Molecular Biology Core Facilities (MBCF)

Coordinates: 42°20′47″N 71°06′07″W / 42.346397°N 71.101853°W / 42.346397; -71.101853 The Molecular Biology Core Facilities (MBCF) was created to allow investigators at the Dana-Farber Cancer Institute (DFCI) access to cutting edge molecular biology tools which would be tested and developed in a shared setting. Collaborations can be set up with anyone in the world. Although these services are primarily focused on Cancer and AIDS research, there is a broad spectrum of research that uses these resources.^[1]

The MBCF logo.

History

The MBCF at DFCI was first started in 1984 to supply small oligonucleotides to researchers. Marvin Caruthers at the University of Colorado determined how to synthesize small oligonucleotides by solid-phase synthesis using the phosphoramidite method.^[2][3] Carruthers and Leroy Hood at the California Institute of Technology constructed the first automated DNA Synthesizer which the MBCF successfully tested after discussions with Don Taylor.

Because of the growing demand for oligonucleotide primers to initiate DNA replication and for probes, a plan was put into place to develop a core facility to produce reagents for molecular biologists as well as instrumentation for the analysis of DNA and protein samples. This plan stated that a charge-back method would be put in place to fairly spread the resources as a shared facility.

A Peptide Synthesizer using Bruce Merrifield's solid phase peptide synthesis^[4] was brought online in 1988 when Fmoc chemistry became commercially available. A Protein Sequencer using Edman degradation^[5][6] was installed in 1989 quickly followed by several DNA Sequencers which were the first to use fluorescent dye terminator chemistry.^[7][8] Mass Spectrometers were acquired to provide analysis of synthesized peptides but soon grew into a stand-alone service in high demand. Biacore^[9] instrumentation added for ligand kinetics in 1996 (and updated by Shared Instrumentation Grant to a Biacore 3000 in 2004). In 2007 a large expansion of high throughput proteomics using mass spectrometry has been funded by private donation. Blais Proteomics Center. (BPC)

The Molecular Biology Core Facilities has had a continuous web presence since 1992 and began receiving primer sequence for high throughput DNA synthesis by web forms in 1995 when new high volume DNA synthesizers were brought on-line. Since 2004 all interactions between researchers and the core services have been moved to a web based LIMS system.

The MBCF is constantly evaluating new instrumentation which could eventually become a shared resource. The future massively parallel DNA sequencers which can resequence entire genomes in just a few days, (454, Solexa+Illumina, Helicos, SOLiD, Visigen, PacBio, ION Torrent), are being made available to researchers by various methods. In 2009 the Heliscope from Helicos BioSciences began being evaluated in the genomics facility.^[10] An Illumina MiSeq has been purchased and will be installed in the fall of 2011. The Mass Spectrometry proteomics facility has also undergone a large expansion to undertake more complex high-throughput projects as part of the Blais Proteomics Center.

All MBCF staff are Association of Biomolecular Resource Facilities ABRF members in good standing.

Research tools available

• DNA sequencing
  • Massively Parallel Sequencing "next-gen sequencing"
  • Full genome sequencing
  • Gene mapping
  • SNP analysis
  • Genotyping
  • Linkage analysis
• Genomic sequencing
  • ChIP-Seq
  • RNA-Seq
  • GRO-Seq
  • Digital gene expression
  • Genome resequencing
• Protein Sequencing
  • N-terminal sequencing
  • Radioactive tracer detection
• Mass spectrometry
  • MALDI-TOF
  • Ion trap
  • Nanospray
• DNA synthesis
• Peptide synthesis
• Amino acid analysis
• Biacore
• HPLC
• Bioinformatics
  • Sequence analysis
  • Genome annotation
  • Gene expression
  • Protein expression
  • Mutational analysis
  • Structure prediction

Funding

The MBCF is for the most part funded as a straight fee for service chargeback core facility. At times other sources of funding for research and development or expansion are incorporated into the overall budget.

• From 1986 to 1999 the MBCF was part of the Dana-Farber Cancer Institute Comprehensive Cancer Center grant funded by the National Cancer Institute of NIH.
• From 1989 to 2004 the MBCF was part of the Harvard Medical School Center for AIDS Research (HMS CFAR).
• From 2004 to the present the MBCF has been part of the Harvard University Center for AIDS Research (HU CFAR).
• The National Center for Research Resources (NCRR) has funded several instruments through Shared Instrumentation Grants.

References

1. ^ "The Molecular Biology Core Facilities at Dana-Farber Cancer Institute/ Harvard Cores". Harvard Catalyst. http://cbmi.catalyst.harvard.edu/cores/cat/core.html?core_id=67&category_id=8&navMode=cat. Retrieved 18 April 2009. 
2. ^ Beaucage SL, Caruthers MH. (1981) Tetrahedron Lett. 22, 1859-62.
3. ^ McBride LJ, Caruthers MH. (1983) Tetrahedron Lett. 24, 245-8.
4. ^ R. B. Merrifield (1963). "Solid Phase Peptide Synthesis. I. The Synthesis of a Tetrapeptide". J. Am. Chem. Soc. 85 (14): 2149–2154. doi:10.1021/ja00897a025. 
5. ^ Edman, P. Acta Chem. Scand. 1950, 4, 283.
6. ^ Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942–1010. doi:10.1016/S0076-6879(73)27039-8. PMID 4773306. 
7. ^ Nature. 1986 Jun 12-18;321(6071):674-9. Fluorescence detection in automated DNA sequence analysis. We have developed a method for the partial automation of DNA sequence analysis. Fluorescence detection of the DNA fragments is accomplished by means of a fluorophore covalently attached to the oligonucleotide primer used in enzymatic DNA sequence analysis. A different coloured fluorophore is used for each of the reactions specific for the bases A, C, G and T. The reaction mixtures are combined and co-electrophoresed down a single polyacrylamide gel tube, the separated fluorescent bands of DNA are detected near the bottom of the tube, and the sequence information is acquired directly by computer.
8. ^ Nucleic Acids Res. 1985 Apr 11;13(7):2399-412. The synthesis of oligonucleotides containing an aliphatic amino group at the 5' terminus: synthesis of fluorescent DNA primers for use in DNA sequence analysis. Note that Oxford University Press, the publishers of the journal Nucleic Acids Research, make the full contents of this journal available online for free - you can download a copy of this paper for yourself !!
9. ^ H. M. Hiep et al. "A localized surface plasmon resonance based immunosensor for the detection of casein in milk" Sci. Technol. Adv. Mater. 8 (2007) 331 free download
10. ^ GenomeWeb InSequence; Oct 13, 2009 | Interview of Paul Morrison discussing Heliscope in a Core Lab| http://www.genomeweb.com/sequencing/dana-farbers-paul-morrison-running-helicos-sequencer-core-facility

External links

• MBCF Molecular Biology Core Facilities
  • MBCF Click the Fish
• DFCI Dana-Farber Cancer Institute
  • DFCI Staff Directory
• HMS Harvard Medical School
  • HMS Staff Directory
  • CFAR HMS Division for AIDS Research
    • MBCF at CFAR
• ABRF Association of Biomolecular Resource Facilities
  • MBCF at ABRF
• NCBI National Center for Biotechnology Information
• ASMS American Society for Mass Spectrometry
• TPS The Protein Society
• NCI National Cancer Institute