Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Method 2: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes above). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

Method 2: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes above). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps

• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Method 2: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Method 2: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes above). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Method 2: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes above). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes above). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

"UUUUU" = Upstream annealing region
"ddddd" = Downsream annealing region (reverse complement)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Golden Gate Part Design Reference:

Method 1: Synthesizing dsDNA containing the required overhang regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required overhang regions

You need to order two primers that will anneal to your desired part sequence and contain overhang sequences necessary for proper Golden Gate Assembly.

For easy primer design you can use the shiny app here: https://spleonard1.shinyapps.io/paRting/

Otherwise reference the table in the diagram at the top of the page to add the necessary prefix (XXXX)/suffix (yyyy) to the primer templates below!

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes below). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

CAUTION In Primer 2, the priming site (dddd...) must be the reverse-complement of your part and you must use the suffix-R sequence for the Golden Gate part overlap because this is on the other strand.

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

• All sequences in the table are written 5' to 3'.

• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

Back to Golden Gate Protocols

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes below). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

CAUTION In Primer 2, the priming site (dddd...) must be the reverse-complement of your part and you must use the suffix-R sequence for the Golden Gate part overlap because this is on the other strand.

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

These part overhangs are used by the YTK (yeast toolkit) and the BTK (Broad-host-range toolkit). More information on the design of parts for Golden Gate assembly using these standards can be found in the reference to the YTK (especially in the supplement). Be aware that some definitions vary between the two toolkits.

• All sequences in the table are written 5' to 3'.
• YTK: yeast toolkit; BTK: broad-host-range toolkit.
• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes below). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

CAUTION In Primer 2, the priming site (dddd...) must be the reverse-complement of your part and you must use the suffix-R sequence for the Golden Gate part overlap because this is on the other strand.

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

These part overhangs are used by the YTK (yeast toolkit) and the BTK (Broad-host-range toolkit). More information on the design of parts for Golden Gate assembly using these standards can be found in the reference to the YTK (especially in the supplement). Be aware that some definitions vary between the two toolkits.

• All sequences in the table are written 5' to 3'.
• YTK: yeast toolkit; BTK: broad-host-range toolkit.
• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

These part overhangs are used by the YTK (yeast toolkit) and the BTK (Broad-host-range toolkit). More information on the design of parts for Golden Gate assembly using these standards can be found in the reference to the YTK (especially in the supplement). Be aware that some definitions vary between the two toolkits.

• All sequences in the table are written 5' to 3'.
• YTK: yeast toolkit; BTK: broad-host-range toolkit.
• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

-- Main.KateElston - 14 Dec 2017

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

CAUTION In Primer 2, the priming site (dddd...) must be the reverse-complement of your part and you must use the suffix-R sequence for the Golden Gate part overlap because this is on the other strand.

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

These part overhangs are used by the YTK (yeast toolkit) and the BTK (Broad-host-range toolkit). More information on the design of parts for Golden Gate assembly using these standards can be found in the reference to the YTK (especially in the supplement). Be aware that some definitions vary between the two toolkits.

• All sequences in the table are written 5' to 3'.
• YTK: yeast toolkit; BTK: broad-host-range toolkit.
• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

-- Main.KateElston - 14 Dec 2017

Designing a new part

Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided in the next sections. The end result is the same: a piece of DNA with the proper flanking regions for BsmBI cloning into the entry vector, while maintaining the BsaI sites used in first stage assembly – with proper overhangs for the type of part that you are designing.

Method 1: Synthesizing dsDNA containing the required flanking regions

When ordering a double-stranded piece of DNA to be synthesized, you can just append the sites needed for cloning in your order. Use this protocol when ordering a gBlock from IDT, for example.

5'-GCATCGTCTCATCGGTCTCAXXXX YOUR PART YYYYTGAGACCTGAGACGGCAT-3'
3'-CGTAGCAGAGTAGCCAGAGTxxxx your part yyyyACTCTGGACTCTGCCGTA-5'

Replace XXXX with the prefix-F sequence for the part type you are designing ( see the table and notes below). Similarly, replace YYYY with the suffix-F sequence for the part.

In general, the amount of DNA synthesized is sufficient for cloning into the entry vector without further PCR amplification of a gBlock.

Method 2: Amplifying a sequence with primers that add the required flanking regions

You need to order two primers that append sequences to the ends of the DNA sequence that you are amplifying. If your template looks like the following, then you should design the two primers like the examples.

Template

5'-UUUUUUUUUUUUUUUUUUUU YOUR PART DDDDDDDDDDDDDDDDDDD-3'
3'-uuuuuuuuuuuuuuuuuuuu your part ddddddddddddddddddd-5'

Primer 1 (forward)

5'-GCATCGTCTCATCGGTCTCAXXXXUUUUUUUUUUUUUUUUUUUU-3'

Primer 2 (reverse)

5'-ATGCCGTCTCAGGTCTCAyyyyddddddddddddddddddd-3'

CAUTION In Primer 2, the priming site (dddd...) must be the reverse-complement of your part and you must use the suffix-R sequence for the Golden Gate part overlap because this is on the other strand.

The overlap with the template can vary from the 20 base pairs that are shown according to the normal rules for designing good PCR primers. If calculating melting temperatures, be sure to only include the overlap region in your calculations, not the stuff that is being added to the ends!

Example PCR Reaction

• PCR Insert
• Use standard 25ul Phusion (or other high fidelity polymerase) protocol
• PCR (25ul reaction)
• 5 ul 5x Buffer
• 1.5 ul dntps
• 1.25 ul primer (A+C)
• 1.25 ul primer (B+D)
• x ul template plasmid (<250ng)

ddH20 to 24.5 µl

then add 0.25 µl Phusion

Set elongation time according to size of insert. Purify PCR products

CAUTION The plasmid you are constructing in the entry vector (pYTK001) is camR, so if your template plasmid also encodes chloramphenicol resistance, you should DpnI digest after your PCR reaction, and probably also gel purify the fragment, as any residual plasmid may be transformed and lead to false-positive colonies.

Part Overlap Quick Reference Table

These part overhangs are used by the YTK (yeast toolkit) and the BTK (Broad-host-range toolkit). More information on the design of parts for Golden Gate assembly using these standards can be found in the reference to the YTK (especially in the supplement). Be aware that some definitions vary between the two toolkits.

• All sequences in the table are written 5' to 3'.
• YTK: yeast toolkit; BTK: broad-host-range toolkit.
• Standard bases that are added before or after the actual Golden Gate overhang in prefix / suffix to maintain part function are shown in red.

-- Main.KateElston - 14 Dec 2017