Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

Abstract

Left-handed Z-DNA has been identified as a transient structure occurred during transcription. DNA B-Z transition has attracted much attention because of not only Z-DNA biological importance but also their relation to disease and DNA nanotechnology. Recently, photoluminescent carbon dots, especially highly luminescent nitrogen-doped carbon dots, have attracted much attention on their applications to bioimaging and gene/drug delivery because of carbon dots with low toxicity, highly stable photoluminescence and controllable surface function. However, it is still unknown whether carbon dots can influence DNA conformation or structural transition, such as B-Z transition. Herein, based on our previous series work on DNA interactions with carbon nanotubes, we report the first example that photoluminescent carbon dots can induce right-handed B-DNA to left-handed Z-DNA under physiological salt conditions with sequence and conformation selectivity. Further studies indicate that carbon dots would bind to DNA major groove with GC preference. Inspired by carbon dots lighting up Z-DNA and DNA nanotechnology, several types of DNA logic gates have been designed and constructed based on fluorescence resonance energy transfer between photoluminescent carbon dots and DNA intercalators.

Nucleic Acids and Smart Materials: Advanced Building Blocks for Logic Systems

“…Photoluminescent carbon dots (CDs), with a diameter less than 10 nm, are considerably attractive for bioimaging and biosensor applications owing to their stable photoluminescence, broad excitation spectrum, tunable emission wavelength, excellent biocompatibility, and abundant functional groups on their surface . Recently, our group found that CDs can induce B‐DNA to Z‐DNA under physiological salt conditions with sequence and conformation selectivity . Compared to canonical right‐handed B‐DNA, Z‐DNA presents the left‐handed double helix and its phosphate backbone has a zigzag pattern.…”

Interfering with DNA High‐Order Structures using Chiral Ruthenium(II) Complexes

“…Transient Z‐DNA plays an important role in cell processes including transcription, chromatin recombination, and nucleosome positioning . Some molecules have been reported that can induce a B–Z DNA conformational transfer . For example, in the presence of a low concentration of [Co(NH 3 ) 6 ] 3+ , B‐DNA conformationally transforms into Z‐DNA .…”

“…[4][5][6][7][8] Somem olecules have been reported that can induce aB-Z DNA conformational transfer. [9][10][11][12][13][14][15][16][17][18] For example, in the presence of al ow concentration of [Co(NH 3 ) 6 ] 3 + ,B-DNA conformationally transforms into Z-DNA. [11] More interestingly,w ith an increasing concentration of [Co(NH 3 ) 6 ] 3 + ,D NA turns into ah igh-orderc ompacts tructure.…”

Novel insights into a major DNA oxidative lesion: its effects on Z-DNA stabilization

“…Commercially available poly(dI-dC)s were used as templates, and Klenow fragments were used to incorporate 8-oxo-2′-deoxyguanosine-5′-triphosphate into the synthetic polymers. 17 We next used the hexamer of 5′-CGCGCG-3′ with substituted 8-oxodG sites for study. To be different from polyCG, a typical Z-DNA conformation could be characterized on the CD spectrum of polyC-oxoG, 17 showing a positive band around 250 nm, an evident positive one around 270 nm and a dominant-negative one around 290 nm in the absence of NaCl (Fig.…”