SlideShare a Scribd company logo
siRNA
Design
Reza Rakhshi
Master student of Med Biotechnology
Find CDS Sequence:
1. Go NCBI
2. Choose Nucleotide Database
3. Write your Gene name
4. Active mRNA and Ref seq
5. Extract CDS
Reza Rakhshi, Master student of Medical Biotechnology
Find CDS Sequence-step2,3:
Reza Rakhshi, Master student of Medical Biotechnology
2
3
Find CDS Sequence-step4:
Reza Rakhshi, Master student of Medical Biotechnology
Find CDS Sequence-step5:
Reza Rakhshi, Master student of Medical Biotechnology
FASTA
Create siRNA-invitrogen Database:
Reza Rakhshi, Master student of Medical Biotechnology
Create siRNA- appoint parameter:
Reza Rakhshi, Master student of Medical Biotechnology
Write Accession
OR
number or paste
FASTA seq.
Create siRNA- appoint
parameter:
Reza Rakhshi, Master student of Medical Biotechnology
Create siRNA- Results:
Reza Rakhshi, Master student of Medical Biotechnology
1. Good seq has AT
at 𝟑′ and CG at 𝟓′
2. Good seq must
not repeated seq
Seem good items
Analyse seq:
– First of all we must get antisense seq from sense seq.
– Use Gene Runner App for this work
– Then use Oligo analyser App.
Reza Rakhshi, Master student of Medical Biotechnology
Antisense seq
Sense seq
Analyse seq:
Reza Rakhshi, Master student of Medical Biotechnology
Paste Antisense seq
and analye frequent
options
Analyse seq:
Reza Rakhshi, Master student of Medical Biotechnology
Temperature and
structure is normal
Analyse seq- immunogenic seq:
– Use Gene Runner App.
– Press Crtl + F and find all of immunogenic seq available below:
1. GTCCTTCAA 2. TGTGT
3. TGT 4. TCA
5. UGGC 6. GT-rich sequences
7. AT-rich sequences 8. T-rich sequences
Reza Rakhshi, Master student of Medical Biotechnology
Reza Rakhshi, Master student of Medical Biotechnology
mRNA accessibility:
– Need RNA Fold app.
1. Paste (whole mRNA) FASTA on box
2. Press PROCEED
3. Find siRNA in whole mRNA
Reza Rakhshi, Master student of Medical Biotechnology
Reza Rakhshi, Master student of Medical Biotechnology
1
2
Analyse RNA Fold:
Reza Rakhshi, Master student of Medical Biotechnology
Find siRNA in whole genome
– We need Gene Runner App.
1. Paste whole mRNA
2. Press Ctrl + F and find siRNa seq (sense seq)
3. Find your siRNA in RNA Fold pic
Reza Rakhshi, Master student of Medical Biotechnology
Reza Rakhshi, Master student of Medical Biotechnology
1
2
3
siRNA position
Reza Rakhshi, Master student of Medical Biotechnology
Start nt
(1197)
finish nt
(1221)
Better
than this
sequence
exist in
loop
because
your siRNA
can stick
easily to it.
Reza Rakhshi, Master student of Medical Biotechnology
Thanks for your attention

More Related Content

Similar to siRNA desiging

Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
QIAGEN
 
Bro gef mi_rna_0212_lr
Bro gef mi_rna_0212_lrBro gef mi_rna_0212_lr
Bro gef mi_rna_0212_lr
Elsa von Licy
 
Rn ai
Rn aiRn ai
Tpa 2013
Tpa 2013Tpa 2013
Tpa 2013
Elsa von Licy
 
Technical Guide to Qiagen PCR Arrays - Download the Guide
Technical Guide to Qiagen PCR Arrays - Download the GuideTechnical Guide to Qiagen PCR Arrays - Download the Guide
Technical Guide to Qiagen PCR Arrays - Download the Guide
QIAGEN
 
Sh rna 2013
Sh rna 2013Sh rna 2013
Sh rna 2013
Elsa von Licy
 
Principle and method of RNAi-Creative Biogene
Principle and method of RNAi-Creative BiogenePrinciple and method of RNAi-Creative Biogene
Principle and method of RNAi-Creative Biogene
Donglin Bao
 
Multiplex Assays for Studying Gene Regulation and Cell Function
Multiplex Assays for Studying Gene Regulation and Cell FunctionMultiplex Assays for Studying Gene Regulation and Cell Function
Multiplex Assays for Studying Gene Regulation and Cell Function
MiraiBio Group of Hitachi Solutions America, Ltd.
 
