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M Simsek

Publications and source records attributed to M Simsek.

30 records · Page 2Linked to original sources
PubMed1988

A precaution when preparing very large plasmids by alkaline lysis procedure.

The extractabilities of plasmids of different sizes by the sodium lauryl sulfate (SDS)-alkali procedure were compared using either sodium acetate or potassium acetate buffer as the neutralizing agent. There was a selective loss of large plasmids (above 100 kb) when the potassium salt was used. When N-lauryl sarcosine instead of SDS was used as the detergent, no loss of large plasmids occurred in the presence of potassium salt. A comparison of the kinetics of precipitate formation with sodium acetate and potassium acetate indicated that the rate and the amount of lauryl sulfate precipitated were lower with the sodium salt. It is suggested that faster precipitation of lauryl sulfate with potassium acetate leads to trapping of large denatured plasmids that cannot renature as fast as the small ones.

Acetates↗
PubMed1982

Nucleotide sequence of wheat germ cytoplasmic initiator methionine transfer ribonucleic acid.

The primary sequence of wheat germ initiator tRNA has been determined using in vitro labelling techniques. The sequence is: pAUCAGAGUm1Gm2GCGCAG CGGAAGCGUm2GG psi GGGCCCAUt6AACCCACAGm7GDm5Cm5CCAGGA psi CGm1AAACCUG*GCUCUGAUACCAOH. As in other eukaryotic initiator tRNAs, the sequence -T psi CG(A)- present in loop IV of virtually all tRNA active in protein synthesis is absent and is replaced by -A psi CG-. The base pair G2:C71 present in all other initiator tRNAs recognized by E. coli Met-tRNA transformylase is absent and is replaced by U2:A71. Since wheat germ initiator tRNA is not formylated by E. coli Met-tRNA transformylase this implies a possible role of the G2:C71 base pair present in other initiator tRNAs in formylation of initiator tRNA species.

Base Sequence↗
PubMed1982

A transposable element from Halobacterium halobium which inactivates the bacteriorhodopsin gene.

We describe the characterization of a transposable element from an archaebacterium. The bacteriorhodopsin genes from the wild-type and two mutant Halobacterium halobium strains have been cloned as BamHI fragments in pBR322. The cloned DNA fragments from the two mutants both contain a 1.1-kilobase-pair insertion sequence (ISH1) near the NH2 terminus of the bacteriorhodopsin coding sequence. ISH1 is present in the two mutants in an identical palindromic site but in opposite orientations. The complete sequence of ISH1 has been determined; it is 1,118 nucleotides long, it has 8-base-pair interrupted inverted repeats at the ends, and it duplicates an 8-base-pair (A-G-T-T-A-T-T-G) target sequence upon insertion. As for most eukaryotic and some prokaryotic transposable elements, the sequence of the ISH1 begins with T-G and ends in C-A. ISH1 contains an open reading frame 810 nucleotides long and codes for an RNA approximately 900 nucleotides long. The copy number of ISH1 ranges from one to five or more in different H. halobium strains. In at least one of the strains, one copy of ISH1 is present also on a plasmid DNA.

Bacteriorhodopsins↗
PubMed1981

The bacteriorhodopsin gene.

The bacteriorhodopsin gene has been identified in a 5.3-kilobase restriction endonuclease fragment isolated from Halobacterium halobium DNA, using a cloned cDNA fragment as the probe. Of the 1229 nucleotides whose sequence was determined in the genomic fragment, 786 correspond to the structural gene of bacteriorhodopsin, 360 are upstream from the initiator methionine codon, and 83 are downstream from the COOH terminus. The bacteriorhodopsin gene codes for a precursor sequence of 13 amino acids at the NH2 terminus, 248 amino acids that are present in the mature protein and an additional aspartic acid at the COOH terminus. This determination of the DNA sequence for an archaebacterial gene reveals that the standard genetic code is used; however, there is a marked preference for either G or C in the third codon position. The gene does not contain any intervening sequences and no prokaryotic promoter can be identified in the region immediately upstream from the structural gene. The bacteriorhodopsin mRNA contains at the 5' terminus only three nucleotides beyond the initiating AUG codon and this terminus can form a hairpin structure. Immediately downstream from this structure there is a sequence complementary to the 3' terminus of H. halobium 16S rRNA.

Amino Acid Sequence↗
PubMed1979

Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts.

