Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Abstract

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40°C by SWNTs but no change for AT-DNA. SWNTs can induce B–A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B–A transition in solution and they bind to the DNA major groove with GC preference.

Insights into the biomedical effects of carboxylated single-wall carbon nanotubes on telomerase and telomeres

“…However, the positively charged amino group-modified SWNTs decreased the i-motif Tm by 2 °C 13 . These results indicate that a negatively charged group on the open end of the side wall enhances the interactions with i-motif CC + base pairs by providing favourable electrostatic attractions 11 . These findings are also consistent with our other works that carboxyl-or hydroxyl-modified SWNTs can facilitate polyrA to form A·A + duplex structure at pH 7.0, whereas no such effect was observed with positively charged amino-modified SWNTs 12 .…”

“…SWNTs (ϕ = 1.1nm, purity > 90%) were purchased from Aldrich (St Louis, MO, USA) and MWNTs (ϕ = 10-20 nm) were purchased from Nanotech Port Co. Ltd. (Shenzhen, China). The preparation and characterization (size and surface charges) of chemically modified CNTs have been described in detail in previous reports [11][12][13][14][15][16][17][18]32 . In brief, the carboxyl- , 2′-O-meRnA or transfection with TRF2 ∆B∆m for 3 weeks, cells were lysed and separated on 10% sDs-PAGE, and probed with anti-p16 InK4a and anti-p21 WAF1 primary antibody, respectively.…”

“…After reduction, samples were successively washed with methanol, diluted HCl and water. The ethylenediamine-modified SWNTs (SWNT-CONHCH 2 CH 2 NH 2 ) were synthesized by a routine method 11,12,16 , suspending the carboxyl-modified SWNTs in thionyl chloride (SOCl 2 ) solution containing 5% dimethylformamide, and circle heating for 24 h at 70 °C, then washing with tetrahydrofuran. Acyl chloride-modified SWNTs (SWNT-COCl) were obtained.…”

“…A piece of double-stranded (ds) DNA wrapped on the surface of a SWNT can serve as sensors SWNT-COOH MWNT-COOH SWNT-CH 2 OH SWNT-CONHCH 2 CH 2 NH 2 A1 A13 A19 G2 G3 G14 G15 G16 G20 G21 G22 G4 G8 G9 G10 T5 T11 T12 T6 T17 T18 A7 C1 T4 T22 A5 A6 C2 C3 C15 C14 C13 C9 T10 T16 in living cells based on the transition of DNA secondary structure from the native, right-handed 'B' form to the alternate, left-handed 'Z' form 10 . A series of DNA interactions with SWNTs have been studied by our group [11][12][13][14][15][16][17][18] . We found that SWNTs can destabilize duplex DNA and induce a sequence-dependent DNA B-A transition 11 and can facilitate self-structuring of ssRNA poly(rA) to form A·A + duplex structure 12 .…”

“…A series of DNA interactions with SWNTs have been studied by our group [11][12][13][14][15][16][17][18] . We found that SWNTs can destabilize duplex DNA and induce a sequence-dependent DNA B-A transition 11 and can facilitate self-structuring of ssRNA poly(rA) to form A·A + duplex structure 12 . Intriguingly, SWNTs, not multi-walled carbon nanotubes (MWNTs), can selectively stabilize human telomeric i-motif DNA and induce i-motif structure formation by binding to the 5′-end major groove under physiological conditions [13][14][15][16] (Supplementary Figs S1 and S2), and even under molecular crowding conditions 17 .…”