Rna seq
Rna seq Rna seq
Rna seq
Amitha Dasari
 
A Study on Genome Editing Tools
A Study on Genome Editing ToolsA Study on Genome Editing Tools
A Study on Genome Editing Tools
Suneet Meena
 
Mi rna array 2013
Mi rna array 2013Mi rna array 2013
Mi rna array 2013
Elsa von Licy
 
Reporter assay and q pcr application 2012
Reporter assay and q pcr application 2012Reporter assay and q pcr application 2012
Reporter assay and q pcr application 2012
Elsa von Licy
 
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
QIAGEN
 
(Rn ai)
(Rn ai)(Rn ai)
Mi rna part ii_2013
Mi rna part ii_2013Mi rna part ii_2013
Mi rna part ii_2013
Elsa von Licy
 
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeqEfficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
Theofilatos Konstantinos
 
PCR Primer Design Tool for Sanger Sequencing Confirmation
PCR Primer Design Tool for Sanger Sequencing ConfirmationPCR Primer Design Tool for Sanger Sequencing Confirmation
PCR Primer Design Tool for Sanger Sequencing Confirmation
Thermo Fisher Scientific
 
31931 31941
31931 3194131931 31941
31931 31941
Amit Gupta
 
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
QIAGEN
 
Mi rna series i-dec 2012
Mi rna series i-dec 2012Mi rna series i-dec 2012
Mi rna series i-dec 2012
Elsa von Licy
 

Similar to siRNA desiging (20)

Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
Advanced miRNA Expression Analysis: miRNA and its Role in Human Disease Webin...
 
Bro gef mi_rna_0212_lr
Bro gef mi_rna_0212_lrBro gef mi_rna_0212_lr
Bro gef mi_rna_0212_lr
 
Rn ai
Rn aiRn ai
Rn ai
 
Tpa 2013
Tpa 2013Tpa 2013
Tpa 2013
 
Technical Guide to Qiagen PCR Arrays - Download the Guide
Technical Guide to Qiagen PCR Arrays - Download the GuideTechnical Guide to Qiagen PCR Arrays - Download the Guide
Technical Guide to Qiagen PCR Arrays - Download the Guide
 
Sh rna 2013
Sh rna 2013Sh rna 2013
Sh rna 2013
 
Principle and method of RNAi-Creative Biogene
Principle and method of RNAi-Creative BiogenePrinciple and method of RNAi-Creative Biogene
Principle and method of RNAi-Creative Biogene
 
Multiplex Assays for Studying Gene Regulation and Cell Function
Multiplex Assays for Studying Gene Regulation and Cell FunctionMultiplex Assays for Studying Gene Regulation and Cell Function
Multiplex Assays for Studying Gene Regulation and Cell Function
 
Rna seq
Rna seq Rna seq
Rna seq
 
A Study on Genome Editing Tools
A Study on Genome Editing ToolsA Study on Genome Editing Tools
A Study on Genome Editing Tools
 
Mi rna array 2013
Mi rna array 2013Mi rna array 2013
Mi rna array 2013
 
Reporter assay and q pcr application 2012
Reporter assay and q pcr application 2012Reporter assay and q pcr application 2012
Reporter assay and q pcr application 2012
 
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...
 
(Rn ai)
(Rn ai)(Rn ai)
(Rn ai)
 
Mi rna part ii_2013
Mi rna part ii_2013Mi rna part ii_2013
Mi rna part ii_2013
 
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeqEfficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
Efficient and accurate analysis of non-coding RNAs with InSyBio ncRNASeq
 
PCR Primer Design Tool for Sanger Sequencing Confirmation
PCR Primer Design Tool for Sanger Sequencing ConfirmationPCR Primer Design Tool for Sanger Sequencing Confirmation
PCR Primer Design Tool for Sanger Sequencing Confirmation
 
31931 31941
31931 3194131931 31941
31931 31941
 
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
Advanced Real-Time PCR Array Technology – Coding and Noncoding RNA Expression...
 