The lysine isoacceptor tRNAs differ in two aspects from the majority of the other mammalian tRNA species: they do not contain ribosylthymine (T) in loop IV, and a 'new' lysine tRNA, which is practically absent in non-dividing tissue, appears at elevated levels in proliferating cells. We have therefore purified the three major isoaccepting lysine tRNAs from rabbit liver and the 'new' lysine tRNA isolated from SV40-transformed mouse fibroblasts, and determined their nucleotide sequences. Our basic findings are as follows. a) The three major lysine tRNAs (species 1, 2 and 3) from rabbit liver contain 2'-O-methylribosylthymine (Tm) in place of T. tRNA1Lys and tRNA2Lys differ only by a single base pair in the middle of the anticodon stem; the anticodon sequence C-U-U is followed by N-threonyl-adenosine (t6A). TRNA3Lys has the anticodon S-U-U and contains two highly modified thionucleosides, S (shown to be 2-thio-5-carboxymethyl-uridine methyl ester) and a further modified derivative of t6 A (2-methyl-thio-N6-threonyl-adenosine) on the 3' side of the anticodon. tRNA3Lys differs in 14 and 16 positions, respectively, from the other two isoacceptors. b) Protein synthesis in vitro, using synthetic polynucleotides of defined sequence, showed that tRNA2Lys with anticodon C-U-U recognized A-A-G only, whereas tRNA3Lys, which contains thio-nucleotides in and next to the anticodon, decodes both lysine codons A-A-G and A-A-A, but with a preference for A-A-A. In a globin-mRNA-translating cell-free system from ascites cells, both lysine tRNAs donated lysine into globin. The rate and extent of lysine incorporation, however, was higher with tRNA2Lys than with tRNA3Lys, in agreement with the fact that alpha-globin and beta-globin mRNAs contain more A-A-G than A-A-A- codons for lysine. c) A comparison of the nucleotide sequences of lysine tRNA species 1, 2 and 3 from rabbit liver, with that of the 'new' tRNA4Lys from transformed and rapidly dividing cells showed that this tRNA is not the product of a new gene or group of genes, but is an undermodified tRNA derived exclusively from tRNA2Lys. Of the two dihydrouridines present in tRNA2Lys, one is found as U in tRNA4Lys; the purine next to the anticodon is as yet unidentified but is known not be t6 A. In addition we have found U, T and psi besides Tm as the first nucleoside in loop IV.

Animals↗
PubMed1973

Absence of the sequence G-T-psi-C-G(A)- in several eukaryotic cytoplasmic initiator transfer RNAs.

The nucleotide sequence G-T-Psi-C-G(A)- has previously been found in every tRNA of known sequence that is active in protein biosynthesis. An exception to this generalization is the recently sequenced initiator tRNA from yeast cytoplasm. It is now reported that cytoplasmic initiator tRNAs from wheat germ, rabbit liver, and sheep mammary gland also lack the G-T-Psi-C-G(A)- sequence. Thus: (i) nucleoside composition analyses show the absence of T in all these tRNAs; (ii) analyses of oligonucleotide fragments produced by T1 ribonuclease show the absence not only of the T-Psi-C-G(A)- sequence, but also of U-Psi-C-G(A)- or U-U-C-G(A)- sequences in such digests. The absence of G-T-Psi-C-G(A)- in the eukaryotic cytoplasmic initator tRNAs is, therefore, not simply due to lack of enzymatic modification of U to T.

Adenosine↗
PubMed1973

Replacement of the sequence G-T-phi-C-G(A)- by G-A-U-C-G- in initiator transfer RNA of rabbit-liver cytoplasm.

Eukaryotic cytoplasmic initiator tRNAs lack the sequence G-T-Psi-C-G(A)-, which is in every tRNA of known sequence that is active in protein biosynthesis. In initiator tRNA of yeast cytoplasm, which is the only eukaryotic initiator tRNA of known sequence, this sequence is replaced by G-A-U-C-G-. We now report the sequence of a 30-nucleotide-long, 3'-terminal fragment of cytoplasmic initiator tRNA of rabbit liver obtained by specific cleavage of the tRNA at the site occupied by the modified nucleoside, 7-methyl guanosine. We show (i) that in rabbit-liver initiator tRNA also, the sequence G-T-Psi-C-G(A)- is replaced by G-A-U-C-G- and (ii) that the sequences of loop IV of both the yeast and rabbit-liver cytoplasmic initiator tRNAs are identical, A-U-C-G-m(1)-A-A-A-.

Adenine Nucleotides↗
PubMedDate not supplied

Pericardial cystic mass with fetal tachycardia.

A pericardial cystic mass is a rare congenital anomaly and may be mistaken for other pericardial and pleural masses. A 31-year-old pregnant woman at 38 weeks of gestation presented with fetal pericardial cyst and fetal tachycardia, which were confirmed by transthoracal echocardiography after delivery. Tachycardia did not persist after delivery. The case is being followed up without any clinical problems at the pediatric cardiology clinic.

Adult↗