Molecular-Basis of Single-Walled Carbon Nanotube Recognition by Single-Stranded DNA
Abstract
Hybrids of biological molecules and single-walled carbon nanotubes (SWCNT) have proven useful for SWCNT sorting and are enabling several biomedical applications in sensing, imaging, and drug delivery. In the DNA-SWCNT system, certain short (10-20mer) sequences of single-stranded DNA recognize specific SWCNT, allowing the latter to be sorted from a chirality diverse mixture. (1) However, little is known about the DNA secondary structures that underlie their recognition of SWCNTs. Using replica exchange molecular dynamics (REMD) of multiple strands on a single SWCNT, we report that DNA forms ordered structures on SWCNTs that are strongly DNA sequence and SWCNT dependent. DNA sequence (TAT)(4) on its recognition partner, the (6,5) SWCNT, (1) forms an ordered right-handed helically wrapped barrel, stabilized by intrastrand, self-stitching hydrogen bonds and interstrand hydrogen bonding. The same sequence on the larger diameter (8,7)-SWCNT forms a different and less-stable structure, demonstrating SWCNT selectivity. In contrast, homopolymer (T)(12), with weaker tendency for intrastrand hydrogen bonding, forms a distinctly left-handed wrap on the (6,5)-SWCNT, demonstrating DNA sequence specificity. Experimental measurements show that (TAT)(4) selectively disperses smaller diameter SWCNTs more efficiently than (T)(12), establishing a relationship between recognition motifs and binding strength. The developing understanding of DNA secondary structure on nanomaterials can shed light on a number of issues involving hybrids of nanomaterials and biological molecules, including nanomedicine, health-effects of nanomaterials, and nanomaterial processing.
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Non-covalent encapsulation of SWCNTs with polymers, including short oligonucleotides, facilitates aqueous suspension and confers molecular selectivity to their optical responses via a molecular masking effect and modulation of optical bandgaps.
“Non-covalent encapsulation with polymers, including short oligonucleotides, facilitates aqueous suspension and confers molecular selectivity to their optical responses via (1) contributing to a molecular masking effect that defines the shape and size of the exposed surface of SWCNTs26-28 and (2) modulating their optical bandgaps29.”
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Self-citation
- Authors
- Roxbury, D., Mittal, J., & Jagota, A.
- Affiliations
- Lehigh University (US)
- Corresponding author
- Mittal, Jeetain
- Jagota, Anand
- Venue
- Nano Letters
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-03-06
- Volume
- 12
- Issue
- 3
- Pages
- 1464-1469
- ISSN
- 1530-6984 (ISSN-L)
- 1530-6992
- OpenAlex
- W2316648814
- Cited by
- 137
- References
- 28
- Citations by year
- 2026: 12 · 2025: 5 · 2024: 5 · 2023: 10 · 2022: 13 · 2021: 2 · 2020: 12 · 2019: 9 · 2018: 6 · 2017: 12 · 2016: 13 · 2015: 10 · 2014: 8 · 2013: 12 · 2012: 8
- FWCI
- 4.88
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nano Letters (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Materials Science › Materials Chemistry › Carbon Nanotubes in Composites
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- single-walled carbon nanotubes, single-stranded DNA, DNA secondary structure, DNA sequence specificity, hydrogen bonding, DNA sequence motifs
- MeSH terms
- Base Sequence, Binding Sites, DNA, Molecular Sequence Data, Molecular Probe Techniques, Nanotubes, Carbon
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