DNA Single Strands Tethered to Fused Quartz/Water Interfaces Studied by Second Harmonic Generation

Abstract

Second harmonic generation (SHG) is used to study oligonucleotides at aqueous/solid interfaces for the first time. Detailed thermodynamic state information for interfacial DNA single strands, namely, the interfacial charge density, the interfacial potential, and the change in the interfacial energy density, is obtained. The phosphate groups on the DNA backbone serve as intrinsic labels that do not require DNA modification other than surface attachment. This approach is broadly applicable for the investigation of DNA during its interaction with biological targets, as well as charged biopolymers in general, and has important implications for predicting and controlling macromolecular interactions, improving biodiagnostics, and understanding life processes.

Importance of Length and Sequence Order on Magnesium Binding to Surface-Bound Oligonucleotides Studied by Second Harmonic Generation and Atomic Force Microscopy

“…The strands were covalently attached to the silica surface via amide bond formation that occurs through the/3AmMO/-3′ modification and the N-hydroxysuccinimide linker. 27,41,42,59,60 Aqueous solutions were prepared using Millipore water and adjusted to pH 7 by the addition of dilute HCl (E.M.D., ACS grade) and dilute NaOH (Sigma-Aldrich, 99.99%). The aqueous solutions of the 0.1 M MgCl 2 stock were prepared by using MgCl 2 (H 2 O)) 6 (Sigma-Aldrich, 99.99%).…”

Interactions of biopolymers with silica surfaces: Force measurements and electronic structure calculation studies

“…Just as silica surfaces, the homopolymers attached to the slide glasses would take smaller fractional charges rather than the (+1) LYS. For example, recent second harmonic generation (SHG) studies have estimated the interfacial charge densities of organic molecules on SAM interface as low as 0.0003 C/m 2 for carboxyl-terminated SAM to 0.02 C/m 2 for 15-mer oligonucleotide SAM at around pH 7 (Konek et al, 2004;Boman et al, 2005). Thus, correction for the surface charge density on the polymeric units would produce more realistic binding energies.…”

Specific and Nonspecific Metal Ion−Nucleotide Interactions at Aqueous/Solid Interfaces Functionalized with Adenine,Thymine, Guanine, and Cytosine Oligomers

“…The lenses were then functionalized with the ssDNA using our previously established method. [1][2][3] The 21-mer DNA sequences (Integrated DNA Technologies) used in theses experiments had the following sequences: (A 15 +T 6 ): 5'-AAA AAA AAA AAA AAA TTT TTT /3AmMO/-3', (C 15 +T 6 ): 5'-CCC CCC CCC CCC CCC TTT TTT /3AmMO/-3', and (T 15 +T 6 ): 5'-TTT TTT TTT TTT TTT TTT TTT /3AmMO/-3'. The strands were covalently attached to the S2 fused silica hemisphere via their -3' end through a peptide bond between the /3AmMO/ modification and an N-hydroxysuccinimide linker, as described in our previous work.…”

“…The strands were covalently attached to the S2 fused silica hemisphere via their -3' end through a peptide bond between the /3AmMO/ modification and an N-hydroxysuccinimide linker, as described in our previous work. [1][2][3] Care was taken to ensure that the substrates were not reacted with the DNA any sooner than 15 hrs before their experimental use.…”