BMB 303 Techniques in Biochemistry & Molecular Biology

Fall 2006

Lab Resources

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Part 1: Basic Bioinformatics & databases

• Background Literature
  • Edmiston, P. L.; Schavolt, K. L.; Kersteen, E. A.; Moore, N. R.; Borders Jr, C. L. 2001. Creatine kinase: a role for arginine-95 in creatine binding and active site organization. Biochim Biophys Acta 1546:291-8. (This link may not work off-campus.)
• Molecular Visualization
  • Protein Molecular Visulaization Using Chimera
  • Protein Molecular Visualization Using Protein Explorer
  • Protein Explorer application
  • PDB Lite (to locate proteins in Protein Data Bank)
  • PDB files: CK dimer (prepared by PE using SwissPDB); Horseshoe crab AK (with bound transition state analog ADP-NO₃-Arg)
• Multiple Sequence Alignment
  • Perfoming a Multiple Sequence Alignment Using MacVector
  • Performing a Multiple Sequence Alignment Using Web-based Resources
  • CLUSTALW: Multiple Sequence Alignment web site

Part 2: Molecular Genetics

• Expression Plasmids
  • pMAL system manual
  • pET E. coli T7 expression vectors
• pET System Manual
• Site-directed mutagenesis
  • ExSite™ PCR-Based Site-Directed Mutagenesis Kit
  • QuikChange® Mutagenesis Kits
• Primer Design
  • Ch. 5, "Design and Use of PCR Primers" in Critical Factors for Successful PCR, (Qiagen)
  • GenomeWeb Primer Design: "A collection of primer design sites.
  • More online programs: Primer3, QIAGEN Operon's Oligo Toolkit
• pMALc2g2 sequence file
  • MacVector file with feature annotations
  • FASTA
• Rabbit muscle CK files
  • FASTA nucleotide
  • MacVector nucleotide
  • FASTA protein
  • MacVector protein
• CK-pET17b Sequence Files
  • MS Word document
  • FASTA format
• CKdel4-pET17b Sequence Files (not used in 2004)
  • FASTA format
• Mutant Oligos (Not created yet)
• Plasmid Mini-preps
  • QIAprep Miniprep Handbook 03/02 at Qiagen's Literature Resources site ; print & bring p. 22-23 to lab
• Manipulating sequences using MacVector (MS word)
  • Conducting a restriction enzyme analysis using MacVector
  • Constructing a virtual clone using MacVector
• Restriction Digests (on-line resources)
• Find sites in a DNA sequence: NEBcutter (see Guide for description) at New England Biolab's site
• "Setting Up a Restriction Endonuclease Reaction" at NEB's Tech Resource site
• Agarose gel electrophoresis
  • Product Information: Agaroses for Molecular Biology at Amresco's site (registration required)
  • "Horizontal Mini-Gel Systems" Catalogue Description at C.B.S. Scientific site
• Gel Documentation and Analysis
  • QuickTips Guide: Using the Kodak EDAS 290 for Capturing DNA Gel Images; Kodak Electrophoresis Documentation and Analysis System (EDAS) 290 Macintosh User's Guide (print manual only; available in 310 Mateer)

Part 3: Protein Biochemistry

• Laboratory Equipment Quiz
• Preparation of Buffers
• Summary of Techniques for Protein Expression, Purification, and Functional Analysis