Molecular Biology Methods

General sources about Molecular Biology Methods

Online Methods Sources:

• Nucleic Acids Research - Methods
• Nature Protocols
• protocolexchange - An open repository (preprint server) of community-contributed protocols sponsored by Nature Portfolio
  
• Technical Tips Online search at BioMedNet- Categories
• Molecular Biology Protocols at Northwest Fisheries Science Center
• Paul N. Hengen Molecular Biology Home Page
• Methods FAQ list
• Protocol Online - Your lab's reference book
• Molecular Biology Protocols on the World Wide Web
• Conversion of Units - Molarity Calculator at GraphPad
  
• General biotech journals: Biotecnologie 2000 (Ita) Lab2000 (Ita)
• Tecnologie Biomolecolari (Ita)

Safety

• MATERIAL SAFETY DATA SHEETS
• Vermont SIRI MSDS Collection
• Material Safety Data Sheets at Cornell University
• MSDS's on the Internet
• MSDS eSearch - More than 2.5+ Million MSDSs
• PENN STATE UNIVERSITY DEPARTMENT OF ENVIRONMENTAL HEALTH AND SAFETY HOMEPAGE

ITALY - Servizio di Sicurezza, Igiene e Medicina del Lavoro dell'Università di Bologna
• Sicurezza 626   |   Norme operative interne di radioprotezione (D Lgs 230/95 - D Lgs 626/94)
• Risorse Internet su Sicurezza, Ambiente e Salute
• Pagine sulla sicurezza (Dipartimento di Biochimica, Università di Bologna)
• ISPESL: Istituto Superiore per la Prevenzione e la Sicurezza del Lavoro - Rischi in Azienda
• Prevenzione degli infortuni nel laboratorio chimico

Laboratory practice guidelines

• OECD Good Laboratory Practice
• NIH Recombinant DNA Guidelines
• Federal Bureau of Investigation Home Page
• Food and Drug Administration Home Page
• Managing your Lab (Science -- Cech and Bond 304 (5678):1717)
• The Academic Scientists' Toolkit - Managing your Lab (Science)
• HHMI Lab Management
• Books about laboratory management: At the Helm: A Laboratory Navigator - At the Bench: A Laboratory Navigator
• LabAssistant - "Get your life organized" - freeware for MacOS X

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Basic

• Practical Information for the Molecular Biologist - Units and formulas
• Water purification in "Laboratorio 2000" (Ita)
• Chemical Calculator (Solutions) - Percent (%) Solutions Calculator
  

Statistic Analysis: GraphPad Library   |   How to choose a statistical test

Microscopy

Laboratorio di Istopatologia - Ospedale Sant'Orsola-Malpighi (Ita)

Cell biology

• Apoptosis: A Laboratory Manual of Experimental Methods - Andrea Cossarizza & Diana Boraschi, Eds.
  

DNA/RNA isolation

• Solid-phase nucleic acid extraction, amplification, and detection - article
• DNA Banking in Epidemiologic Studies - review at CDC
• Nuclease control: The Basics and exploration - RNA isolation: The Basics and exploration - by Ambion
• Quantitation of RNA - RNA quality: exploration - The Basics: mRNA quantitation - by Ambion

Nucleic Acids Electrophoresis - Blots

• The Basics: Northern analysis and Nuclease protection assay - by Ambion
• GelReader: software for analyzing gel (Mac version)
• NIH Image Home Page
• RAM GENE-1 mark II

DNA gel purification

Recombinant DNA Technology

CloneIt!- an online program finding sub-cloning strategies

Molecular Biology Programs - EnzymeX, a digestion simulator for MacOS X

Common vectors:

pT7T3D-PAC

pCS2 Plasmid - Map (Word file) http://bioinformatics.org/JaMBW/

PCR

• MAKING PCR (Polymerase Chain Reaction) - includes Fundational Papers   |   Kary Mullis website
• PCR: A short introduction (with animated tutorial) - at: Sequence Analysis with distributed Resources
• DNALC: PCR Animation
• PCR Manual - 2nd Edition , 1999 at Roche site
• PCR Protocols & Reference at Promega site
• RT-PCR Methodology at Davidson College   |   RT-PCR:The Basics - Problem Solver, tips at Ambion
• The Polymerase Chain Reaction (PCR) Jump Station - Web page about all aspects of PCR
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• PCR Primers design software on the Web
• Primer BLAST
  
