Quantum dot-DNA interaction

Computational issues and preliminary insights on use of quantum dots as biosensors

S. Anandampillai, X. Zhang, P. Sharma, Gillian C. Lynch, M. A. Franchek, K. V. Larin

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

In recent years, quantum dots have generated enormous interest from the life sciences community due to their (largely) untapped potential in biomedical applications; particularly in bio-labeling and sensing. While empirical work already exists on the use of quantum dots as bio-labels, their development as biosensors requires a thorough scientific understanding of their interactions with conjugated biomolecules that together 'sense' the molecule of interest. Some recent experiments have claimed a marked variation in the luminescence of cadmium selenide quantum dots conjugated to macromolecules linked to bacteria. The origin of this large shift in luminescence of the quantum dot (and thus by implication, the band gap) appears to be poorly understood. The knowledge of the exact nature of the interaction causing the 'shift' may hold the key to designing better biosensors. The objective of the present work is to address the aforementioned interaction and to that end, we have chosen a prototypical model consisting of a capped cadmium selenide quantum dot interacting with a DNA molecule. This problem is inherently multiscale due to the relatively large number of atoms, complex nature of the interactions involved in the quantum dot-DNA system and the disparate length scales present in the problem requiring a combination of methods ranging from approaches that utilize empirical molecular mechanics force fields on one hand and ab initio electronic structure (based on density functional theory) calculations on the other hand. We discuss several modeling issues that arise in the simulations of this complex problem and present some preliminary insights. Our initial results indicate a wavelength shift of roughly 19 nm in the spectrum of a 1.1 nm sized dot upon interaction with a typical DNA molecule. However, upon increase of quantum dot size, the shift decreases and thus suggests a re-examination of singular experimental data available in the literature. Our results, which are performed in vacuum rather than a solvent, may be considered as an upper-bound to the true interaction.

Original languageEnglish (US)
Pages (from-to)3378-3385
Number of pages8
JournalComputer Methods in Applied Mechanics and Engineering
Volume197
Issue number41-42
DOIs
StatePublished - Jul 1 2008
Externally publishedYes

Fingerprint

bioinstrumentation
Biosensors
Semiconductor quantum dots
DNA
deoxyribonucleic acid
quantum dots
cadmium selenides
interactions
shift
Cadmium
Molecules
Luminescence
luminescence
molecules
Molecular mechanics
life sciences
Biomolecules
Macromolecules
macromolecules
Labeling

Keywords

  • Biomedical applications
  • DNA
  • Quantum dots

ASJC Scopus subject areas

  • Computer Science Applications
  • Computational Mechanics

Cite this

Quantum dot-DNA interaction : Computational issues and preliminary insights on use of quantum dots as biosensors. / Anandampillai, S.; Zhang, X.; Sharma, P.; Lynch, Gillian C.; Franchek, M. A.; Larin, K. V.

In: Computer Methods in Applied Mechanics and Engineering, Vol. 197, No. 41-42, 01.07.2008, p. 3378-3385.

Research output: Contribution to journalArticle

Anandampillai, S. ; Zhang, X. ; Sharma, P. ; Lynch, Gillian C. ; Franchek, M. A. ; Larin, K. V. / Quantum dot-DNA interaction : Computational issues and preliminary insights on use of quantum dots as biosensors. In: Computer Methods in Applied Mechanics and Engineering. 2008 ; Vol. 197, No. 41-42. pp. 3378-3385.
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