Stabilization of Unstable CGC+ Triplex DNA by Single-walled Carbon Nanotubes Under Physiological Conditions

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 May 18

PMID 21576218

Citations 3

Authors

Yujun Song

Lingyan Feng

Jinsong Ren

Xiaogang Qu

Affiliations

Soon will be listed here.

Abstract

Triplex formation is a promising strategy for realizing artificially controlling of gene expression, reversible assembly of nanomaterials and DNA nanomachine and single-walled nanotubes (SWNTs) have been widely used as gene and drug delivery vector or as 'building blocks' in nano-/microelectronic devices. CGC(+) triplex is not as stable as TAT triplex. The poor stability of CGC(+) triplex limits its use in vitro and in vivo. There is no ligand that has been reported to selectively stabilize CGC(+) triplets rather than TAT. Here, we report that SWNTs can cause d(CT) • d(AG) duplex disproportionation into triplex d(C(+)T) • d(AG) • d(CT) and single-strand d(AG) under physiological conditions. SWNTs can reduce the stringency of conditions for CGC(+) triplex formation studied by UV-vis, CD, DNA melting, light scattering and atomic force microscopy. Further studies indicate that electrostatic interaction is crucial for d(CT) • d(AG) repartition into triplex d(C(+)T) • d(AG) • d(CT). Our findings may facilitate utilization of SWNTs-DNA complex in artificially controlling of gene expression, nanomaterials assembly and biosensing.

Citing Articles

Switchable electrochemical aptasensor for amyloid-β oligomers detection based on triple helix switch coupling with AuNPs@CuMOF labeled signaling displaced-probe.

Wang X, Li L, Gu X, Yu B, Jiang M Mikrochim Acta. 2021; 188(2):49.

PMID: 33495901 DOI: 10.1007/s00604-021-04704-5.

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

Feng L, Zhao A, Ren J, Qu X Nucleic Acids Res. 2013; 41(16):7987-96.

PMID: 23814186 PMC: 3763558. DOI: 10.1093/nar/gkt575.

Biophysical characterization of the strong stabilization of the RNA triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) alkyl ether berberine analogs.

Bhowmik D, Das S, Hossain M, Haq L, Suresh Kumar G PLoS One. 2012; 7(5):e37939.

PMID: 22666416 PMC: 3362543. DOI: 10.1371/journal.pone.0037939.

References

Gigliotti B, Sakizzie B, Bethune D, Shelby R, Cha J . Sequence-independent helical wrapping of single-walled carbon nanotubes by long genomic DNA. Nano Lett. 2006; 6(2):159-64. DOI: 10.1021/nl0518775. View

Sugimoto N, Wu P, Hara H, Kawamoto Y . pH and cation effects on the properties of parallel pyrimidine motif DNA triplexes. Biochemistry. 2001; 40(31):9396-405. DOI: 10.1021/bi010666l. View

Mergny J, De Cian A, Ghelab A, Sacca B, Lacroix L . Kinetics of tetramolecular quadruplexes. Nucleic Acids Res. 2005; 33(1):81-94. PMC: 546136. DOI: 10.1093/nar/gki148. View

Htun H, Dahlberg J . Topology and formation of triple-stranded H-DNA. Science. 1989; 243(4898):1571-6. DOI: 10.1126/science.2648571. View

Li X, Peng Y, Ren J, Qu X . Carboxyl-modified single-walled carbon nanotubes selectively induce human telomeric i-motif formation. Proc Natl Acad Sci U S A. 2006; 103(52):19658-63. PMC: 1750900. DOI: 10.1073/pnas.0607245103. View

Zhao C, Ren J, Qu X . Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: more water molecules released. Chemistry. 2008; 14(18):5435-9. DOI: 10.1002/chem.200800280. View

Zheng M, Jagota A, Semke E, Diner B, McLean R, Lustig S . DNA-assisted dispersion and separation of carbon nanotubes. Nat Mater. 2003; 2(5):338-42. DOI: 10.1038/nmat877. View

Zhao C, Song Y, Ren J, Qu X . A DNA nanomachine induced by single-walled carbon nanotubes on gold surface. Biomaterials. 2009; 30(9):1739-45. DOI: 10.1016/j.biomaterials.2008.12.034. View

Zhang L, Huang C, Li Y, Xiao S, Xie J . Label-free detection of sequence-specific DNA with multiwalled carbon nanotubes and their light scattering signals. J Phys Chem B. 2008; 112(23):7120-2. DOI: 10.1021/jp800092r. View

10.

Campbell J, Tessmer I, Thorp H, Erie D . Atomic force microscopy studies of DNA-wrapped carbon nanotube structure and binding to quantum dots. J Am Chem Soc. 2008; 130(32):10648-55. DOI: 10.1021/ja801720c. View

11.

Soto A, Loo J, Marky L . Energetic contributions for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks. J Am Chem Soc. 2002; 124(48):14355-63. DOI: 10.1021/ja026952h. View

12.

Li X, Peng Y, Qu X . Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution. Nucleic Acids Res. 2006; 34(13):3670-6. PMC: 1540735. DOI: 10.1093/nar/gkl513. View

13.

Cassidy S, Asensio Alvarez J, Fox K, Brown T, Lane A . Coralyne has a preference for intercalation between TA.T triples in intramolecular DNA triple helices. Nucleic Acids Res. 1997; 25(10):1890-6. PMC: 146695. DOI: 10.1093/nar/25.10.1890. View

14.

Zhao C, Peng Y, Song Y, Ren J, Qu X . Self-assembly of single-stranded RNA on carbon nanotube: polyadenylic acid to form a duplex structure. Small. 2008; 4(5):656-61. DOI: 10.1002/smll.200701054. View

15.

Keren K, Berman R, Buchstab E, Sivan U, Braun E . DNA-templated carbon nanotube field-effect transistor. Science. 2003; 302(5649):1380-2. DOI: 10.1126/science.1091022. View

16.

Peng Y, Wang X, Xiao Y, Feng L, Zhao C, Ren J . i-Motif quadruplex DNA-based biosensor for distinguishing single- and multiwalled carbon nanotubes. J Am Chem Soc. 2009; 131(38):13813-8. DOI: 10.1021/ja9051763. View

17.

Moser H, Dervan P . Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987; 238(4827):645-50. DOI: 10.1126/science.3118463. View

18.

Wells R, Collier D, Hanvey J, Shimizu M, WOHLRAB F . The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988; 2(14):2939-49. View

19.

Plum G, Breslauer K . Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. J Mol Biol. 1995; 248(3):679-95. DOI: 10.1006/jmbi.1995.0251. View

20.

Song Y, Wang X, Zhao C, Qu K, Ren J, Qu X . Label-free colorimetric detection of single nucleotide polymorphism by using single-walled carbon nanotube intrinsic peroxidase-like activity. Chemistry. 2010; 16(12):3617-21. DOI: 10.1002/chem.200902643. View