Protein-Sized Quantum Dot Luminescence Can Distinguish between 'Straight', 'Bent', and 'Kinked' Oligonucleotides

摘要

There is increasing evidence from X-ray crystal structures, gel electrophoresis, enzyme cyclization, and electron microscopy experiments that DNA sequence can dictate overall DNA structure. In particular, double-stranded DNAs that contain 5′-A_n-3′ (where n = 3-7) phased one full double-helical twist apart appear to induce curvature in the context of a long strand (～10~2 bp) of DNA in gel mobility and enzyme cyclization experiments. The sequence 5′-d(CATGGCCATG)-3′ has been crystallized as a self-complementary duplex and shows a definite kink of 23° across the central 5′-GGCC-3′. However, packing forces and the presence of highly-charged counterions might also influence the DNA structure in the solid state. Here we describe a novel method for probing DNA structure in dilute solution: the adsorption of oligonucleotides of defined sequence to protein-sized particles. The particles are "quantum dots" of the semiconductor CdS, and we find that the surface-sensitive luminescence of these particles can discriminate between "straight", "bent", and "kinked" oligonucleotides in dilute solution.