Isomorphic repeat units for putative information-bearing H-bonded duplexes. Part I. Pyrimidine base pairs with polyamide backbone

2018 ◽  
Vol 1126 ◽  
pp. 33-43 ◽  
Author(s):  
Esther Chingbiaknem ◽  
Siamkhanthang Neihsial ◽  
R.H. Duncan Lyngdoh
Keyword(s):  
Base Pairs ◽  
Pyrimidine Base ◽  
Repeat Units

scholarly journals Three Small Nucleolar RNAs Identified from the Spliced Leader-Associated RNA Locus in Kinetoplastid Protozoans

1998 ◽  
Vol 18 (8) ◽  
pp. 4409-4417 ◽  
Author(s):  
T. Guy Roberts ◽  
Nancy R. Sturm ◽  
Billy K. Yee ◽  
Michael C. Yu ◽  
Toinette Hartshorne ◽  
...  
Keyword(s):  
Large Subunit ◽  
Small Subunit ◽  
Cell Fractionation ◽  
Small Nucleolar Rnas ◽  
Small Subunit Rrna ◽  
Base Pairs ◽  
Spliced Leader ◽  
Repeat Units ◽  
Large Subunit Rrna ◽  
Nucleolar Rnas

ABSTRACT First characterized in Trypanosoma brucei, the spliced leader-associated (SLA) RNA gene locus has now been isolated from the kinetoplastids Leishmania tarentolae and Trypanosoma cruzi. In addition to the T. brucei SLA RNA, bothL. tarentolae and T. cruzi SLA RNA repeat units also yield RNAs of 75 or 76 nucleotides (nt), 92 or 94 nt, and ∼450 or ∼350 nt, respectively, each with significant sequence identity to transcripts previously described from the T. brucei SLA RNA locus. Cell fractionation studies localize the three additional RNAs to the nucleolus; the presence of box C/D-like elements in two of the transcripts suggests that they are members of a class of small nucleolar RNAs (snoRNAs) that guide modification and cleavage of rRNAs. Candidate rRNA-snoRNA interactions can be found for one domain in each of the C/D element-containing RNAs. The putative target site for the 75/76-nt RNA is a highly conserved portion of the small subunit rRNA that contains 2′-O-ribose methylation at a conserved position (Gm1830) in L. tarentolae and in vertebrates. The 92/94-nt RNA has the potential to form base pairs near a conserved methylation site in the large subunit rRNA, which corresponds to position Gm4141 of small rRNA 2 in T. brucei. These data suggest that trypanosomatids do not obey the general 5-bp rule for snoRNA-mediated methylation.

scholarly journals Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 306 ◽  
Author(s):  
Pablo Mora ◽  
Jesús Vela ◽  
Areli Ruiz-Mena ◽  
Teresa Palomeque ◽  
Pedro Lorite
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Repeat Unit ◽  
Pericentromeric Region ◽  
Fish Analysis ◽  
Agricultural Pests ◽  
Base Pairs ◽  
Satellite Dnas ◽  
Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

Genetic transcription

1966 ◽  
Vol 164 (995) ◽  
pp. 181-197 ◽  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Messenger Rna ◽  
Cellular Protein ◽  
Base Sequence ◽  
Structural Members ◽  
Base Pairs ◽  
Pyrimidine Base ◽  
Form Part

The purine and pyrimidine base sequence of DNA , permanent repository of the genetic information, must be transcribed on to ribopolynucleotides before genotype can be translated into phenotype. This transcription gives rise to three recognizably different classes of RNA molecules: (1) two species of ribosomal RNA , one about 1500 and the other 3000 nucleotides in length, that form part of the structural members of the engine for cellular protein synthesis; (2) several dozen species of transfer RNA , each about 100 nucleotides in length, that provide adaptors in protein synthesis for the twenty ‘standard’ amino acids; and (3) hundreds, or thousands, of species of messenger RNA , probably of variable length, but reaching into the tens of thousands of nucleotides, that furnish the templates for orderly copolymerization of amino acids into specific polypeptides. To the particular purine and pyrimidine base sequence of every one of these multifarious RNA species there corresponds some homologous sector of the DNA where this sequence recurs in one of the complementary deoxypolynucleotide strands. It is generally assumed that the DNA strand of base sequence complementary to that of the RNA transcript acts as the template in transcription, because, in analogy with the mechanism of DNA replication, one imagines that formation of the complementary base pairs (Watson & Crick 1953) is responsible for specific alinement of the ribonucleotide monomers. But this point has not yet been firmly established, at least for the actual in vivo transcription. It would be prudent, therefore, to keep in mind for the time being that for transcription some other basepairing mechanism might conceivably obtain. For instance, pairing might also involve identical, rather than complementary, bases (Donohue & Stent 1956), in which case the DNA strand of identical base sequence could act as transcription template, or pairing might involve base triplets, rather than pairs (Stent 1958), in which case both DNA strands of the homologous sector could act jointly as transcription template.

scholarly journals The Stage-regulated Expression ofLeishmania mexicanaCPB Cysteine Proteases Is Mediated by an Intercistronic Sequence Element

