UK Research and Innovation - Oligonucleotide Synthesis and Nucleic Acid Sequencing Services Framework

UKRI wish to put in place a Framework for the purchase of a range of user selectable DNA Sequencing services (Sanger/ ~800-1000 base pair read) from a range of samples and formats including tubes, microtiter plates, preparation & extractions services including from colonies and tissue, with the capability of sequencing from High GC and AT samples.

UKRI wish to put in place a Framework for the purchase of a user selectable range of Custom Gene Synthesis.

It is anticipated that this will be divided into 4 sub lots:

• Sub lot 2.1 - Custom Gene fragment synthesis (sub 2000bp)
• Sub lot 2.2 - Custom Gene fragment synthesis (sub 3000bp)
• Sub lot 2.3 - Custom Gene synthesis (3001-5000bp)
• Sub lot 2.4 - Custom Gene synthesis (5001+ bp)

For the above sub-lots, a range of user selectable additional services should be available. These are to include, but not limited to the following:

• Genes produced with additional synthetic Nucleotides (AGTC + XY)
• Custom vector production
• Codon optimized sequences - all species
• Site-directed mutagenesis
• Bacterial, yeast, Baculovirus and mammalian gene expression services
• Complex sequence synthesis - GC rich, AT rich, complex repeats & hairpin structures and toxic sequences

UKRI wish to put in place a Framework for the purchase of a user selectable (via supplier engagement) range of advanced DNA services.

It is anticipated that this will be divided into 3 sub lots:

• Sub-lot 3.1 - Gene Specific DNA Methylation
• Sub-lot 3.2 - Global DNA Methylation
• Sub-lot 3.3 - Allele quantification

A range of additional advanced DNA services are required to include, but not limited to:

• Perform Bisulfite modification.
• Perform PCR reactions.
• Perform Pyrosequencing analysis.
• LC MS DNA-methylation analysis.
• ELISA that enables the direct quantitation of genomic DNA methylation.
• PCR based methods e.g.; Alu and LINE1.
• Methylation sensitive restriction assays e.g.; luminometric methylation assay (LUMA).
• SNP detection and quantification.
• Assay development for SNP detection and quantification from pooled DNA with a defined 100bp target region in murine DNA.
• Validation of the above assay.
• Sample testing if required for the above assay.

UKRI wish to put in place a framework for the purchase of a range of custom Oligonucleotide synthesis services including Custom DNA oligo's in tubes, plates and RNA/siRNA, to be user selectable via supplier engagement with a range of purification and modification options.

It is anticipated that this will be split into 2 sub lots:

• Sub lot 4.1 - synthesis of DNA oligonucleotides.
• Sub lot 4.2 - synthesis of Custom RNA oligo's (both Single and double stranded RNA oligoes, siRNA) the supply of siRNA Libraries and the production of custom SiRNA Libraries

UKRI wish to put in place a framework for the purchase of a range of custom Oligonucleotide synthesis services including Custom DNA oligo's in tubes, plates and RNA/siRNA, to be user selectable via supplier engagement with a range of purification and modification options. Synthesis of DNA oligonucleotides, synthesis of Custom RNA oligo's (both Single and double stranded RNA oligoes, siRNA) the supply of siRNA Libraries and the production of custom SiRNA Libraries but not limited to:

The production of custom user defined oligonucleotides in the following ranges are required (Inc. plates)

• 0.01UM bases standard
• 0.05UM bases standard
• 0.2UM bases standard
• 1.0UM bases standard
• 0.025 UM / 3OD
• Microtiter plates

Sub lot 1.1 - First Generation Nucleic Acid sequencing services

For the above sub lot, UKRI wish to put in place a framework for the purchase of a range of user selectable Nucleic Acid sequencing (Sanger/ ~800-1000 base pair read) services to be provided. This could include but is not limited to the following:

• Provide Phred 20 quality for as many nucleotides per sample as possible (min 800 bp or above for 5' 3' reads).
• Provide purification and sequencing of plasmids and PCR products in both 1.5 ml tubes and microtiter plates (must offer 96 well as a minimum).
• Provide purification and sequencing of plasmids supplied as Escherichia coli clones in both 1.5 ml tubes and microtiter plates (must offer 96 well as a minimum).
• Provide sequencing services using both primers synthesized by supplier and those with user provided primers.
• Provide Primer walking services in both double and single stranded DNA.

Sub lot 1.2 - Second Generation Nucleic Acid sequencing services

For the above sub lot, UKRI wish to put in place a framework for the purchase of a range of Second Generation sequencing services from a range of samples and formats including tubes, microtiter plates, preparation & extractions services including from colonies and tissue samples.

A range of user selectable Nucleic Acid sequencing services are required that could include but not limited to:

• Ligation or sequencing by synthesis
• Pyrosequencing
• Dye sequencing
• Semiconductor based sequencing
• Provide sample pick-up or sample mailing/courier service as required.
• Provide purification and sequencing of samples supplied
• Offer suitable solutions to templates failing to give readable results

Sub lot 1.3 - Third Generation Nucleic Acid sequencing services

For the above Sub Lot, UKRI wish to put in place a framework for the purchase of a range of Third generation sequencing services from a range of samples and formats including tubes, microtiter plates, preparation & extractions services including from colonies and tissue samples utilising novel or 'next generation technologies.

