Preparation Of High Molecular Weight DNA Research Articles

Preparation of High-Molecular-Weight DNA from Drosophila Embryos: Figure 1.

Standard methods for extracting DNA from cells or organisms (e.g., phenol extraction and ethanol precipitation) produce fragments with an average size of 50-200 kb under optimal conditions. The shearing forces that are applied to DNA in solution during mechanical vortexing or mixing and pipetting produce frequent double-stranded breaks. To prepare high-molecular-weight (HMW) DNA, it is necessary to guard against such damaging forces by performing all extractions and manipulations on DNA that is embedded within a protective matrix. Preparation of HMW DNA from Drosophila embryos is described in detail here because, in our hands, it is the simplest and most reliable protocol and can be used for large- or small-scale preparations. The overall strategy is to purify nuclei, gently embed them in molten agarose, and then extract proteins and perform other enzymatic reactions by transferring the solidified agarose block into the appropriate solutions. Salts, soaps, and enzymes act on the DNA by diffusing through the agarose matrix, while the matrix protects the DNA from shearing forces.

Construction of Bacterial Artificial Chromosome (BAC/PAC) Libraries

Large-insert genomic libraries are necessary for physical mapping of large chromosomal regions, for isolation of complete genes, and for use as intermediates in DNA sequencing of entire genomes. Construction of BAC and PAC libraries is detailed in the unit, including preparation of PAC or BAC vector DNA for cloning by digestion with BamHI or EcoRI, dephosphorylation with alkaline phosphatase, and purification through pulsed-field gel electrophoresis (PFGE). For the preparation of high-molecular weight DNA for cloning, procedures for embedding total genomic DNA from lymphocytes or animal tissue cells are also provided. Other protocols detail partial digestion of genomic DNA with MboI or with a combination of EcoRI endonuclease and EcoRI methylase (including methods for optimizing the extent of digestion), and subsequent size fractionation by preparative PFGE. Finally, the isolation of BAC and PAC plasmid DNA for analyzing clones is also presented.

Construction of Bacterial Artificial Chromosome (BAC/PAC) Libraries

This unit describes the construction of BAC and PAC libraries. Two vectors, pCYPAC2 and pPAC4 have been used for preparing PAC libraries, and a new BAC vector pBACe3.6 has been developed for construction of BAC libraries. A support protocol describes preparation of PAC or BAC vector DNA for cloning by digestion with BamHI or EcoRI, simultaneous dephosphorylation with alkaline phosphatase, and subsequent purification through pulsed-field gel electrophoresis (PFGE). For the preparation of high-molecular weight DNA for cloning, support protocols provide procedures for embedding total genomic DNA from lymphocytes or animal tissue cells, respectively, in InCert agarose. Another support protocol details the next steps for the genomic DNA: partial digestion with MboI or with a combination of EcoRI endonuclease and EcoRI methylase, and subsequent size fractionation by preparative PFGE. The final support protocol covers the isolation of BAC and PAC plasmid DNA for analyzing clones.

Rapid and efficient method for isolating plant high molecular weight (HMW) DNA with high purity

PREPARATION of HMW DNA (Megabase-size) is the basis for construction of genomic library with large DNA inserts such as bacterial artificial chromosome (BAC) and yeast artificial chromosome (YAC), and for long-range physical mapping. It can also be used for the macro-study of repeat sequences. Since HMW DNA during preparation is inclined to be sheared physically and digested by internal nucleases, it is very difficult to prepare the HMW DNA. Initially, plant HMW DNA was prepared by embedding protoplasts in the low melting-point (LMP) agarose; however, it had several disadvantages: (ⅰ) Culture of protoplasts was time-consuming, costly and tedious. ( ⅱ ) It was only used successfully for limited plant

Large-scale preparation of high-molecular weight DNA from buccal mucosa

Four non-invasive methods of sampling DNA from buccal mucosa, simple rinses, scrubbing with cotton balls, scrubbing with toothbrushes and rinses after scrubbing with toothbrushes, were investigated. Scrubbing with toothbrushes yielded 5.79 ± 5.56 μg of DNA rich in high-molecules, while less than one eighth the amount was recovered by scrubbing with cotton balls. Rinses after scrubbing with toothbrushes gave 50.0 ± 46.0 μg of DNA and simple rinses 34.4 ± 35.7 μg, although the DNA was considerably degraded. DNA specimens obtained from buccal cells were shown to be more or less in the process of degradation including apoptosis. For minisatellite analysis, only DNA prepared by scrubbing with toothbrushes could be used, while all specimens could be applied to PCR analyses. Since scrubbing with toothbrushes is painless and harmless, we recommend this method. Subsequent rinsing will yield a large amount of DNA suitable for many PCR analyses.