Curvature-Induced Base Pair “Slipping” Effects in DNA-Nanoparticle Hybridization

Abstract

Experiments are presented that suggest DNA strands chemically immobilized on gold nanoparticle surfaces can engage in two types of hybridization, one that involves complementary strands and normal base pairing interactions and a second one assigned as a "slipping" interaction, which can additionally stabilize the aggregate structures through non-Watson Crick type base pairing or interactions less complementary than the primary interaction. The curvature of the particles appears to be a major factor that contributes to the formation of these "slipping" interactions as evidenced by the observation that flat gold triangular nanoprism conjugates of the same sequence do not support them. Finally, these "slipping" interactions significantly stabilize nanoparticle aggregate structures, leading to large increases in T m s and effective association constants as compared with free DNA and particles that do not have the appropriate sequence to maximize their contribution. Main TextOver the past decade, polyvalent oligonucleotide-gold nanoparticle conjugates (DNA-AuNPs) have become the focus of intense research. 1-3 These structures exhibit properties that are often different from the properties of the nanoparticle and free-oligonucleotides from which they are derived, 4,5 and from their monovalent analogues. 6 They have been utilized in the development of novel materials assembly schemes, 7-12 useful and, in certain cases, commercially viable detection systems, 13-28 and intra-cellular gene regulation agents. 29-31 Despite their extensive utility, however, there remain several fundamental questions pertaining to DNA hybridization with these polyvalent structures.When two types of DNA-AuNPs, functionalized with complementary oligonucleotide sequences, are introduced in one solution, under the appropriate conditions, they will assemble into large polymeric amorphous or crystalline aggregates (Scheme 1A). 1,7,8,[32][33][34] This assembly is accompanied by a concomitant dampening and red-shifting of their surface plasmon resonance (SPR) band and a color change from red to blue. This process is reversible, and when heated, the DNA linkages holding the particles together dehybridize (melting of the DNA-AuNPs) in a highly cooperative manner resulting in a recovery of their original spectroscopic signatures and intense red color. These structures typically melt at temperatures higher than one would predict based upon the melting properties of the particle-free DNA. 1,35,36 This unique behavior has been explained, in part, by the multivalent character of the particles and their ability to engage in multiple hybridization events, which lead to enhanced stability. 36 However, the exact nature of the DNA base interactions contained within these structures *Corresponding author e-mail: E-mail: chadnano@northwestern.edu. has not been completely resolved. Herein, we describe experiments that suggest that these curved particles can engage in two types of hybridization, one that involves complementary strands and normal base pairin...

One-pot synthesis and strong near-infrared upconversion luminescence of poly(acrylic acid)-functionalized YF3:Yb3+/Er3+ nanocrystals

“…We have successfully prepared luminescent YF 3 surfactant, only large nanorice particles were obtained. These nanorice particles are very large (∼700 nm in length) and show strong red upconversion fluorescence visible to the naked eye.…”

“…The fluorescence emission spectra were obtained on a Hitachi F-4500 fluorescence spectrophotometer with a 980 nm laser diode as the excitation source. Figure 1 shows SEM images of the YF 3 Fig. 1(a)) have a high degree of uniformity with a narrow dispersion of particle size.…”

“…The PAA coating can be easily characterized by FTIR spectroscopy. Figure 3 shows the FTIR spectra of YF 3 (Fig. 3(b) Fig.…”

“…In order to investigate the luminescence under direct Er 3+ excitation, we also prepared nanocrystals doped only with Er 3+ using the same protocol employed for YF 3 :Yb 3+ /Er 3+ @PAA nanoparticles. Not only the downconversion but also the upconversion emission of the as-prepared YF 3 :Er 3+ @PAA nanoparticles was investigated.…”

“…During the past decades, magnetic nanoparticles [1,2], noble metal nanocrystals [3], quantum dots (QDs) [4][5][6][7], and other kinds of luminescent nanomaterials [8][9][10] have been successfully prepared and widely used in the biological and medical fields. Due to their novel optical properties, QDs are preferable to organic dyes for biotagging applications.…”