double-helical structure of dna  (Double Helix)

Journal: ACS Biomaterials Science & Engineering

Article Title: Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement

doi: 10.1021/acsbiomaterials.5c00228

Figure Lengend Snippet: Characterization of aptamer Broccoli fluorescence enhancement by DNA brick nanostructures. (A) Illustration of aptamer Broccoli on DNA brick-based structures with different sizes. The sizes are presented as width by length. (B) Agarose gel image of DNA brick-based structures connecting with aptamer Broccoli (8–1, 4–1, 2–1, and 1–1) and without aptamer Broccoli (8, 4, 2, and 1). The band shifts indicate a combination of aptamers with nanostructures. (C) Normalized fluorescence intensities of aptamer Broccoli on DNA brick-based structures or free aptamer Broccoli in the presence of DFHBI-1T (10 μM). The corresponding concentrations are 100 nM 8–1, 4–1, 2–1, and 1–1 with 100 nM Broccoli. Free Broccoli (B) is 100 nM ( N = 3).

Article Snippet: For DNA double helices, 10 μL of DNA nanostructures mixed with 2 μL of glycerol were separated using 8% native PAGE at 100 V for 1–2 h. Gels were prepared with 1× TBE buffer containing 10 mM MgCl 2 and left to solidify at room temperature for at least 1 h. The gels were stained by the SYBR Safe DNA gel stain ( S33102 , Invitrogen) for 30 min after the electrophoresis was finished.

Techniques: Fluorescence, Agarose Gel Electrophoresis

Journal: ACS Biomaterials Science & Engineering

Article Title: Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement

doi: 10.1021/acsbiomaterials.5c00228

Figure Lengend Snippet: Characterization of aptamer Broccoli fluorescence enhancement by DNA double helices. (A) Illustration of aptamer Broccoli in the middle of double helices with different lengths (M0 is 0 bp, M3 is 22 bp, M7 is 66 bp, and M15 is 154 bp). (B) Illustration of aptamer Broccoli on the end of double helices with different lengths (S0 is 0 bp, S3 is 22 bp, S7 is 66 bp, and S15 is 154 bp). (C) Normalized fluorescence intensities of aptamer Broccoli on DNA double helices or free aptamer Broccoli in the presence of DFHBI-1T (10 μM). The corresponding concentrations are 100 nM M0, M3, M7, and M15 with 100 nM Broccoli. Free Broccoli (B) is 100 nM ( N = 3). (D) Normalized fluorescence intensities of aptamer Broccoli on DNA double helices or free aptamer Broccoli in the presence of DFHBI-1T (10 μM). The corresponding concentrations are 100 nM S0, S3, S7, and S15 with 100 nM Broccoli. Free Broccoli (B) is 100 nM ( N = 3).

Article Snippet: For DNA double helices, 10 μL of DNA nanostructures mixed with 2 μL of glycerol were separated using 8% native PAGE at 100 V for 1–2 h. Gels were prepared with 1× TBE buffer containing 10 mM MgCl 2 and left to solidify at room temperature for at least 1 h. The gels were stained by the SYBR Safe DNA gel stain ( S33102 , Invitrogen) for 30 min after the electrophoresis was finished.

Techniques: Fluorescence

Journal: ACS Biomaterials Science & Engineering

Article Title: Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement

doi: 10.1021/acsbiomaterials.5c00228

Figure Lengend Snippet: Characterization of aptamer Baby Spinach fluorescence enhancement by DNA nanostructures. (A) Secondary structures of aptamers Broccoli and Baby Spinach and the cognate fluorogen DFHBI-1T. The green bases are the same in both aptamers. The orange bases are the different bases in both aptamers. (B) Normalized fluorescence of hairpins, double helices, and DNA brick-based nanostructures (100 nM) with aptamer Baby Spinach (100 nM). Free aptamer Baby Spinach (S) is 100 nM.

Article Snippet: For DNA double helices, 10 μL of DNA nanostructures mixed with 2 μL of glycerol were separated using 8% native PAGE at 100 V for 1–2 h. Gels were prepared with 1× TBE buffer containing 10 mM MgCl 2 and left to solidify at room temperature for at least 1 h. The gels were stained by the SYBR Safe DNA gel stain ( S33102 , Invitrogen) for 30 min after the electrophoresis was finished.

Techniques: Fluorescence