Examples Level 2

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January 7, 2009

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Examples level 2 service

Example 1: designing hydroleasy^® assay

A customer wanted a HydrolEasy^® assay to quantify expression of his favorite gene. He therefore sent us the sequence of that gene. PentaBase designed primers and probes according to the best standards including primers spanning an intron, short amplicon to ensure linearity of standard curve, correct positioning of the probe to ensure proper cleavage of fluorophore, correct design of the probe to ensure high signal-to-noise ratio and correct design of primers to ensure specific and efficient priming.

If you would like us to design your HydrolEasy^® assay please send us:

The NCBI reference e.g: J04038^aor your sequence electronically: e.g.

     exon            <1..29
                     /gene="GAPD"
                     /note="glyceraldehyde-3-phosphate dehydrogenase, (first
                     expressed exon) (EC 1.2.2.12)"
                     /number=2
     exon            30..129
                     /gene="GAPD"
     exon            130..236
                     /gene="GAPD"
                     /number=4
     exon            237..327
                     /gene="GAPD"
                     /number=5
     exon            328..443
                     /gene="GAPD"
                     /number=6
     exon            444..525
                     /gene="GAPD"
                     /number=7
     exon            526..938
                     /gene="GAPD"
                     /number=8
     exon            939..>1008
                     /gene="GAPD"
                     /note="glyceraldehyde-3-phosphate dehydrogenase"
                     /number=9
ORIGIN
        1 atggggaagg tgaaggtcgg agtcaacgga tttggtcgta ttgggcgcct ggtcaccagg
       61 gctgctttta actctggtaa agtggatatt gttgccatca atgacccctt cattgacctc
      121 aactacatgg tttacatgtt ccaatatgat tccacccatg gcaaattcca tggcaccgtc
      181 aaggctgaga acgggaagct tgtcatcaat ggaaatccca tcaccatctt ccaggagcga
      241 gatccctcca aaatcaagtg gggcgatgct ggcgctgagt acgtcgtgga gtccactggc
      301 gtcttcacca ccatggagaa ggctggggct catttgcagg ggggagccaa aagggtcatc
      361 atctctgccc cctctgctga tgcccccatg ttcgtcatgg gtgtgaacca tgagaagtat
      421 gacaacagcc tcaagatcat cagcaatgcc tcctgcacca ccaactgctt agcacccctg
      481 gccaaggtca tccatgacaa ctttggtatc gtggaaggac tcatgaccac agtccatgcc
      541 atcactgcca cccagaagac tgtggatggc ccctccggga aactgtggcg tgatggccgc
      601 ggggctctcc agaacatcat ccctgcctct actggcgctg ccaaggctgt gggcaaggtc
      661 atccctgagc tgaacgggaa gctcactggc atggccttcc gtgtccccac tgccaacgtg
      721 tcagtggtgg acctgacctg ccgtctagaa aaacctgcca aatatgatga catcaagaag
      781 gtggtgaagc aggcgtcgga gggccccctc aagggcatcc tgggctacac tgagcaccag
      841 gtggtctcct ctgacttcaa cagcgacacc cactcctcca cctttgacgc tggggctggc
      901 attgccctca acgaccactt tgtcaagctc atttcctggt atgacaacga atttggctac
      961 agcaacaggg tggtggacct catggcccac atggcctcca aggagtaa

Synthesis scale of your choice: 5 nmol¹, 40 nmol, 200 nmol or 1 umol and
Delivery and payment details (or username from our home page)

You will then receive:

An order confirmation followed by
A HydrolEasy^® probe e.g: FAM-AGCTTCCCGTTCTCAG-TAMRA comprising 4 HyNAs (not shown)
Two SuPrimers e.g: 5'-GAAGGTGAAGGTCGGAGT and 5'-AAGATGGTGATGGGATTTC each comprising 1-2 HyNAs (not shown)
A short report explaining the design and assay suggestion.

Order online or send an email with your order or inquiry.

Questions? Why not contact us on our online support.

Example 2: Designing an EasyBeacon™ assay

Another customer wanted an EasyBeacon™ assay to detect a complex SNP. He therefore sent us the sequence of his target underlining the position of the SNP. PentaBase designed primers and probes according to the best standards, including primers amplifying the correct region without amplifying off-target regions. We positioned the probe in relation to the SNP to obtain a very specific signal, designed the probe to anneal before the primers and designed the primers to ensure specific and efficient priming.

If you would like us to design your EasyBeacon™ assay please send us:

The NCBI reference e.g: J04038^aor your sequence electronically. Make sure to underline or in other ways clarify the positions of variation. Describe the alleles that you want to differentiate between.
Synthesis scale of your choice: 5 nmol¹, 40 nmol, 200 nmol or 1 umol and
Delivery and payment details (or username from our home page)

You will then receive:

An order confirmation followed by
An EasyBeacon™ e.g: FAM-TAGGGTAACAGCGGCG-DABCYL comprising 4 HyNAs (not shown)
Two SuPrimers e.g: 5'-GAAGGTGAAGGTCGGAGT and 5'-AAGATGGTGATGGGATTTC each comprising 1-2 HyNAs (not shown)^a,b
A short report explaining the design and assay suggestion.

Order online or send an email with your order or inquiry.

Questions? Why not contact us on our online support.

Example 3: changing DNA primers to SuPrimers™

Do you want PentaBase to design your DNA primers or SuPrimers™? We at PentaBase design primers/SuPrimers™ according to the best standards including primers amplifying the correct region without amplifying of target regions and reduced or removed primer dimer formation. In short primers that ensure specific and efficient priming.

If you would like us to design your primers, please send us:

The NCBI reference e.g: J04038^aor your sequence electronically.
Synthesis scale of your choice: 40 nmol, 200 nmol or 1 umol
Primer type of your choice: DNA primers or SuPrimers™ and
Delivery and payment details (or username from our home page)

You will then receive:

An order confirmation followed by
The corresponding primers/SuPrimers™ e.g: 5'-GAAGGTGAAGGTCGGAGT and 5'-AAGATGGTGATGGGATTTC each comprising 1-2 HyNAs (not shown)^b

Order online or send an email with your order or inquiry.

Questions? Why not contact us on our online support.

General notes

^a Sequence is taken from Kelly et al. PNAS | 2006 | vol. 103 | no. 40 | 14935-14940

^bSequence is taken from Abd El Galil et al. APPL. ENV. MICROBIOL. | 2005 | Vol. 71 | No. 11 | 7113–7116.

Sequence shown is just an example and not necessarily actually ordered or re-designed. The customer story is however correct, but the identity of the customer and his research project and sequences are kept confidential.

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