Dependence of the ligation efficiency of large DNA fragments isolated from agarose gels on the purification method. 1998

E Fransen, and G Van Camp, and B Winnepenninckx
Dept. of Medical Genetics, University of Antwerp, Belgium.

The isolation of large DNA fragments (> 5 kb) from agarose gels can be problematic. The DNA yield is often low, and the purification may be insufficient for subsequent reactions such as sequencing or ligation. Here we have compared a number of commonly used methods and commercial kits for DNA recovery. Large DNA fragments (12 and 14 kb, respectively) were isolated from agarose gel and purified, the recovery yield was tested, and a well-defined amount of purified DNA was used in a standard ligation reaction. We observed dramatic differences in the efficiency of this ligation reaction depending on which recovery method had been used. However, the respective ligation efficiencies of the different methods were not related to their recovery yields.

UI MeSH Term Description Entries
D008562 Membrane Glycoproteins Glycoproteins found on the membrane or surface of cells. Cell Surface Glycoproteins,Surface Glycoproteins,Cell Surface Glycoprotein,Membrane Glycoprotein,Surface Glycoprotein,Glycoprotein, Cell Surface,Glycoprotein, Membrane,Glycoprotein, Surface,Glycoproteins, Cell Surface,Glycoproteins, Membrane,Glycoproteins, Surface,Surface Glycoprotein, Cell,Surface Glycoproteins, Cell
D009835 Oligochaeta A class of annelid worms with few setae per segment. It includes the earthworms such as Lumbricus and Eisenia. Earthworms,Eisenia foetida,Eisenia worm,Lumbricus,Lumbricus terrestris,Eisenia fetida,Earthworm,Eisenia fetidas,Eisenia foetidas,Eisenia worms,Lumbricus terrestri,Oligochaetas,fetida, Eisenia,foetidas, Eisenia,terrestris, Lumbricus,worm, Eisenia
D010957 Plasmids Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS. Episomes,Episome,Plasmid
D011088 DNA Ligases Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD). DNA Joinases,DNA Ligase,Polydeoxyribonucleotide Ligases,Polydeoxyribonucleotide Synthetases,T4 DNA Ligase,DNA Ligase, T4,Joinases, DNA,Ligase, DNA,Ligase, T4 DNA,Ligases, DNA,Ligases, Polydeoxyribonucleotide,Synthetases, Polydeoxyribonucleotide
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004587 Electrophoresis, Agar Gel Electrophoresis in which agar or agarose gel is used as the diffusion medium. Electrophoresis, Agarose Gel,Agar Gel Electrophoresis,Agarose Gel Electrophoresis,Gel Electrophoresis, Agar,Gel Electrophoresis, Agarose
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D018509 DNA, Helminth Deoxyribonucleic acid that makes up the genetic material of helminths. Helminth DNA
D019006 Neural Cell Adhesion Molecules Cell adhesion molecule involved in a diverse range of contact-mediated interactions among neurons, astrocytes, oligodendrocytes, and myotubes. It is widely but transiently expressed in many tissues early in embryogenesis. Four main isoforms exist, including CD56; (CD56 ANTIGEN); but there are many other variants resulting from alternative splicing and post-translational modifications. (From Pigott & Power, The Adhesion Molecule FactsBook, 1993, pp115-119) Cell Adhesion Molecule, Neural,NCAM,Neural Cell Adhesion Molecule,Cell Adhesion Molecules, Neural
D039841 Leukocyte L1 Antigen Complex A member of the S-100 protein family that is present at high levels in the blood and interstitial fluid in several infectious, inflammatory, and malignant disorders, including rheumatoid arthritis, inflammatory bowel disease, and cystic fibrosis. It is a complex of a light chain (CALGRANULIN A) and a heavy chain (CALGRANULIN B). L1 binds calcium through an EF-hand motif, and has been shown to possess antimicrobial activity. L1 Antigen,Leukocyte L1 Protein,27E10 Antigen,Calcium-Binding Myeloid Protein P8,14,Calgranulin,Calprotectin,Migratory Inhibitory Factor-Related Protein MRP,Myelomonocytic Antigen L1,Antigen L1, Myelomonocytic,Antigen, 27E10,Antigen, L1,Calcium Binding Myeloid Protein P8,14,L1 Protein, Leukocyte,Migratory Inhibitory Factor Related Protein MRP

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