Loren Data's SAM Daily™

FBO DAILY ISSUE OF FEBRUARY 22, 2007 FBO #1914
SOLICITATION NOTICE

99 -- PROVIDE DESIGN AND ANALYSIS OF FATHEAD MINNOW NORMATIZED AND LIQUOTED OLIGONUCLEOTIDES FOR PRODUCTION OF MICRO ARRAYS.

Notice Date

2/20/2007
 

Notice Type

Solicitation Notice
 

NAICS

325413 — In-Vitro Diagnostic Substance Manufacturing
 

Contracting Office

Vicksburg Consolidated Contracts Office, Vicksburg, ATTN: ERDC, 4155 Clay Street, Vicksburg, MS 39183-3435
 

ZIP Code

39183-3435
 

Solicitation Number

W912HZ07T0015
 

Response Due

3/7/2007
 

Archive Date

5/6/2007
 

Small Business Set-Aside

N/A
 

Description

The Engineer Research and Development Center is soliciting for a custom designed 70-mer oligonucleotides representing all known Fathead minnow genes with appropriate controls for hybridization (approximately 20,992). THIS REQUIREMENT IS AN UNRESTRICT ED PROCUREMENT. DNA must be synthesized at 50 nanomolar scale. The service must be fast, accurate and able to deliver oligonucleotides within one week of placing the order. The oligonucleotides must be designed to detect the publicly available fathead 1842 4 UniGene clusters present on the GenBank database for which orientation is known. Oligonucleotides must be designed for each strand of the additional 880 Unigene clusters that have contradicting information regarding their orientation. Oligonucleotides mu st be designed for each strand of 699 unique cDNA sequences not present in GenBank public database. The 699 sequences are derived from clustering and BLAST analysis of 4,200 cDNA sequences provided by ERDC Vicksburg, MS. Oligonucleotides suitable to assess quality and specificity of hybridization must be design to include at least 90 control oligonucleotides to assess cDNA position effects, at least 50 negative control oligonucleotides, at least 150 control oligonucleotides with different percentages of seq uence identity to a target cDNA in order to assess specificity of hybridization. Oligonucleotide design must ensure that oligonucleotide melting temperatures are optimal within the designed set of all oligonucleotides. Oligonucleotide secondary structure a s determined by self alignment using dynamic programming must not interfere with hybridization. The oligonucleotide sequence specificity with regard to other target sequences in the set must be sufficiently low as to eliminate cross hybridization. The sequ ence quality of CDNA sequences used for oligonucleotides design must account for sequencing quality scores. The design process must use global optimization where all possible probes in all sequences are considered. The oligonucleotide quality scoring proce ss must consider all design criteria simultaneously to guarantee the best overall probe. The oligonucleotide specificity must be assessed by comparison of all possible pairwise alignments with all other sequences in the set and against all publicly availab le sequences to guarantee specificity in a conservative manner. The following information about all probes must be supplied with synthesized oligonucleotides: The probe ID, target sequence name and class (genes/controls), position of the probe on the targe t sequence, probe oligonucleotide sequence, global probe score, and individual probe scores for Tm, secondary structure, lowcomplexity, specificity, position. Quality Control for oligonucleotide synthesis must include: 100% Trityl monitoring of each base a ddition on every oligonucleotide  A real-time in-process digital Trityl monitoring system must be used to identify both base addition success and presence of full length product. Measurements must be taken at the capping, oxidation, and coupling steps for every base addition of every oligonucleotide in every well of every plate. Measurements must be taken without stopping or disrupting the synthesis process. Measurements must be compared to standard, length dependant absorbance curves. Absorbance values be low established threshold criteria should trigger failure of the synthesis. 100% of the oligonucleotides must be analyzed by OD260 absorbance measurement. 100% of the oligonucleotides must be analyzed by capillary electrophoresis - A CE system capable of s ingle base resolution must be used for quantitative determination of purity and full-length yield for oligonucleotide synthesis. Reagent delivery and oligonucleotide synthesis must be in an enclosed, inert environment. Oligonucleotide synthesis must take p lace in a 384-well microplate. Oligonucleotides must be normalized to equivalent concentrations and aliquoted into a 384 well format. All remaining oligonucleot ide yields should be placed in a 96 well format. The Request for Quote (RFQ) will be issued on February 20, 2007, with a closing date of March 7, 2007. The RFQ will be available the Army Single Face to Industry at https://acquisition.army.mil/asfi. Hard co pies will not be available. It is the offerors responsibility to monitor the web page for the release of the RFQ (and amendments, if any). Potential offerors will be responsible for downloading their own copy of the RFQ and any amendments. The NAICS Code i s 325413 and the Size Standard is 500.
 

Place of Performance

Address: Vicksburg Consolidated Contracts Office, Vicksburg ATTN: ERDC, 4155 Clay Street Vicksburg MS

Zip Code: 39183-3435

Country: US
 

Record

SN01235277-W 20070222/070220222802 (fbodaily.com)
 

Source

FedBizOpps Link to This Notice
(may not be valid after Archive Date)

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