Sequencing of large double-stranded DNA using the dideoxy sequencing technique

1982 ◽  
Vol 2 (11) ◽  
pp. 907-912 ◽  
Author(s):  
G. F. Hong
Keyword(s):  
Sequence Analysis ◽  
Direct Sequencing ◽  
Dna Molecules ◽  
Coding Region ◽  
Base Pairs ◽  
Dideoxy Sequencing ◽  
Double Stranded Dna ◽  
Sequencing Technique ◽  
Eukaryotic Dna

The dideoxy sequencing technique has been applied to the direct sequencing of large double-stranded DNA molecules with a small single-stranded primer. For instance, the method was applied to the lambda genome, which contains 48 502 base-pairs (Sanger F, Coulson AR, Hong GF, Hill D & Petersen GB, 1982, J. Mol. Biol., in press), and the coding region for gene W identified. The procedure proves useful in the sequence analysis of a large number of different mutations in a particular region and in the analysis of eukaryotic DNA cloned in plasmids, phages, and cosmids.

scholarly journals Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 241
Author(s):  
Enrique Maciá
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Three Dimensional ◽  
Dna Molecules ◽  
Analytical Treatment ◽  
Dynamical Equations ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Collective Oscillations ◽  
Triplet Codon

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

Sequence-dependent twist-bend coupling in DNA minicircles

Nanoscale ◽  
2021 ◽  
Author(s):  
Minjung Kim ◽  
Sehui Bae ◽  
Inrok Oh ◽  
Jejoong Yoo ◽  
Jun Soo Kim
Keyword(s):  
Dna Bending ◽  
Dna Molecules ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Sequence Dependent ◽  
Potential Tool

Looping of double-stranded DNA molecules with 100∼200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a...

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

scholarly journals Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium castaneum, is Associated With a Recent Mutation

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 417-426
Author(s):  
Richard W Beeman ◽  
M Scott Thomson ◽  
John M Clark ◽  
Marco A DeCamillis ◽  
Susan J Brown ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Tribolium Castaneum ◽  
Frameshift Mutation ◽  
Open Reading Frames ◽  
Red Flour Beetle ◽  
Intron Sequence ◽  
Coding Region ◽  
Long Terminal Repeats ◽  
Flour Beetle ◽  
Reading Frames

Abstract A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

scholarly journals Hoogsteen Base Pairs Increase the Susceptibility of Double-Stranded DNA to Cytotoxic Damage

2021 ◽  
Vol 120 (3) ◽  
pp. 9a
Author(s):  
Akanksha Manghrani ◽  
Yu Xu ◽  
Emily Cannistraci ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Base Pairs ◽  
Double Stranded Dna

scholarly journals Direct Sequencing from the Minimal Number of DNA Molecules Needed to Fill a 454 Picotiterplate

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e97379 ◽  
Author(s):  
Mária Džunková ◽  
Marc Garcia-Garcerà ◽  
Llúcia Martínez-Priego ◽  
Giussepe D’Auria ◽  
Francesc Calafell ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Dna Molecules

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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