scholarly journals KARAKTERISASI FRAGMEN DNA GEN GLUKOAMILASE (GLU1) PRODUK PCR DENGAN ANALISIS RESTRIKSI

2005 ◽  
Vol 11 (1) ◽  
pp. 81-79
Author(s):  
Sofijan Hadi
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequencing ◽  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
Positive Control ◽  
Recognition Site ◽  
Base Pairs ◽  
Saccharomycopsis Fibuligera ◽  
Glucoamylase Gene ◽  
Eco Ri

Characterization used retriction enzyme on the 1784 bp (base pairs) DNA fragmen of glucoamylase gene (GLUI) of E. fibuligera ITB. R. cc. 64 has been done. The rectriction enzyme usage was Stu 1, Eco RI, Eco RV, Bam HI and Sau 3A. The purpose of this research were: First was to know recognition site of 1784 bp DNA fragmen of glucoamylase gene (GLUI) by the restriction enzyme above. The second was to know homologyst the glucoamylase gene (GLUI) E. fibuligera ITB. R. cc. 64 and the glucoamylase gene (GLUI) Saccharomycopsis fibuligera HUT 7212 (pSf GLUI). The result of amplification glucoamylase gene (GLUI) indicated that 1784 bp DNA fragmen on GLUI locus has succesfully isolated and gave the same size with the positive control pSf GLUI. Analysis of those DNA fragmen by StuI, Eco RV, Eco RI, Bam HI and Sau 3A indicated that 1784 bp of DNA fragmen from E. fibuligera ITB.R.cc.64. has the same result with 1784 bp of DNA fragmen from pSf GLUI. The result of the fragments after incubated by restriction enzymes are as follows: 997 bp and 787 bp by Eco RI, 1000 bp and 1780 bp by Bam H) and 850 bp and 760 bp by Sau 3A. Digestion using StuI and Eco RI was failed. To ensure that the DNA fragmen 1784 bp has characteristic as glucoamylase gene, it should be expressed into S. cerevisiae and/or should be determined the nucleotide sequence by DNA sequencing.

scholarly journals EVOLUTIONARY RELATIONSHIPS AMONG FIVE SUBSPECIES OF MUS MUSCULUS BASED ON RESTRICTION ENZYME CLEAVAGE PATTERNS OF MITOCHONDRIAL DNA

Genetics ◽  
1981 ◽  
Vol 98 (4) ◽  
pp. 801-816
Author(s):  
Hiromichi Yonekawa ◽  
Kazuo Moriwaki ◽  
Osamu Gotoh ◽  
Jun-Ichi Hayashi ◽  
Junko Watanabe ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Sequence ◽  
Restriction Enzyme ◽  
Mus Musculus ◽  
Sequence Divergence ◽  
Restriction Enzymes ◽  
Genetic Distances ◽  
The Other ◽  
Enzyme Cleavage ◽  
The Times

ABSTRACT The intra- and intersubspecific genetic distances between five subspecies of Mus musculus were estimated from restriction enzyme cleavage patterns or maps of mitochondrial DNA (mtDNA). The European subspecies, M. m. domesticus and Asian subspecies, M. m. bactrianus, M. m. castaneus, M. m. molossinus and M. m. urbanus were examined. For each subspecies, except M. m. urbanus, at least two local races from widely separated localities were examined. Intrasubspecific heterogeneity was found in the mtDNA cleavage patterns of M. m. bactrianus and M. m. castaneus. M. m. molossinus and M. m. domesticus, however, revealed no intrasubspecific heterogeneity. Four of the subspecies had distinct cleavage patterns. The fifth, M. m. urbanus, had cleavage patterns identical to those of M. m. castaneus with several enzymes. Estimates of genetic distances between the various races and subspecies were obtained by comparing cleavage maps of the mtDNAs with various restriction enzymes. Nucleotide sequence divergences of mtDNA between local races were estimated to be less than 0.4% in M. m. bactrianus and less than 0.3% in M. m. castaneus. The times of divergence of both subspecies were calculated to be 0.1-0.2 × 106 years. These values suggest that the intrasubspecific divergence began some 0.1-0.2 × 106 years ago. On the other hand, nucleotide sequence divergences between European subspecies M. m. domesticus and Asian subspecies M. m. bactrianus and M. m. castaneus were 7.1% and 5.8%, respectively. The times of divergence were calculated to be 2.1-2.6 × 106 years. Further, the nucleotide sequence divergence and time of divergence between M. m. molossinus and the other two Asian subspecies were comparable to those between M. m. molossinus and M. m. domesticus (about 3% and 1 × 106 years, respectively). These results suggest that M. m. molossinus is situated in a unique evolutionary position among Asian subspecies.

