Base Motif Recognition and Design of DNA Templates for Fluorescent Silver Clusters by Machine Learning

Abstract

Discriminative base motifs within DNA templates for fluorescent silver clusters are identified using methods that combine large experimental data sets with machine learning tools for pattern recognition. Combining the discovery of certain multibase motifs important for determining fluorescence brightness with a generative algorithm, the probability of selecting DNA templates that stabilize fluorescent silver clusters is increased by a factor of >3.

A Segregated, Partially Oxidized, and Compact Ag10 Cluster within an Encapsulating DNA Host

“…27–30 Finally, their spectra span the visible and near-infrared spectral regions and are encoded by the primary sequence and secondary structure of the DNA host. 28,29,31–33 …”

Research Update: Density functional theory investigation of the interactions of silver nanoclusters with guanine

“…30 Gwinn's group and Dickson's group have done studies especially on short singlestranded DNA. 8,9,[33][34][35][36] Yeh, Martinez, Werner, and co-workers have carried out investigations on DNA detection probes with a greater focus on guanine bases. 12,23,[37][38][39] In addition to the experimental work, theoretical investigations have also been performed on DNA-AgNCs by several groups.…”

DNA-stabilized bimetallic nanozyme and its application on colorimetric assay of biothiols

“…DNA is a superior ligand for aqueous synthesis of monodisperse metal nanoclusters/nanoparticles since nucleobases can coordinate metal cations for surface passivation and phosphate backbones are able to prevent irreversible aggregation (Copp et al 2014;Kennedy et al 2012;Ma et al 2010;Rotaru et al 2010). Selective coordination interactions between transition metal ions and DNA templates provide fundamental principles to modulate size (Fu et al 2011), morphology , photoluminescence (Copp et al 2014), surface enhanced Raman scattering (SERS) , electrical conductivity (Pearson et al 2012), as well as catalytic activity of monometallic nanomaterials (Tiwari et al 2013).…”

“…Selective coordination interactions between transition metal ions and DNA templates provide fundamental principles to modulate size (Fu et al 2011), morphology , photoluminescence (Copp et al 2014), surface enhanced Raman scattering (SERS) , electrical conductivity (Pearson et al 2012), as well as catalytic activity of monometallic nanomaterials (Tiwari et al 2013). For example, Pd 8~P d 9 clusters encapsulated in i-motif DNA were designed consisting of metallic 5 atoms as well as positively charged Pd ligated by N3 of cytosines.…”