Binding between DNA and Carbon Nanotubes Strongly Depends upon Sequence and Chirality

Shankar, A. N.; Mittal, Jeetain; Jagota, Anand

doi:10.1021/la500013c

Cited by 48 publications

(77 citation statements)

References 35 publications

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“…The ability of these sequences to exhibit stronger chirality dependence than the other recognition sequences tested could be caused by an increased sensitivity of binding strength on SWNT chirality. This phenomenon was previously reported for the sequences (TAT) 4 , (CCA) 10 and (TTA) 4 TT, where surfactant exchange experiments indicated that the difference in binding strength across various chiralities was much larger for (TAT) 4 than for the other sequences [34].…”

Section: Resultssupporting

confidence: 82%

“…Thus, the chirality dependence observed in this study can be explained by corona structure variability-and hence, variability in analyte accessibility to the SWNT surface-across different chiralities for the same ssDNA wrapping. Molecular dynamics simulations have been extensively used to study the corona architecture of DNA-SWNT hybrids and a combination of molecular dynamics and surfactant exchange experiments have shown that corona architecture and binding strength vary across different chiralities for several sequences exhibiting separation capability including (TAT) 4 [32][33][34]. Both corona structure and binding strength are dependent on a combination of nanotube diameter and electronic properties, which can be clearly observed in the chirality dependent responses of (TAT) 4 -wrapped SWNTs.…”

Section: Resultsmentioning

confidence: 99%

“…However, the impact of sequence length and composition on the strength and conformation of binding to SWNTs have been the focus of numerous studies [28][29][30][31][32][33][34]. In particular, Tu and coworkers identified specific DNA oligonucleotide sequences known to recognize and interact uniquely with certain (n,m) SWNTs enabling their enrichment in ion exchange chromatography [35].…”

Section: Introductionmentioning

confidence: 99%

“…In particular, Tu and coworkers identified specific DNA oligonucleotide sequences known to recognize and interact uniquely with certain (n,m) SWNTs enabling their enrichment in ion exchange chromatography [35]. Follow-up studies investigated the structure and binding strength of select recognition sequences and concluded that the sequences were able to bind more tightly to their respective chirality partners than to other chiralities [31,33,34].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Salem

Landry

Bisker

et al. 2016

Carbon

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a b s t r a c tCorona phase molecular recognition (CoPhMoRe) is a phenomenon whereby a polymer or surfactant corona phase wrapped around a nanoparticle selectively recognizes a particular molecule. The method can potentially generate non-biological, synthetic molecular recognition sites, analogous to antibodies, for a broad range of biomedical applications, including new types of sensors, laboratory and clinical assays, as well as inhibitors and targeted therapeutics. In this work, we utilize near infrared fluorescent single-walled carbon nanotubes (SWNTs) wrapped with specific single stranded DNA sequences to explore the (n,m) chirality dependence of CoPhMoRe. Specific DNA oligonucleotide sequences are known to recognize and interact uniquely with certain (n,m) SWNTs enabling their enrichment in ion exchange chromatography. We explore the CoPhMoRe effect using corona phases constructed from a library of 24 such sequences, screening against a biomolecule panel that includes common neurotransmitters, amino acids, saccharides and riboflavin. Example sequences include (ATT) 4 , (TAT) 4 and (ATTT) 3 which recognize (7,5), (6,5) and (8,4) SWNTs, respectively. We find that these recognition sequences indeed form CoPhMoRe phases that are distinct among SWNT chiralities, and appear to pack more densely as to exclude analyte adsorption on the chirality they recognize. These results have encouraging implications for the controlled design of CoPhMoRe phases for biomedical applications.

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Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Salem

Landry

Bisker

et al. 2016

Carbon

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“…1 SWCNT have been used for the development of nanocomposite materials, 2 molecular detection agents, 3 molecular delivery vehicles, 4 electrochemical sensors, 5,6 optical sensors, 7–11 biologically compatible nanoconjugates, 12,13 and nanotube partitioning. 14–19 Many SWCNT applications rely on their noncovalent functionalization with physisorbed polymers, such that the sp2 hybridization of the honeycomb carbon lattice of the SWCNT surface remains intact and fluorescent. Adsorbed polymers create a molecular corona around the SWCNT, which can facilitate the incorporation of SWCNT into bulk materials, 20 make SWCNT water-soluble and biocompatible, 21 appropriate for targeted delivery into organelles, 7 or enable SWCNT-based sensing.…”

