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

Landry, Markita P.; Vuković, Lela; Kruss, Sebastian; Bisker, Gili; Landry, Alexandra M.; Islam, Shahrin; Jain, Rishabh; Schulten, Klaus; Strano, Michael S.

doi:10.1021/jp511448e

Cited by 84 publications

(88 citation statements)

References 58 publications

(127 reference statements)

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“…Recently, Landry et al reported that RNA-wrapped SWNTs slowly equilibrated upon dilution in PBS, as manifested by a gradual fluorescence modulation over several hours [36], whereas DNA wrappings showed a much more stable fluorescence signal after dilution. Although 23 of the 24 sequences used in this study were DNA, many sequences were much shorter than the 30-mer oligonucleotides used in the previous work and may not bind as tightly.…”

Section: Resultsmentioning

confidence: 99%

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: Resultsmentioning

confidence: 99%

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

Salem

Landry

Bisker

et al. 2016

Carbon

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“…Single walled carbon nanotubes dispersion can be assisted by surfactants like sodium dodecyl sulfate (SDS) or sodium cholate (SC) [38], DNA or RNA [39,40] or other amphiphilic copolymers [27]. Tsai and co-workers, for example, immobilized glucose oxidase (GOx) onto SWCNTs and determined that the enzyme retained 75% of its activity upon adsorption.…”

Section: Non-covalent Immobilizationmentioning

confidence: 99%

“…However, there is lack of, and need for, a systematic and predictable understanding of the parameters that determine protein-SWCNT fates in their interactions with biological systems. Advances in experimental and theoretical tools to study SWCNTbiomolecule conjugate systems at the molecular scale [37,40,87] have emerged, but many remain to be extended for molecularscale SWCNT-protein studies. The risk of CNPs triggering an immune response should be also considered, since the protein components of the complement system can bind to carbon nanotubes.…”

Section: Toxicity Of Delivered Swcnt-protein Conjugatesmentioning

confidence: 99%

Protein functionalized carbon nanomaterials for biomedical applications

Oliveira

Bisker

Bakh

et al. 2015

Carbon

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188

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a b s t r a c tSince the discovery of low-dimensional carbon allotropes, there is increasing interest in using carbon nanomaterials for biomedical applications. Carbon nanomaterials have been utilized in the biomedical field for bioimaging, chemical sensing, targeting, delivery, therapeutics, catalysis, and energy harvesting. Each application requires tailored surface functionalization in order to take advantage of a desired property of the nanoparticles. Herein, we review the surface immobilization of bio-molecules, including proteins, peptides, and enzymes, and present the recent advances in synthesis and applications of these conjugates. The carbon scaffold and the biological moiety form a complex interface which presents a challenge for achieving efficient and robust binding while preserving biological activity. Moreover, some applications require the utilization of the protein-nanocarbon system in a complex environment that may hinder its performance or activity. We analyze different strategies to overcome these challenges when using carbon nanomaterials as protein carriers, explore various immobilization techniques along with characterization methods, and present recent demonstrations of employing these systems for biomedical applications. Finally, we consider the challenges and future directions of this field.

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“…59 Landry and co-workers have extended this platform to study ribonucleic acid (RNA) contributions to fluorescence response. 72 Recent experimental measurements suggest that the differences in (GU) 15 -RNA and (GT) 15 -DNA conformations have a significant impact on fluorescence response. A comparison of both polymers shows that the (GU) 15 -RNA has a lower conformational stability on the SWCNT than the corresponding DNA-based complex.…”

Section: Engineering Sensor Selectivity Of Nir Fluorescence Sensors Bmentioning

confidence: 99%

Review—Engineering the Selectivity of the DNA-SWCNT Sensor

Kupis-Rozmysłowicz¹,

Antonucci²,

Boghossian³

2016

ECS J. Solid State Sci. Technol.

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Single-walled carbon nanotubes (SWCNTs) demonstrate a unique combination of optical, chemical, and physical properties that render them suitable for a variety of sensing applications. Their photostable near-infrared (nIR) fluorescence emissions are highly sensitive to perturbations in the surrounding SWCNT environment, enabling optical sensors with single-molecule detection limits. Despite these immanent advantages, SWCNTs lack the inherent molecular recognition capabilities required for selective sensing applications. One approach to tuning sensor selectivity is to engineer synthetic and biological wrappings that cover the nanotube's surface in a manner that limits chemical access to the surface to specific target analytes. Among the numerous possible wrappings, deoxyribonucleic acid (DNA) has emerged as the most studied polymeric wrapping. In addition to the sequence-dependent tunability DNA offers in engineering selectivity, DNA assumes a peculiar helical wrapping conformation along the SWCNT surface that has been the focus of many experimental and computational studies. In this review, we summarize some of the major findings in the field, focusing on the underlying molecular interactions responsible for the conformational and molecular recognition elements of the wrapping. Special focus is given to characterizing the nucleotide binding affinity, DNA sequence dependency, DNA length variation, SWCNT chirality, and sugar backbone (RNA vs. DNA) contributions to the wrapping conformation and SWCNT fluorescence. This article concludes with an assessment of the latest DNA-SWCNT-based sensing platforms used for the selective, single-and multi-modal detection of target analytes. Since their introduction in the early 60s, 1 biosensors have become an indispensable part of our daily lives, finding disparate applications in a variety of analytical fields ranging from biomedical diagnostics to environmental monitoring to food technology.2 Notably, optical biosensors based on fluorescent-light emission, which exploit diverse fluorescent probes as labeling agents for the recognition units, have emerged as highly sensitive, rapid, reproducible, and simple-to-operate analytical tools capable of quantitatively monitoring specific molecular interactions in real time.3,4 However, several drawbacks limit their application in more complex chemical and biological environments. For example, typical fluorescence-based sensors conventionally employ organic fluorophores that emit fluorescence with visible wavelengths that do not penetrate well through biological tissue.5 Furthermore, such fluorophores are often subject to rapid photobleaching, thus compromising their sensor lifetimes. These limitations are unfavorable for long-term in vivo sensing 6 for diagnostic applications. Recent research is thus focused on finding new technologies and materials to engineer novel sensing platforms with increased sensitivity and selectivity over extended periods of time.Single-walled carbon nanotubes (SWCNTs) have become widely used in a new genera...

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

Cited by 84 publications

References 58 publications

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

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

Protein functionalized carbon nanomaterials for biomedical applications

Review—Engineering the Selectivity of the DNA-SWCNT Sensor

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