Journal: Biochemistry and Biophysics Reports

Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field

doi: 10.1016/j.bbrep.2016.10.006

Figure Lengend Snippet: Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles in the absence of a magnetic field on the ambient temperature. The ordinate axis represents the ligation efficiency, which is normalized by that at 16 °C. The standard deviations are obtained from 6 independent experiments.

Article Snippet: In summary, we carried out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on ferromagnetic particles and found that the ligation efficiency was increased under a radio frequency alternating magnetic field caused by heat generation from the particles.

Techniques: DNA Ligation, Ligation

Journal: Biochemistry and Biophysics Reports

Article Title: Efficient DNA ligation by selective heating of DNA ligase with a radio frequency alternating magnetic field

doi: 10.1016/j.bbrep.2016.10.006

Figure Lengend Snippet: Dependence of the efficiency of DNA ligation using T4 DNA ligase immobilized on ferromagnetic particles under an ac magnetic field of 0.34 MHz on the amplitude of the magnetic field. The ambient temperature is 16 °C. The ordinate axis represents the ligation efficiency under an ac magnetic field, which is normalized by that in the absence of a magnetic field. The inset shows the ligation efficiency under the ac magnetic field as a function of the average surface temperature of ferromagnetic particles, noting that the surface temperature increases with an increase in the field amplitude. The standard deviations are obtained from 6 independent experiments.

Article Snippet: In summary, we carried out the ligation of DNA fragments with cohesive ends using T4 DNA ligase immobilized on ferromagnetic particles and found that the ligation efficiency was increased under a radio frequency alternating magnetic field caused by heat generation from the particles.

Techniques: DNA Ligation, Ligation

Journal: The Plant Journal

Article Title: Single-nucleotide and long-patch base excision repair of DNA damage in plants

doi: 10.1111/j.1365-313X.2009.03994.x

Figure Lengend Snippet: Partial stimulation of uracil repair by the addition of exogenous proteins. Duplex DNA containing U opposite G at a Hpa II site was incubated at 30°C for 3 h with Arabidopsis cell extract in a reaction mixture containing either deoxycytidine triphosphate (dCTP) or all four deoxyribonucleotide triphosphates (dNTPs), as indicated, and different combinations of T4 DNA ligase (1.5 U), Arabidopsis AtXRCC1 (65 n m ) and human Pol β (2.4 U). Reaction products were digested with Hpa II, separated in a 12% denaturing polyacrylamide gel and quantified by fluorescence scanning. The percentage of fully repaired DNA product is shown. Values are means with standard errors from two independent experiments.

Article Snippet: E. coli T4 DNA ligase was purchased from Promega ( http://www.promega.com ) and Hpa II was purchased from Roche ( http://www.roche-applied-science.com ).

Techniques: Incubation, Fluorescence

Journal: PLoS ONE

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray

doi: 10.1371/journal.pone.0090920

Figure Lengend Snippet: Optimization of D-probe complementary sequence length. (A) Complementary sequences of four probe sets for miR-143. (B) The fluorescence intensities of D-probes bound to C-probes in the presence of T4 DNA ligase. Data represent the mean ± S.E. (n = 3). (C) Correlation between input miR-143 and the signal of D-probe-143-(8) in the presence (filled circle) or absence (open circle) of T4 DNA ligase. The upper axis indicates the final concentration of input miR-143 in the hybridization chamber while the lower axis indicates the total amount of input miR-143. Data in the linear range were fitted by a linear expression (gray lines). Data represent the mean ± S.E. (n = 3).

Article Snippet: Silane-PEG-Maleimide (MW 5000), betaine solution, PEG 6000 solution, bovine serum albumin (BSA) and T4 DNA ligase were purchased from NANOCS Inc. (Boston, MA, USA), WAKO (Osaka, Japan), Hampton Research (Aliso Viejo, CA, USA), Sigma Aldrich Japan (Tokyo, Japan) and TAKARA (Shiga, Japan), respectively.

Techniques: Sequencing, Fluorescence, Concentration Assay, Hybridization, Expressing

Journal: PLoS ONE

Article Title: Label-Free Quantification of MicroRNAs Using Ligase-Assisted Sandwich Hybridization on a DNA Microarray

doi: 10.1371/journal.pone.0090920

Figure Lengend Snippet: Experimental design of the LASH assay. (A) Schematic representation of the ligase-assisted sandwich hybridization assay (LASH assay) for detection of non-labeled miRNA. A target miRNA hybridizes to complimentary D-probe and C-probe, resulting in a tertiary complex. Both C-probe and D-probe are capped with a phosphate group at the 5′ end and a hydroxyl group at the 3′ end; this permits T4 DNA ligase to ligate the 5′ end of C-probe to the 3′ end of D-probe, and to ligate the 5′ end of D-probe to the 3′ end of the target miRNA. (B) A bright-field image of droplets spotted on a coverslip by an ink-jet machine. Scale bar, 400 µm. (C) Fluorescence images of 6-FAM-labeled C-probe (left) immobilized on a substrate and Alexa647-labeled D-probe (right) bound to C-probe in the presence of 1.25 nM miR-143. Scale bar, 100 µm.

Article Snippet: Silane-PEG-Maleimide (MW 5000), betaine solution, PEG 6000 solution, bovine serum albumin (BSA) and T4 DNA ligase were purchased from NANOCS Inc. (Boston, MA, USA), WAKO (Osaka, Japan), Hampton Research (Aliso Viejo, CA, USA), Sigma Aldrich Japan (Tokyo, Japan) and TAKARA (Shiga, Japan), respectively.

Techniques: Hybridization, Labeling, Fluorescence