Targeting of mixed sequence double-stranded DNA using pyrene-functionalized 2′-amino-α-l-LNA

2005 ◽  
pp. 4279 ◽  
Author(s):  
Patrick J. Hrdlicka ◽  
T. Santhosh Kumar ◽  
Jesper Wengel
Keyword(s):  
Double Stranded Dna ◽  
Mixed Sequence

Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

RSC Advances ◽  
2016 ◽  
Vol 6 (90) ◽  
pp. 87400-87404 ◽  
Author(s):  
P. Chilka ◽  
P. R. Patlolla ◽  
B. Datta
Keyword(s):  
Selective Recognition ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Carbocyanine Dye ◽  
G Quadruplex

A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

scholarly journals Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

Molecules ◽  
2015 ◽  
Vol 20 (8) ◽  
pp. 13780-13793 ◽  
Author(s):  
Brooke Anderson ◽  
Saswata Karmakar ◽  
Patrick Hrdlicka
Keyword(s):  
Sequence Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence

scholarly journals Identification and Characterization of Second-Generation Invader Locked Nucleic Acids (LNAs) for Mixed-Sequence Recognition of Double-Stranded DNA

2013 ◽  
Vol 78 (19) ◽  
pp. 9560-9570 ◽  
Author(s):  
Sujay P. Sau ◽  
Andreas S. Madsen ◽  
Peter Podbevsek ◽  
Nicolai K. Andersen ◽  
T. Santhosh Kumar ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Second Generation ◽  
Sequence Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Locked Nucleic Acids ◽  
Identification And Characterization

scholarly journals Impact of non-nucleotidic bulges on recognition of mixed-sequence dsDNA by pyrene-functionalized Invader probes

2020 ◽  
Vol 18 (24) ◽  
pp. 4645-4655
Author(s):  
Dale C. Guenther ◽  
Raymond G. Emehiser ◽  
Allison Inskeep ◽  
Saswata Karmakar ◽  
Patrick J. Hrdlicka
Keyword(s):  
Specific Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence

Invader probes featuring non-nucleotidic bulges are energetically activated for highly specific recognition of complementary double-stranded DNA targets.

scholarly journals Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

2014 ◽  
Vol 12 (39) ◽  
pp. 7758-7773 ◽  
Author(s):  
Saswata Karmakar ◽  
Andreas S. Madsen ◽  
Dale C. Guenther ◽  
Bradley C. Gibbons ◽  
Patrick J. Hrdlicka
Keyword(s):  
Single Nucleotide ◽  
Double Stranded Dna ◽  
Mixed Sequence

Energetically activated double-stranded probes with interstrand arrangements of intercalator-functionalized nucleotides enable recognition of mixed-sequence DNA with single nucleotide fidelity.

Head-to-head comparison of LNA, MPγPNA, INA and Invader probes targeting mixed-sequence double-stranded DNA

2020 ◽  
Vol 18 (1) ◽  
pp. 56-65 ◽  
Author(s):  
Raymond G. Emehiser ◽  
Eric Hall ◽  
Dale C. Guenther ◽  
Saswata Karmakar ◽  
Patrick J. Hrdlicka
Keyword(s):  
Specific Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Modified Dna ◽  
Dna Strands

Double-stranded (ds) Invader and INA probes allow for efficient and specific recognition of mixed-sequence dsDNA targets, whereas recognition is less efficient and specific with single-stranded LNA-modified DNA strands and fully modified MPγPNAs.

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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