A rapid and efficient PCR-based mutagenesis method applicable to cell physiology study

2005 ◽  
Vol 288 (6) ◽  
pp. C1273-C1278 ◽  
Author(s):  
Jae-Kyun Ko ◽  
Jianjie Ma
Keyword(s):  
Molecular Biology ◽  
Protein Engineering ◽  
Restriction Enzyme ◽  
Cost Effective ◽  
Restriction Enzymes ◽  
Recognition Site ◽  
Cell Physiology ◽  
Multiple Site ◽  
Functional Studies ◽  
Engineering Studies

PCR-based mutagenesis is a cornerstone of molecular biology and protein engineering studies. Herein we describe a rapid and highly efficient mutagenesis method using type IIs restriction enzymes. A template gene is amplified into two separate PCR fragments using two pairs of anchor and mutagenic primers. Mutated sequences are located near the recognition site of a type IIs restriction enzyme. After digestion of two fragments with a type IIs enzyme, exposed cohesive ends that are complementary to each other are then ligated together to generate a mutated gene. We applied this method to introduce multiple site-directed mutations in EGFP and Bcl-2 family genes and observed perfect mutagenesis efficiency at the desired sites. This efficient and cost-effective mutagenesis method can be applied to a wide variety of structural and functional studies in cell physiology.

scholarly journals Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes ψent1 and ψent2 and the selu or selu v gene using PCR-RFLP

2007 ◽  
Vol 56 (2) ◽  
pp. 208-216 ◽  
Author(s):  
Mark M. Collery ◽  
Cyril J. Smyth
Keyword(s):  
Dna Sequencing ◽  
Restriction Enzyme ◽  
Sequence Similarity ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Restriction Enzyme Digestion ◽  
Pcr Rflp ◽  
Intergenic Regions ◽  
Unique Restriction ◽  
Genomic Regions

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, ψent1 and ψent2, or the selu or selu v gene. While these two alternative sei–seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or selu v gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3′ end of the sei gene through the 5′ first quarter of the seln gene allowed pseudogene- and selu- or selu v-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or selu v gene, while selu- or selu v-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or selu v-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei–seln egc locus type.

scholarly journals The presence of zinc in the restriction enzyme Eco RI.

1982 ◽  
Vol 257 (14) ◽  
pp. 7911-7914
Author(s):  
J K Barton ◽  
L A Basile ◽  
S R Paranawithana
Keyword(s):  
Restriction Enzyme ◽  
Eco Ri

scholarly journals Nucleotide sequence of the putative regulatory region of mouse lactate dehydrogenase-A gene

1986 ◽  
Vol 235 (2) ◽  
pp. 435-439 ◽  
Author(s):  
K M Fukasawa ◽  
S S L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Nucleotide Sequence ◽  
Cyclic Amp ◽  
Regulatory Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Untranslated Sequence ◽  
Eukaryotic Genes ◽  
Putative Regulatory Region ◽  
Processed Pseudogene

The nucleotide sequence of approx. 3 kilobases including the regulatory region, a non-coding exon and the first protein-coding exon from mouse lactate dehydrogenase-A (LDH-A) gene has been determined. The putative initiation sites of transcription and translation were deduced by comparing the nucleotide sequence of mouse LDH-A gene with those of a mouse LDH-A processed pseudogene and the LDH-A full-length cDNAs from rat and human. The tentative TATA and CAAT boxes, and the hexanucleotides CCGCCC have been identified. The sequence of AAATCTTGCTCAA of mouse LDH-A gene has also been found to show striking homology to the cyclic AMP-responsive sequences of eukaryotic genes regulated by cyclic AMP. It has been reported previously that the protein-coding sequence of mouse LDH-A gene is interrupted by six introns and the 3′ untranslated sequence of 485 nucleotides is not interrupted [Li, Tiano, Fukasawa, Yagi, Shimiza, Sharief, Nakashima & Pan (1985) Eur. J. Biochem. 149, 215-225]. An additional intron of 1653 base-pairs was found in the 5′ untranslated sequence of 101 nucleotides at 24 nucleotides upstream to the translation start site. Thus, mouse LDH-A gene containing seven introns spans approx. 11 kilobases and its length of mature mRNA is 1582 nucleotides, excluding the poly(A) tail.

RAD3 gene of Saccharomyces cerevisiae: nucleotide sequence of wild-type and mutant alleles, transcript mapping, and aspects of gene regulation

1985 ◽  
Vol 5 (1) ◽  
pp. 17-26
Author(s):  
L Naumovski ◽  
G Chu ◽  
P Berg ◽  
E C Friedberg
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Coding Region ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Calculated Molecular Weight ◽  
Base Pair Deletion ◽  
S1 Nuclease Mapping ◽  
Essential Function ◽  
Nuclease Mapping

We determined the complete nucleotide sequence of the RAD3 gene of Saccharomyces cerevisiae. The coding region of the gene contained 2,334 base pairs that could encode a protein with a calculated molecular weight of 89,796. Analysis of RAD3 mRNA by Northern blots and by S1 nuclease mapping indicated that the transcript was approximately 2.5 kilobases and did not contain intervening sequences. Fusions between the RAD3 gene and the lac'Z gene of Escherichia coli were constructed and used to demonstrate that the RAD3 gene was not inducible by DNA damage caused by UV radiation or 4-nitroquinoline-1-oxide. Two UV-sensitive chromosomal mutant alleles of RAD3, rad3-1 and rad3-2, were rescued by gap repair of a centromeric plasmid, and their sequences were determined. The rad3-1 mutation changed a glutamic acid to lysine, and the rad3-2 mutation changed a glycine to arginine. Previous studies have shown that disruption of the RAD3 gene results in loss of an essential function and is associated with inviability of haploid cells. In the present experiments, plasmids carrying the rad3-1 and rad3-2 mutations were introduced into haploid cells containing a disrupted RAD3 gene. These plasmids expressed the essential function of RAD3 but not its DNA repair function. A 74-base-pair deletion at the 3' end of the RAD3 coding region or a fusion of this deletion to the E. coli lac'Z gene did not affect either function of RAD3.

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