Activation of Double-stranded DNA by One pcPNA Strand for Its Site-selective Scission with CeIV/EDTA

2007 ◽  
Vol 36 (6) ◽  
pp. 780-781 ◽  
Author(s):  
Yuichiro Aiba ◽  
Yoji Yamamoto ◽  
Makoto Komiyama
Keyword(s):  
Double Stranded Dna ◽  
Site Selective

Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity

2008 ◽  
Vol 3 (4) ◽  
pp. 655-662 ◽  
Author(s):  
Makoto Komiyama ◽  
Yuichiro Aiba ◽  
Yoji Yamamoto ◽  
Jun Sumaoka
Keyword(s):  
Double Stranded Dna ◽  
Artificial Restriction ◽  
Site Selective

scholarly journals Rapid site-selective hydrolysis of double-stranded DNA by use of Ce(IV)/EDTA and PNA bearing phosphate group

2005 ◽  
Vol 49 (1) ◽  
pp. 277-278 ◽  
Author(s):  
Yuichiro Aiba ◽  
Masao Mori ◽  
Yoji Yamamoto ◽  
Makoto Komiyama
Keyword(s):  
Phosphate Group ◽  
Selective Hydrolysis ◽  
Double Stranded Dna ◽  
Site Selective ◽  
Hydrolysis Of

scholarly journals PNA–NLS conjugates as single-molecular activators of target sites in double-stranded DNA for site-selective scission

2013 ◽  
Vol 11 (32) ◽  
pp. 5233 ◽  
Author(s):  
Yuichiro Aiba ◽  
Yuya Hamano ◽  
Wataru Kameshima ◽  
Yasuyuki Araki ◽  
Takehiko Wada ◽  
...  
Keyword(s):  
Double Stranded Dna ◽  
Target Sites ◽  
Site Selective

Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid “Invasion”

ACS Nano ◽  
2011 ◽  
Vol 5 (4) ◽  
pp. 2467-2474 ◽  
Author(s):  
Andrea L. Stadler ◽  
Dazhi Sun ◽  
Mathew M. Maye ◽  
Daniel van der Lelie ◽  
Oleg Gang
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Selective Binding ◽  
Double Stranded Dna ◽  
Site Selective

Site-selective Scission of Double-stranded DNA by Combining a Triplex-forming bis-PNA and Ce(IV)/EDTA

2013 ◽  
Vol 42 (10) ◽  
pp. 1300-1302 ◽  
Author(s):  
Yuichiro Aiba ◽  
Kohei Yasuda ◽  
Makoto Komiyama
Keyword(s):  
Double Stranded Dna ◽  
Site Selective

Discrimination of monomer from multimer DNA disk-shaped toruses by freezeetch TEM

1984 ◽  
Vol 42 ◽  
pp. 210-211
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Biochemical Data ◽  
Dna Structures ◽  
Ice Surface ◽  
Double Stranded Dna ◽  
Data Support ◽  
Dna Organization ◽  
Trivalent Cations

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.

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.

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