Optical Properties of an Immobilized DNA Monolayer from 255 to 700 nm

Abstract

The real (n) and imaginary (k) refractive indices of an immobilized monolayer of 27 nucleotide (nt) single stranded DNA (ssDNA) and the corresponding double stranded DNA (dsDNA) are measured in the 255-700 nm range. Multiple techniques are used to obtain consistent estimation. The coverage is approximately 6.5% with an average interchain distance of tethered ssDNA molecules of approximately 11.8 nm, which is significantly larger than the "footprint" of the chain on the surface. The measured increase in n by approximately 5% between the ssDNA and the dsDNA is 20% smaller than the expected change due to doubling of the molecular weight. The change in k is not significant, indicating that the electron delocalization effect expected in dsDNA due to base pair stacking is not important at optical frequencies.

Label-free DNA sequence detection using oligonucleotide functionalized optical fiber

“…Since the dsDNA is very stiff and may be modeled as a wormlike chain using merely linear elasticity of a thin, uniform rod, the 26 base pair dsDNA can be regarded as a rod with a contour length of about 9 nm. 5 If the average effect of ss-DNA and dsDNA is considered, this film thickness change is reasonable. 123.8 nmol/ ml solutions of noncomplementary ssDNA-C were used as the negative control.…”

“…This is mainly due to the change in density of the DNA monolayer. 5 In this study, the change in optical thickness is measured by a multicavity Fabry-Pérot ͑FP͒ interferometer formed by a short piece of hollow fiber sandwiched between two pieces of optical fiber, 6 as shown in Fig. 1.…”

“…This is larger than the unperturbed radius of gyration of the ssDNA chain of about 2 nm, and smaller than the end-to-end distance of about 5 nm, if a Gaussian coil of a Kuhn step length model is used for the unstretched conformation of the immobilized ssDNA. 5 This may be caused by the salt concentration. At low NaCl concentrations, the negative charges on the DNA chain tend to repel each other, stretching the DNA strands.…”

Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy

“…In fact, the lack of clear experimental data for single DNA molecules hinders the establishment of the theories. Experimental data such as optical spectra, in which a structure of one broad peak of the coupled levels is observed 26,27 , are not refined enough to determine the single-molecule electronic structure.Here, we present STS results on long homogeneous single novel poly(G)-poly(C) DNA molecules 28 deposited on gold 13 : such results enable us for the first time to resolve conductance peaks that are associated with the electronic levels of the nucleic acids. In parallel, insight into the nature of such levels is gained by ab initio DFT calculations for the very same base sequence, eventually enabled by the existence of clear experimental data.…”

“…In fact, the lack of clear experimental data for single DNA molecules hinders the establishment of the theories. Experimental data such as optical spectra, in which a structure of one broad peak of the coupled levels is observed 26,27 , are not refined enough to determine the single-molecule electronic structure.…”