Nucleic Acids Research

Scholten, Petra, M.;Nordheim,, Alfred

doi: 10.1093/nar/14.10.3981pmid: 3714469

Abstract Two palindromic DNA sequences were analyzed with respect to their chemical reactivities with diethyl pyrocarbonate. In negatively supercoiled plasmid templates enhanced N7 carbethoxy-lation was found with individual purines located in presumptive single-stranded loops of DNA cruciform structures. No enhanced reactivity at these positions was observed in linear, relaxed or low superhelical density plasmids. Hyperreactivity was found over a narrow region only, indicating that stable cruciforms contain loops of minimal size. No enhanced chemical reactivity was found with the four-way junction at the base of cruciforms. Diethyl pyrocarbonate has proved a sensitive structural probe for the analysis, with single nucleotide resolution, of DNA cruciform structures. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Furlong, Judy, C.;Lilley, David M., J.

doi: 10.1093/nar/14.10.3995pmid: 3012460

Abstract Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T) 34 cruciforms of pColIR315 and pXG540. In each case we observe maximal modification at the most central adenosine of the loop, and an overall pattern of modification corresponding to a total loop size of about six bases. The results may be interpreted in terms of a model in which the loop has a defined tertiary structure. No modification was detected at either cruciform four-way junction, suggesting that this region is fully base-paired. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Hajnsdorf,, E.;Favre,, A.;Expert-Bezancon,, A.

doi: 10.1093/nar/14.10.4009pmid: 2423965

Abstract Functionally active 70S rtbosomes containing 4-thiouracil in place of uracil (substitution level 2%) were prepared by an in vivo substitution method. RNA-protein crosslinks were introduced by 366nm photoactlvation of 4-thlouracll in the purified 305 subunlts. Seven single stranded Ml3 probes containing rDNA inserts complementary to domains 3 and 4 of 16S RNA were constructed. These inserts approximately 100 nucleotides long starting at nucleotide 868 and ending at the 3' OH terminus were used to select contiguous RNA sections. The proteins covalently linked to each selected RNA section were identified by 20 gel electrophoresis. Proteins S7, 59, SI3 were shown to be efficiently crosslinked to multiple sites belonging to both domains. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Ridley, Robert, G.;Patel, Hasmukh, V.;Gerber, Gerhard, E.;Morton, Robert, C.;Freeman, Karl, B.

doi: 10.1093/nar/14.10.4025pmid: 3012461

Abstract A cDNA clone spanning the entire amino acid sequence of the nuclear-encoded uncoupling protein of rat brown adipose tissue mitochondria has been isolated and sequenced. With the exception of the N-terminal methionine the deduced N-terminus of the newly synthesized uncoupling protein is identical to the N-terminal 30 amino acids of the native uncoupling protein as determined by protein sequencing. This proves that the protein contains no N-terminal mitochondrial targeting prepiece and that a targeting region must reside within the amino acid sequence of the mature protein. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Sun, Lee, K.;Showe, Lousie, C.;Croce, Carlo, M.

doi: 10.1093/nar/14.10.4037pmid: 3714470

Abstract We have cloned and mapped the sequences extending 38 kb 3' of the c-myc gene. This region is found to be highly repetitive in nature and hybridizes extensively with a BLUR 8 Alu probe. Unique sequence probes derived from this region were used to map the chromosomal breakpoints of a number of lymphoma cell lines with t(2;8) or t(8;22) translocations. In five of the cell lines (PA682, LY67, LY47, LY66 and LY91), the immunoglobulin light chain locus translocates into a region which is greater than 47 kb downstream of c-myc. For one of the cell lines, JI, the location of the breakpoint on the 8q+ chromosome was found to be 25–32 kb 3' of c-myc. The breakpoint for the BL2 cell line had been previously mapped at 10 kb 3' of the c-myc oncogene. Analyses of steady-state levels of c-myc mRNA in cell lines with chromosomal break points ranging from 10 kb to greater than 47 kb 3' of c-myc range from 0.5 to 10X the levels in lymphoblast controls. The different levels of c-myc transcripts is not a direct function of the distance between the c-myc gene and the translocated immunoglobulin light chain locus. This content is only available as a PDF. Author notes + Present address: Malvern, Philadelphia, USA © IRL Press Limited, Oxford, England

Leutwiler, Leslie, S.;Meyerowitz, Elliot, M.;Tobin, Elaine, M.

