Center for Infectious Disease & Immunity

DNA Research Services

 

DNA Research Services provides technical services in DNA synthesis (automated single-stranded oligonucleotide synthesis), and DNA sequencing (electrophorectic separation and spectral detection of dye-labeled DNA fragments).

505-272-5792
Biomedical Research Facility, room 338

Services
DNA Synthesis Order form
DNA Sequencing Order form
DNA Sizing Order form

 

About the order forms

Order forms are in Microsoft Excel 97/2000 format. It should be possible to open them in any recent version of Excel, OpenOffice Calc, or any of several Excel file viewers, such as Microsoft's Excel Viewer 2003. You can either print the form and fill it out by hand, or open the file, fill out the form in your spreadsheet application, and then print it (recommended). If you are asked for a password after clicking on the link, just click on Cancel and the opening process will continue. Alternately, right-click the link and select the option to save the file locally, save it to your desktop and open it from there.

For DNA sequencing and sizing services, completed order forms should be brought, along with samples, to the Biomedical Research Facility (BRF) room 338. Synthesis requests can be brought by hand, faxed to 505-272-8084, or attached to an email to DNAServices@salud.unm.edu.  

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DNA synthesis services

Oligonucleotide synthesis order form

DNA and RNA may be synthesized at 0.2 μmole, 1.0 μmole, and 10 μmole scales. The normal method of synthesis is 3' to 5', but oligonucleotide segments can be synthesized in the opposite sense, 5' to 3', for the production of 5'-5' or 3'-3' linkages for antisense studies or structural studies.

In addition to the standard nucleotide codes (a, c, g, t, u), please use the following Ambuguous Nucleotide codes when filling out the order form:

	  R → puRine (A or G)
	  Y → pYrimidine (C or T/U)
	  M → A or C
	  W → A or T/U
	  S → C or G
	  K → G or T/U
	  D → A, G, or T/U
	  H → A, C, or T/U
	  V → A, C, or G
	  B → C, G, or T/U
	  N → A, C, G, or T/U

Other modifications include:

Phosphorylation (of the 5'-terminus), duplex effects, degeneracy strategies, chain terminators, structural/activity relationships, incorporation of: Biotin, Inosine, Cholesterol, DNP, Acridine (intercalating agent), Psoralen (cross linking), and dyes: 5'-Fluorescein (6-FAM), 5'-Tetrachloro-Fluorescein (TET), 5'-Hexachloro-Fluorescein (HEX), Cyanines (Cy3, Cy3.5, Cy5, Cy5.5), Yakima Yellow, Redmond Red, Rhodamine (TAMRA). We can also incorporate: Black Hole Quenchers, Dabcyl (universal quencher), the Eclipse quencher, halogenated nucleosides, 8-oxo purine, 2'-5' Linkages, spacers, 3'-terminus modifiers, convertible nucleosides, cyclic oligonucleotides, fluorescent nucleosides, the anti-viral drug Cytosine Arabanoside, and many others.

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DNA sequencing services

DNA Sequencing request form

An automated instrument system performs electrophoretic separation and spectral detection of dye-labeled DNA fragments, to determine base sequence, fragment size, or relative quantity.

SEQUENCING reactions are performed with fluorescent labels: four different dyes identify the A,C, G, and T extension reactions. Commonly employed polymerases provide primer extension.

The Center requests that you provide the primer for the sequencing reaction. For each reaction requested, please provide 5 μL of primer, at a concentration of 1 pmol/μL.

Sample Requirements:

Sample type PROVIDE 10 μL/reaction
AT THIS CONCENTRATION
Plasmid Double-stranded 100 ng/μL
PCR product 100-199 bp 0.5 ng/μL
200-499 bp 1.0 ng/μL
500-999 bp 2.5 ng/μL
1000-2000 bp 5.0 ng/μL
< 2000 bp 10.0 ng/μL

 

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DNA sizing services

Gene scanning request form

For DNA sizing, labeling reactions use one fluorescent dye for each sample. The Gene Mapper analysis software uses the automated fluorescence detection capabilities of the 3100 Genetic Analyzer instrument to size and quantify DNA fragments. Running a size standard in the same lane promotes accurate quantitative results. Two size standards are available, depending on the other dyes used: ROX (red) or LIZ (orange).

The ROX size standard can be used with the following fluorescent dye labels: 6-FAM (blue), HEX (green), & NED (yellow).

GeneScan™ 500 ROX® Size Standard is designed for sizing DNA fragments in the 35-500 bp range and providess 16 single-stranded fragments of 35, 50, 75, 100, 139, 150, 160, 200, 250, 300, 340, 350, 400, 450, 490, and 500 bps.

The LIZ size standard can be used with the following fluorescent dye labels: 6-FAM (blue), VIC (green), NED (yellow), & PET (red).

GeneScan™ 500 LIZ™ Size Standard, (designed for use with the AmpFLSTR® Identifiler™ Kit and 5-dye ABI PRISM® Custom Primers).

Used for sizing DNA samples in the 50-500 nucleotides range and provides sixteen single-stranded labeled fragments labeled fragments of: 35, 50, 75, 100, 140, 150, 160, 200, 250, 300, 340, 350, 400, 450, 490, and 500 nucleotides.

GeneScan™ 600 LIZ® Size Standard is a new size standard that has been designed for improved fragment sizing and increased throughput enabling accurate and reproducible allele calls in fragment analysis and genotyping assays. The standard, which can be used for sizing in the 20-600 bp range contains 35 fragments that are labeled with the 5th dye LIZ®. The size standard peaks are 20, 40, 60, 80, 100, 114, 120, 140, 160, 180, 200, 214, 220, 240, 260, 280, 300, 314, 320, 340, 360, 380, 400, 414, 420, 440, 460, 480, 500, 514, 520, 540, 560, 580 and 600 bps.

Other size standards are available for different nucleotide ranges: 120 LIZ, 350 ROX, 1000 ROX, and 2500 ROX.

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