Due to the very large number of applications, developments in DNA-coated colloids have been increasing in different branches of science including biomedicine, spectroscopy and material science. Undoubtedly, genetic engineering appears to be very promising today not only theoretically but also experimentally, sheding light on the next generation of new nanomaterials.
Multiple features of nanotechnology are involved when programmability and self-assembly properties of DNA and plasmonic optical properties of metallic nanoparticles are considered.
Surface Enhanced Raman Spectroscopy (SERS) or Tip-enhanced Raman Spectroscopy (TERS) reveal to be ideal contenders for the copious procedures in specific DNA-sequencing or in gene detections, thanks to the high field amplification and sensitivity when light-matter interaction occurs.
The hybridization processes - programmed with single-stranded DNA - can trigger the creation of peculiar structures - in two and/or three dimensions - whose properties are controlled with extreme precision outside their biological environment.
Obtaining SERS signal of specific DNA-chains attached to different metallic nanoparticles is the first aim of this project; subsequently, the leading properties of more complex DNA-nanoparticle structures are attained. Studying the main characteristics of DNA-nanoparticle assemblies both theoretically - by means of computer simulations - and experimentally is the final purpose of this proposal.
Since the first experiments on DNA-coated colloids started in 1996 [1,2], the interest in the peculiar properties of these systems has overwhelmingly grown and is consistently developed with the use of cutting edge techniques and theoretical calculations. In spite of its biological and genetic relevance, DNA has recently been introduced as a keystone of the implementation of new nanomaterials [3].
The first innovation of the project regards the characterisation of DNA chains using Surface Enhanced Raman Spectroscopy (SERS) in both direct and label-free analysis [4]. Indeed, traditional DNA approaches, which use fluorescent reporters and complex procedures for DNA detection, suffer from high cost and loss of information about the intrinsic chemical and structural properties of DNA oligonucleotides. As an alternative to techniques which use fluorescent labelling, we are developing a direct spectroscopic characterisation, by means of SERS, aimed at detecting specific and purposely programmed single-stranded DNA attached on metallic nanoparticles (NPs). Unlike fluorescent techniques, which lack of signal reproducibility due to the photobleaching effect that fluorophores undergo, label-free strategies are likely to be a powerful procedure in DNA detection, mainly, for the reproducibility of spectroscopic signal as well as inexpensive and highly sensitive.
Nevertheless, obtaining a definite spectroscopic signature of DNA, well controlled and high-reproducible is a very challenging goal: up to now, the current scientific literature does not show a general consistency in the spectroscopy signals of this type of systems.
In addition, the complexity of metallic-NP-functionalisation protocols present in literature do not guarantee the optimum DNA loading onto NP surfaces. For this reason, we are considering to develop a new and more precise synthesis method accomplished in collaboration with a Chemistry Department Group of Sapienza University specialized in nanoparticles' fabrication.
Then, I am willing to focalize the attention on the optical properties of single nanostructures like dimers, trimers, etc, whose dimensions can be tested with Dynamic Light Scattering (DLS) experiments and whose structural conformation investigated with a new experimental apparatus has just been made in our laboratory. This employs a considerable number of applications including spectroscopy, nanobiosensors [5] and drug-delivery systems [6].
The project will be also supported by numerical simulations to provide additional understanding of the self-assembly processes of specific DNA-based structures as well as their phase behaviour and aggregation. Simulations based on accurate coarse grained potentials can indeed provide information on the collective behaviour of DNA-functionalized particles, under different
temperature and salt concentration [7] . For this part of the work, the oxDNA model, developed in Oxford recently, will be employed [8]. This model, despite it describes the sugar-phosphate group and the associated base pair as a rigid body with several interaction sites, is able to accurately reproduce the melting curves of arbitrary base sequences and their salt dependence.
In this framework, the still unknown and not totally investigated properties of DNA-colloids open a vast scenario of possible theoretical and experimental implementations as well as future developments in nanotechnology and materials science.
This is what motivates us to investigate and deepen the properties of these systems, not to mention the devotion in research and particularly in Physics.
[1] A. P. Alivisatos et al., "Organisation of `nanocrystal molecules¿ using DNA", (1996)
[2] J.J. Storhoff et al., "What controls the Optical Properties of DNA-linked gold nanoparticle Assemblies?", (1996)
[3] N. Seeman, "Nanomaterials Based on DNA", (2012)
[4] L-J. Xu et al., "Label-Free Surface-Enhanced Raman Spectroscopy Detection of DNA with Single-Base Sensitivity", (2015)
[5] M. Cottat et al., "High sensitivity, High Selectivity SERS Detection of MnSOD Using Optical Nanoantennas Functionalized with Aptamers", (2015)
[6] J. Kopecek, "Smart and genetically engineered biomaterials and drug delivery systems", (2003)
[7] M. N. O'Brien et al., "Programming Colloidal Crystal Habit with Anisotropic Nanoparticle Building Blocks and DNA Bonds",
(2016)
[8] J. P. K. Doye et al., "Coarse-graining DNA for simulations of DNA nanotechnology", (2013)