An Efficient System for Finding Functional Motifs in Genomic DNA Sequences by Using Nature-Inspired Algorithms

2016 ◽  
pp. 215-224
Author(s):  
Ebtehal S. Elewa ◽  
Mohamed B. Abdelhalim ◽  
Mai S. Mabrouk
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Efficient System ◽  
Nature Inspired Algorithms

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Rapid Amplification of Uncharacterized Transposon-tagged DNA Sequences from Genomic DNA

Yeast ◽  
1997 ◽  
Vol 13 (3) ◽  
pp. 233-240 ◽  
Author(s):  
KRISTIN T. CHUN ◽  
HOWARD J. EDENBERG ◽  
MARK R. KELLEY ◽  
MARK G. GOEBL
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Rapid Amplification

scholarly journals Distribution of sequence-dependent curvature in genomic DNA sequences

FEBS Letters ◽  
1997 ◽  
Vol 406 (1-2) ◽  
pp. 69-74 ◽  
Author(s):  
Andrei Gabrielian ◽  
Kristian Vlahovicek ◽  
Sándor Pongor
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Sequence Dependent

scholarly journals Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2748 ◽  
Author(s):  
Ae-Ree Lee ◽  
Na-Hyun Kim ◽  
Yeo-Jin Seo ◽  
Seo-Ree Choi ◽  
Joon-Hwa Lee
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Multiple Sequence ◽  
Left Handed ◽  
Transition Mechanism ◽  
Dna Strands ◽  
Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

Characterization of human genomic DNA sequences homologous to the interleukin 2 cDNA

1986 ◽  
Vol 138 (2) ◽  
pp. 966-973
Author(s):  
Shuji Mita ◽  
Shuichiro Maeda ◽  
Kazunori Shimada
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Interleukin 2 ◽  
Human Genomic ◽  
Human Genomic Dna

scholarly journals Genomic DNA sequences of mitochondrial tRNA genes in fungiPenicillium chrysogenumKCTC1262: tRNAarg, tRNAasnand tRNAtyrgenes

1992 ◽  
Vol 20 (21) ◽  
pp. 5842-5842
Author(s):  
Joonho Sheen ◽  
Seungmoak Kim ◽  
Yung Hee Kho ◽  
Kyung Sook Bae
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Trna Genes ◽  
Mitochondrial Trna ◽  
Mitochondrial Trna Genes

Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 716-728 ◽  
Author(s):  
Pavel Neumann ◽  
Marcela Nouzová ◽  
Jirí Macas
Keyword(s):  
Pisum Sativum ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Chromosome Morphology ◽  
Plant Genome ◽  
Genomic Repeats ◽  
Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211–212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

Analyses of solanaceous species using repetitive genomic DNA sequences isolated from Solanum brevidens

Plant Science ◽  
1996 ◽  
Vol 117 (1-2) ◽  
pp. 121-129 ◽  
Author(s):  
U. Malkamäki ◽  
M.S. Clark ◽  
H. Rita ◽  
J.P.T. Valkonen ◽  
E. Pehu
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Solanum Brevidens ◽  
Solanaceous Species
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