doi: 10.1093/nar/14.10.4051pmid: 3012462

Abstract The genome of Arabidopsis thaliana is exceedingly small, in part because it lacks the large middle repetitive DNA component characteristic of other plants. In this paper we have characterized a member of the low copy DNA component: the gene family for the light-harvesting chlorophyll a/b-protein. This gene family is unusual in that it contains far fewer members tTTan the 7-16 coding sequences for this protein found in other plants. We used cross-hybridization with a Lemna gene encoding a light-harvesting chlorophyll a/b-protein to isolate 3 genes from Arabidopsis, all of which are clustered on an 11-kb genomic clone. Southern blot analysis suggests that there is a fourth related gene in Arabidopsis. Sequence analysis of the three genes demonstrates that a) within the translated region the nucleic acid sequence homology is 96%, b) the deduced amino acid sequence of the mature proteins is identical for the three genes, and c) two of the genes have a high degree of sequence homology in both their 5' and 3' immediate flanking regions. The genes have regulatory sequences typical of eukaryotic genes upstream of the translation start sites. However, not all of these genes are equally expressed in plants grown under normal light-dark conditions. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Vlassov, V., V.;Zarytova, V., F.;Kutiavin, I., V.;Mamaev, S., V.;Podyminogin, M., A.

doi: 10.1093/nar/14.10.4065pmid: 3714471

Abstract A single stranded DNA fragment was modified with alkylating derivatives of oligonucleotides complementary to a certain nuc-leotide sequences in the fragment. The derivatives carried aromatic 2-chloroethylamino groups at their 3'- or 5'-terminal nucleotide residues. Some of the derivatives carried both alkylating group and intercalating phenazine group which stabilized complementary complexes. It was found that these oligonucleotide derivatives modify the DNA fragment in a specific way near the target complementary nucleotide sequences, and the DNA fragment can be cleaved at the alkylated nucleotides positions. Alkylating derivatives carrying phenazine groups were found to be the most efficient in reaction with the DNA fragment. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Lahiri, Debomoy, K.;Thomas, John, O.

doi: 10.1093/nar/14.10.4077pmid: 3754960

Abstract A cDNA clone which expresses a protein that cross-reacts immunologi-cally with the human Cl and C2 hnRNP core proteins has been isolated. The done was selected by a sensitive immunochemical assay employing an avidin-biotin complex for detection, and identified as a clone for the hnRNP C proteins by a highly sensitive antibody select assay that is described here. The clone contains 677 nucleotides, and, as shown by northern blotting, is derived from a 1.5 Kb poly(A) + mRNA. There are regions of strong homology between the human and mouse genes, weak homology is seen with chicken DNA, and very little, if any, homology can be detected with Drosophila. Artemia. sea urchin, or yeast DNAs. Two peptides (a total of 24 amino acids) of the calf thymus single-stranded DNA binding protein UP2 show perfect homology with the deduced amino acid sequence of the clone, suggesting that UP2 is related to the hnRNP C proteins. There is also a region that has a sequence very similar to two regions of the single-stranded DNA binding protein UP1 that contain proposed DNA binding sites. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Datta,, Dipak;Changchien,, Li-Ming;Craven, Gary, R.

doi: 10.1093/nar/14.10.4095pmid: 3520481

Abstract We have found that all E. coli ribosomal proteins strongly bind to an agarose affinity column derivatized with the dye Cibacron Blue F3GA. We have also shown that the capacity to bind the dye is lost when the proteins are organized within the structure of the ribosome or are members of pre-formed protein-RNA complexes. We conclude that the binding of ribosomal proteins to this dye involves specific protein-RNA recognition sites. These observations led us to discover that Cibacron Blue can be used to inhibit in vitro ribosome assembly at any stage of the assembly process. This has allowed us to determine a kinetic order of ribosome assembly. This content is only available as a PDF. © IRL Press Limited, Oxford, England

Frayne, Elizabeth, G.;Kellems, Rodney, E.

doi: 10.1093/nar/14.10.4113pmid: 3714472

Abstract Structural features of the transcription termination region for the mouse dihydrofolate reductase gene have been determined and compared with those of several other known termination regions for protein coding genes. A common feature identified among these termination regions was the presence of a 20 bp consensu DNA sequence element (ATC GA AA GA TAG GA AA GA AGCAAT). The results imply that the 20 bp consensus DNA sequence element is importnat for signaling RNA polymerase II transcription termination at least in the several vertebrate species investigated.Furthermore, the results suggest that for the dhfr gene and possibly for other genes in mice as well, the potential termination consensus sequence can exist as part of a long interspersed repetitive DNA element. This content is only available as a PDF. © IRL Press Limited, Oxford, England