A range of user selectable Nucleic Acid sequencing services are required that could include but not limited to:

• PCR determination
• combinatorial probe-anchor synthesis (cPAS)
• fluorescently labelled antibody binding sequencing
• Single-molecule real-time (SMRT) sequencing
• zero-mode waveguide sequencing
• sequencing of DNA via Nano pore transition

Sub lot 2.1 - Custom Gene fragment synthesis (sub 2000bp)

UKRI wish to put in place a framework for the purchase of a user selectable (via supplier engagement) range of Custom Gene Synthesis (sub 2000bp).

For the above sub lot, a range of user selectable additional services should be available (but are not mandatory). This could include but is not limited to the following:

• Genes produced with additional synthetic Nucleotides (AGTC + XY)
• Custom vector production
• Codon optimized sequences - all species
• Site-directed mutagenesis
• Bacterial, yeast, Baculovirus and mammalian gene expression services
• Complex sequence synthesis - GC rich, AT rich, complex repeats & hairpin structures and toxic sequences

UKRI wish to put in place a framework for the purchase of a user selectable (via supplier engagement) range of Custom Gene Synthesis (2001 - 3000bp).

For the above sub lot, a range of user selectable additional services should be available (but are not mandatory). This could include but is not limited to the following:

• Genes produced with additional synthetic Nucleotides (AGTC + XY)
• Custom vector production
• Codon optimized sequences - all species
• Site-directed mutagenesis
• Bacterial, yeast, Baculovirus and mammalian gene expression services
• Complex sequence synthesis - GC rich, AT rich, complex repeats & hairpin structures and toxic sequences

Sub Lot 2.3 - Custom Gene synthesis (3001-5000bp)

UKRI wish to put in place a framework for the purchase of a user selectable (via supplier engagement) range of Custom Gene Synthesis (3001 - 5000bp).

For the above sub lot, a range of user selectable additional services should be available (but are not mandatory). This could include but is not limited to the following:

• Genes produced with additional synthetic Nucleotides (AGTC + XY)
• Custom vector production
• Codon optimized sequences - all species
• Site-directed mutagenesis
• Bacterial, yeast, Baculovirus and mammalian gene expression services
• Complex sequence synthesis - GC rich, AT rich, complex repeats & hairpin structures and toxic sequences

UKRI wish to put in place a framework for the purchase of a user selectable (via supplier engagement) range of Custom Gene Synthesis (5001 + bp).

For the above sub lot, a range of user selectable additional services should be available (but are not mandatory). This could include but is not limited to the following:

• Genes produced with additional synthetic Nucleotides (AGTC + XY)
• Custom vector production
• Codon optimized sequences - all species
• Site-directed mutagenesis
• Bacterial, yeast, Baculovirus and mammalian gene expression services
• Complex sequence synthesis - GC rich, AT rich, complex repeats & hairpin structures and toxic sequences

Sub Lot 3.1 - Gene Specific DNA Methylation

UKRI wish to put in place a Framework for the purchase of a range of Gene Specific DNA Methylation services are required to include, but not limited to:

o Perform Bisulfite modification.

o Perform PCR reactions.

o Perform Pyrosequencing analysis.

Sub Lot 3.2 - Global DNA Methylation

UKRI wish to put in place a Framework for the purchase of a range of global DNA methylation services are required to include, but not limited to:

o LC MS DNA-methylation analysis.

o ELISA that enables the direct quantitation of genomic DNA methylation.

o PCR based methods e.g.; Alu and LINE1.

o Methylation sensitive restriction assays e.g.; luminometric methylation assay (LUMA).

Sub Lot 3.3 - Allele quantification

UKRI wish to put in place a Framework for the purchase of a range of Allele quantification services are required to include, but not limited to:

o SNP detection and quantification.

o Assay development for SNP detection and quantification from pooled DNA with a defined 100bp target region in murine DNA.

o Validation of the above assay.

o Sample testing if required for the above assay.

Sub Lot 4.1 - Synthesis of DNA oligonucleotides.

UKRI wish to put in place a framework for the purchase of a range of custom Oligonucleotide synthesis services including Custom DNA oligo's in tubes, plates and RNA/siRNA, to be user selectable via supplier engagement with a range of purification and modification options.

The production of custom user defined oligonucleotides in the following ranges are required (Inc. plates).

• 0.01UM bases standard
• 0.05UM bases standard
• 0.2UM bases standard
• 1.0UM bases standard
• 0.025 UM / 3OD
• Microtiter plates

Sub Lot 4.2 - Synthesis of Custom RNA oligo's (both Single and double stranded RNA oligoes, siRNA) the supply of siRNA Libraries and the production of custom SiRNA Libraries

UKRI wish to put in place a framework for the purchase of a range of custom Oligonucleotide synthesis services including Custom DNA oligo's in tubes, plates and RNA/siRNA, to be user selectable via supplier engagement with a range of purification and modification options.

The production of custom user defined oligonucleotides in the following ranges are required (Inc. plates).

• 0.01UM bases standard
• 0.05UM bases standard
• 0.2UM bases standard
• 1.0UM bases standard
• 0.025 UM / 3OD
• Microtiter plates