DNA(mtDNA) ： mainly applied in phylogenetic and
evolutionary studies of animal, as well as the identification of animal
medicines. cyt-b、12Sr DNA are most important markers.
3. nuclear DNA(nDNA) ： important DNA markers for phylogeny and
identification of angiosperms. Further ,we will give emphasis to rDNA.

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 IDEAL MOLECULAR MARKER

MOLECULAR MARKER = DNA sequence that is readily detected and whose inheritance can easily
be monitored.

GENETIC POLYMORPHISM = simultaneous occurence of a trait in the same population of two

discontinuous variants or genotypes.

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Characteristic of markers
phenotype
subjective
• Shape、colour、odor—morphologic markers
• tissue、cell— cellular markers
• Chemical component and content—metabolic product markers

Effect of gene with environment together

polymorphic DNA — molecular markers

genotype
objective

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METABOLOMICS WORKFLOW

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 DNA PATTERNS

Data Preprocessing

HIERARHICAL
CLUSTER
ANALYSIS

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 PCR – RAPD on ITS region of DNA of
S.androgynus from different locations
(Oeke Yunita & Sulisetiorini, 2013, Shaker Verlag)

OPF-07

OPF-12

OPF-15
Sauropus androgynus
katuk, star gooseberry,
SB ST TI BI BJI BJIII PWSI PWD or sweet leaf, phakwan
baan
SP M TII BJI M PWSII
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 SIMILARITY INDEX OF 12 Samples
Katuk (Primer OPF-7, OPF-12, OPF-15)
(Yunita and Sulisetiorini, 2013)
SIMPLE MATCHING MEASURE
SB SP ST T-I T-II B-I BJ-I BJ-II BJ-III PWS-I PWS- PWD
II
SB 1,000
SP 0,821 1,000
ST 0,852 0,865 1,000
T-I 0,803 0,817 0,847 1,000
T-II 0,808 0,812 0,852 0,795 1,000
B-I 0,799 0,821 0,843 0,803 0,790 1,000
BJ-I 0,808 0,821 0,852 0,803 0,799 0,799 1,000
BJ-II 0,821 0,825 0,856 0,808 0,803 0,803 0,821 1,000
BJ-III 0,852 0,865 0,895 0,847 0,843 0,843 0,852 0,856 1,000
PWS-I 0,843 0,856 0,886 0,847 0,834 0,834 0,843 0,847 0,886 1,000
PWS- 0,799 0,812 0,843 0,795 0,790 0,799 0,799 0,803 0,843 0,834 1,000
II
PWD 0,803 0,808 0,838 0,799 0,795 0,786 0,795 0,799 0,838 0,83 0,803 1,000
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DENDOGRAM of KATUK (Sauropus androgynus)
(Yunita and Sulisetiorini, 2013)

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 PLANT DNA BARCODING
Barcoding is a standardized approach to identifying plants and animals by
minimal sequences of DNA, called DNA barcodes.

DNA Barcode: A short DNA sequence, from a uniform locality on the

genome, used for identifying species.
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