• Primer3 - pick primers from a DNA sequence | The PCR Suite - (van Baren and Heutink, 2004)
• PCR Primer design and PCR setup
• MEDUSA - selection and visual assessment of PCR primer pairs
• Primer selection - WWW interface at Virtual Genome Center | Primo - primer design tool | Virtual PCR at CRIBI | JaMBW
• PROBEmer - a web-based software tool for selecting optimal DNA oligos (Emrich et al., 2003)
• Primer Design Assistant (PDA) - a web-based primer design tool (Chen et al., 2003)
• PUNS - Primer-UniGene Selectivity Testing
• PCR Designer for Restriction Analysis of Sequence Mutations
• CODEHOP - PCR primers design from protein multiple sequence alignments (Rose et al., 2003)
• DePIE - Designing Primers for Protein Interaction Experiments (Lu et al., 2003)
• GenePrimer - Prediction of PCR Primers for Experimental Gene Identification
• UniFrag and GenomePrimer - selection of primers for genome-wide production of unique amplicons (Sacha et al., 2003)
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• PCR Primers design software for personal computer
• Amplify, Primers! and other freeware PCR primers design for the Mac
• Primer Premier - PCR Primer Design Software for PCR, multiplex and SNP genotyping assays (commercial)
  
• MeltCalc - probe design with thermodynamic knowledge
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• RACE
• SMART(TM) RACE cDNA Amplification Kit - from Clontech
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• Quantitative PCR
• Balanced PCR - quantitative difference between two complex genomes - Nat Biotechnol, Sep 2002

DNA sequencing

• Freeware for reading ABI-PRISM 4-color trace: EditView (Mac), FourPeaks (MacOS X) or Chromas (Win95)
• Flourescently Hexamer Sequencing - protocol
• Genetic Analysis home at Applied Biosytems
• Branton Lab - Nanopore Sequencing Description
• Pyrosequencing / Technology
• Sequence information can be obtained from single DNA molecules - PNAS, Mar 21, 2003
• Microscopic sequencing of DNA - Atomic Force Microscopy (AFM)
• Genomics

Cytogenetics

• Cytogenetic Aberrations
• The Cytogenetics Gallery

Linkage Analysis

• Genetic linkage analysis site at Rockfeller University
• DCRT/CBEL/BIMAS Genetic Linkage Analysis Home Page
• BIONET.MOLBIO.GENE-LINKAGE FREQUENTLY ASKED QUESTIONS (FAQ)
• Bib: allele-sharing linkage
• An Alphabetic List of Genetic Analysis Software

Gene therapy

• Pier-Luigi Lollini - Terapia Genica (Ita)
• Pier-Luigi lollini - terapia Genica - Il Libro (Ita) (password required)
• Insulin gene therapy (Review in "Trends in Molecular Medicine", Feb 2002)

Functional Genomics

• Proteomics
• NPG web focus: Proteomics - Focus home
• SWISS-2DPAGE Two-dimensional polyacrylamide gel electrophoresis Database
• Proteomics: A Trends Guide
• A Trends Guide to Proteomics II
• DynaProt 2D - database for proteomes and two-dimensional electrophoresis gels (Drews and Gorg, 2005)
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• Gene expression
• New Technologies for Life Sciences: A Trends Guide
• The Basics: In vitro transcription and translation - by Ambion
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• Gene knock out - RNA interference
• Nature Reviews journals web focus on RNAi - Animations on RNA interference - RNAi Poster
• RNA Interference (RNAi) and Gene Silencing - History and Overview (May 2002) at Ambion
• The RNA interference resource - The microRNA resource - RNA structure/function resource - at Ambion
• Silencer - siRNA cocktail kit from Ambion
• TechNotes 10(3): Five Ways to Produce siRNAs at Ambion
• iRNAi oligo designer for MacOS X

Arrays of DNA

ONTOLOGYÂ¥General - Consumables · Software: · Image, Data, Analysis - Ontology
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NEURAL NETWORKS AND MICROARRAYS

• Gene expression profiling diagnosis through DNA molecular computation
  

NANOTECHNOLOGY

Methylome

• RnBeads software
  

Next Generation Sequencing

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Last updated May 28, 2011

DNA