Mi rna series i-dec 2012
Mi rna series i-dec 2012Mi rna series i-dec 2012
Mi rna series i-dec 2012
 

Recently uploaded

Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdfApplied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
University of Hertfordshire
 
Basics of crystallography, crystal systems, classes and different forms
Basics of crystallography, crystal systems, classes and different formsBasics of crystallography, crystal systems, classes and different forms
Basics of crystallography, crystal systems, classes and different forms
MaheshaNanjegowda
 
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
University of Maribor
 
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titrationCompexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
Vandana Devesh Sharma
 
SAR of Medicinal Chemistry 1st by dk.pdf
SAR of Medicinal Chemistry 1st by dk.pdfSAR of Medicinal Chemistry 1st by dk.pdf
SAR of Medicinal Chemistry 1st by dk.pdf
KrushnaDarade1
 
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
AbdullaAlAsif1
 
aziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobelaziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobel
İsa Badur
 
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdfwaterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
LengamoLAppostilic
 
Phenomics assisted breeding in crop improvement
Phenomics assisted breeding in crop improvementPhenomics assisted breeding in crop improvement
Phenomics assisted breeding in crop improvement
IshaGoswami9
 
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
yqqaatn0
 
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defectsThe binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
Sérgio Sacani
 
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityDeep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless Reproducibility
University of Rennes, INSA Rennes, Inria/IRISA, CNRS
 
Micronuclei test.M.sc.zoology.fisheries.
Micronuclei test.M.sc.zoology.fisheries.Micronuclei test.M.sc.zoology.fisheries.
Micronuclei test.M.sc.zoology.fisheries.
Aditi Bajpai
 
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero WaterSharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Texas Alliance of Groundwater Districts
 
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically youngThe debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Sérgio Sacani
 
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốtmô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
HongcNguyn6
 
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdfTopic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
TinyAnderson
 
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Leonel Morgado
 
Thornton ESPP slides UK WW Network 4_6_24.pdf
Thornton ESPP slides UK WW Network 4_6_24.pdfThornton ESPP slides UK WW Network 4_6_24.pdf
Thornton ESPP slides UK WW Network 4_6_24.pdf
European Sustainable Phosphorus Platform
 
NuGOweek 2024 Ghent programme overview flyer
NuGOweek 2024 Ghent programme overview flyerNuGOweek 2024 Ghent programme overview flyer
NuGOweek 2024 Ghent programme overview flyer
pablovgd
 

Recently uploaded (20)

Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdfApplied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
 
Basics of crystallography, crystal systems, classes and different forms
Basics of crystallography, crystal systems, classes and different formsBasics of crystallography, crystal systems, classes and different forms
Basics of crystallography, crystal systems, classes and different forms
 
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
 
Compexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titrationCompexometric titration/Chelatorphy titration/chelating titration
Compexometric titration/Chelatorphy titration/chelating titration
 
SAR of Medicinal Chemistry 1st by dk.pdf
SAR of Medicinal Chemistry 1st by dk.pdfSAR of Medicinal Chemistry 1st by dk.pdf
SAR of Medicinal Chemistry 1st by dk.pdf
 
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
 
aziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobelaziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobel
 
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdfwaterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
 
Phenomics assisted breeding in crop improvement
Phenomics assisted breeding in crop improvementPhenomics assisted breeding in crop improvement
Phenomics assisted breeding in crop improvement
 
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
 
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defectsThe binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
 
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityDeep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless Reproducibility
 
Micronuclei test.M.sc.zoology.fisheries.
Micronuclei test.M.sc.zoology.fisheries.Micronuclei test.M.sc.zoology.fisheries.
Micronuclei test.M.sc.zoology.fisheries.
 
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero WaterSharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
 
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically youngThe debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
 
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốtmô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
mô tả các thí nghiệm về đánh giá tác động dòng khí hóa sau đốt
 
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdfTopic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf
 
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
 
Thornton ESPP slides UK WW Network 4_6_24.pdf
Thornton ESPP slides UK WW Network 4_6_24.pdfThornton ESPP slides UK WW Network 4_6_24.pdf
Thornton ESPP slides UK WW Network 4_6_24.pdf
 
NuGOweek 2024 Ghent programme overview flyer
NuGOweek 2024 Ghent programme overview flyerNuGOweek 2024 Ghent programme overview flyer
NuGOweek 2024 Ghent programme overview flyer
 

siRNA desiging