Disorder in DNA-Linked Gold Nanoparticle Assemblies

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a nonmonotonic “zigzag” pattern in the melting temperature as a function of DNA linker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.

Figure 1

Basic building block of DNA-linked gold nanoparticle aggregates. There are no bonds between the 2 G bases in the probe DNA. Linker DNA sequences used are the following: (a) sequences of varying length and (b) sequences with the same length, but different base distribution. All linkers are named such that the number of bases from the $5^{\prime }$ end to the middle of the sequence are listed first, followed by the number of bases from the $3^{\prime }$ end to the middle.

Figure 2

Melting curves at 260 nm for gold-attached DNA assemblies formed using linkers with between 16 and 24 bases.

Figure 3

(a) Melting temperature as a function of linker sequence length for free, unattached DNA, and 10 and 20 nm gold-attached DNA. Solid line represents predicted values using empirically determined thermodynamic parameters. (b) Change in melting temperature as linker sequence length increases. Values and error bars (one standard error) for 10 nm gold-attached DNA data are taken from four separate experiments.

Figure 4

(a) Melting curves at 260 nm for aggregates formed using linkers with an equal number of bases, but a different distribution of bases among the probe duplexes. (b) Melting temperature as a function of the shortest DNA duplex created using linkers of specific length and base distribution.