Section: Introductionmentioning

confidence: 99%

Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes

Landry

Vuković²,

Kruss

et al. 2015

J. Phys. Chem. C

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Noncovalent polymer-single walled carbon nanotube (SWCNT) conjugates have gained recent interest due to their prevalent use as electrochemical and optical sensors, SWCNT-based therapeutics, and for SWCNT separation. However, little is known about the effects of polymer-SWCNT molecular interactions on functional properties of these conjugates. In this work, we show that SWCNT complexed with related polynucleotide polymers (DNA, RNA) have dramatically different fluorescence stability. Surprisingly, we find a difference of nearly 2500-fold in fluorescence emission between the most fluorescently stable DNA-SWCNT complex, C30 DNA-SWCNT, compared to the least fluorescently stable complex, (AT)7A-(GU)7G DNA-RNA hybrid-SWCNT. We further reveal the existence of three regimes in which SWCNT fluorescence varies nonmonotonically with SWCNT concentration. We utilize molecular dynamics simulations to elucidate the conformation and atomic details of SWCNT-corona phase interactions. Our results show that variations in polynucleotide sequence or sugar backbone can lead to large changes in the conformational stability of the polymer SWCNT corona and the SWCNT optical response. Finally, we demonstrate the effect of the coronae on the response of a recently developed dopamine nanosensor, based on (GT)15 DNA- and (GU)15 RNA-SWCNT complexes. Our results clarify several features of the sequence dependence of corona phases produced by polynucleotides adsorbed to single walled carbon nanotubes, and the implications for molecular recognition in such phases.

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Oncometabolite Fingerprinting Using Fluorescent Single‐Walled Carbon Nanotubes

Amir

Hendler‐Neumark

Wulf

et al. 2021

Adv Materials Inter

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These local changes in the levels of involved metabolites or products can indicate an ongoing process of a cancerous transformation, and even further contribute to its escalation, rendering them oncometabolites. [1][2][3][4][5][6][7][8][9] D-2-hydroxyglutarate (D2HG) is a product of the gain-of-function-mutated enzymes isocitrate dehydrogenase (IDH1/ IDH2), whereas the normal mitochondrial form plays a role in the tricarboxylic acid (TCA) cycle by producing α-ketoglutarate. [1,2,[4][5][6][7][8][9] Hence, an accumulation of D2HG in the mitochondria indicates a mutagenesis of isocitrate dehydrogenase (IDH) and interruption of the TCA cycle, implying that the cell is in a state of pseudo-hypoxia (resembling a state of low oxygen levels), and mainly relying on glycolysis for energy production (Scheme 1). [4] Normally, as a minor metabolic byproduct, D2HG levels are kept low as D-2-hydroxyglutarate dehydrogenase (D2HGDH) converts it to α-ketoglutarate. [1,10] However, D2HGDH does not prevent D2HG accumulation in the case of overproduction. [10] Moreover, a congenital loss of D2HGDH causes D2HG accumulation, which can lead to a severe brain damage in a rare condition called D-2-hydroxyglutarate aciduria. [1,10] The accumulation of D2HG was shown to inhibit a group of enzymes named a-ketoglutarate-dependent dioxygenases (aKGdd), resulting in the promotion of mutagenesis by epigenetic modification of DNA and histone hypermethylation. [1,4,5,7] Notably, IDH1-mutated tumors were shown to exhibit DNA hypermethylation in gliomas and leukemia, and also histone hypermethylation. [1,[5][6][7]9,11] Accumulation of 2-hydroxyglutarate (both D and L optical isomers) was found to suppress cell-proliferation regulation. [1,9] As a demonstration of D2HG cellular potency, it was shown that incubating hematopoietic stem cells with D2HG alters differentiation patterns and promotes immune resistance. [1,6] IDH mutations and D2HG accumulation were found in gliomas and glioblastomas, and D2HG accumulation is suspected to be sufficient for promoting the development of acute myeloid leukemia (AML). [1,6] Another possible oncogenic mechanism linked to D2HG abundance, is its ability to shift cellular redox equilibrium toward overproduction of reactive oxygen species (ROS), which are well-known oncogenic agents. [4] The same mechanism was also found to impair immune antitumor activity. [1,8] The production of oncometabolites is the direct result of mutagenesis in key cellular metabolic enzymes, appearing typically in cancers such as glioma, leukemia, and glioblastoma. Once accumulated, oncometabolites promote cancerous transformations by interfering with important cellular functions. Hence, the ability to sense and quantify oncometabolites is essential for cancer research and clinical diagnosis. Here, the authors present a near-infrared optical nanosensor for a known oncometabolite, D-2-hydroxyglutarate (D2HG), discovered in a screening of a library of fluorescent single-walled carbon nanotubes (SWCNTs) functionalized with ssDNA. The screening r...

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Binding between DNA and Carbon Nanotubes Strongly Depends upon Sequence and Chirality

Cited by 48 publications

References 35 publications

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes

Oncometabolite Fingerprinting Using Fluorescent Single‐Walled Carbon Nanotubes

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