2001 ◽  
Vol 276 (50) ◽  
pp. 47061-47069 ◽  
Author(s):  
Darren R. Brooks ◽  
Hubert Denise ◽  
Gareth D. Westrop ◽  
Graham H. Coombs ◽  
Jeremy C. Mottram
Keyword(s):  
Untranslated Region ◽  
Regulatory Element ◽  
Cysteine Proteases ◽  
Specific Gene ◽  
Base Pairs ◽  
Specific Expression ◽  
Sequence Element ◽  
Repeat Units ◽  
Regulated Expression ◽  
Specific Stage

The tandemly arrangedCPBgenes ofLeishmania mexicanaare polycistronically transcribed and encode cysteine proteases that are differentially stage-specific;CPB1andCPB2are expressed predominantly in metacyclics, whereasCPB3–CPB18are expressed mainly in amastigotes. The mechanisms responsible for this differential expression have been studied via gene analysis and re-integration of individualCPBgenes, and variants thereof, into aCPB-deficient parasite mutant. Comparison of the nucleotide sequences of the repeat units ofCPB1andCPB2withCPB2.8(typical ofCPB3–CPB18) revealed two major regions of divergence as follows: one of 258 base pairs (bp) corresponding to the C-terminal extension of CPB2.8; another, designated InS, of 120 bp, with insertions totaling 57 bp, localized to the intercistronic region downstream ofCPB1andCPB2. Cell lines expressingCPB2.8orCPB2with the 3′-untranslated region and intercistronic sequence ofCPB2.8showed up-regulation in amastigotes. Conversely, metacyclic-specific expression occurred withCPB2orCPB2.8with the 3′-untranslated region and intercistronic sequence ofCPB2. Moreover, the InS down-regulated expression in amastigotes of a reporter gene integrated into theCPBlocus. It is proposed that the InS mediates metacyclic-specific stage-regulated expression ofCPBby affecting the maturation of polycistronic pre-mRNA. This is the first well definedcis-regulatory element implicated in post-transcriptional stage-specific gene expression inLeishmania.

scholarly journals Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs

1994 ◽  
Vol 22 (16) ◽  
pp. 3293-3303 ◽  
Author(s):  
Elisabeth M. Evertsz ◽  
Karsten Rippe ◽  
Thomas M. Jovin
Keyword(s):  
Duplex Dna ◽  
Base Pairs ◽  
Pyrimidine Base ◽  
Purine Pyrimidine

scholarly journals Regulation of DIM-2-dependent repeat-induced point mutation (RIP) by the recombination-independent homologous DNA pairing in Neurospora crassa

2021 ◽  
Author(s):  
Florian Carlier ◽  
Tinh-Suong Nguyen ◽  
Alexey K. Mazur ◽  
Eugene Gladyshev
Keyword(s):  
Neurospora Crassa ◽  
Point Mutation ◽  
Base Pairs ◽  
Substrate Preferences ◽  
Relative Contribution ◽  
Repeat Units ◽  
Sequence Recognition ◽  
Cytosine Methyltransferase ◽  
Flanking Regions ◽  
Repeat Induced Point Mutation

ABSTRACTRepeat-induced point mutation (RIP) is a genetic process that creates cytosine-to-thymine (C-to-T) transitions in duplicated genomic sequences in fungi. RIP detects duplications irrespective of their origin, particular sequence, coding capacity, or genomic positions. Previous studies suggested that RIP involves a cardinally new mechanism of sequence recognition that operates on intact double-stranded DNAs. In the fungus Neurospora crassa, RIP can be mediated by a putative C5-cytosine methyltransferase (CMT) RID or/and a canonical CMT DIM-2. These distinct RIP pathways feature opposite substrate preferences: RID-dependent RIP is largely limited to the duplicated sequences, whereas DIM-2-dependent RIP preferentially mutates adjacent non-repetitive regions. Using DIM-2-dependent RIP as a principal readout of repeat recognition, here we show that GC-rich repeats promote stronger RIP compared to AT-rich repeats (independently of their intrinsic propensities to become mutated), with the relative contribution of AT base-pairs being close to zero. We also show that direct repeats promote much more efficient DIM-2-dependent RIP than inverted repeats; both the spacer DNA between the repeat units (the linker) and the flanking regions are similarly affected by this process. These and other results support the idea that repeat recognition for RIP involves formation of many short interspersed quadruplexes between homologous double-stranded DNAs, which need to undergo concomitant changes in their linking number to accommodate pairing.SUMMARYDuring repeat-induced point mutation (RIP) gene-sized duplications of genomic DNA are detected by a mechanism that likely involves direct pairing of homologous double-stranded DNAs. We show that DIM-2-dependent RIP, triggered by closely-positioned duplications, is strongly affected by their relative orientations (direct versus inverted). We also show that GC-rich repeats promote RIP more effectively than AT-rich repeats. These results support a model in which homologous dsDNAs can pair by establishing interspersed quadruplex-based contacts with concomitant changes in their supercoiling status.

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