Toward an Effective Control of DNA’s Submolecular Conformation on a Surface

Abstract

DNA adopts different conformations based on its environment. We reveal conditions that either preserve the DNA’s physiological B-conformation, even upon its placement in UHV, or lead to a partial B-form to A-form reorganization upon DNA’s deposition on a surface. We use high-resolution AFM to image DNA with a well-defined number of base pairs deposited on mica. To enable the DNA’s adhesion, we either add divalent cations to the DNA solution or functionalize the surface with a silane layer. The contour length of DNA on the silane is always in perfect agreement with the B-form conformation, whereas cation-deposited DNA is always, in some cases up to 20% shorter. We varied the equilibration time, the DNA length, and sequence and compared nicked to non-nicked molecules, thus identifying several factors controlling the DNA’s length. We performed TERS measurements confirming spectroscopically that cation-deposited DNA undergoes a partial B-form to A-form conformational transition upon drying and pinpointed positions along the DNA where this transition was more probable, namely the ends of the molecules. Controlling the conformation of DNA is essential for its nanotechnology applications such as nanotemplating. Our findings could also shed a whole new light on DNA polymer physics, the mechanisms of DNA binding to surfaces, or the abundant contradictory data on DNA’s electrical behavior.

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

“…However, all these exceeded the lengths measured for the pBR322 control. We verified these differences by imaging the nucleoprotein complexes on the APTES-modified mica surface, which was due to strong charge interactions kinetically trapping the complexes and, thus, better preserving their three-dimensional configuration (38–41). When deposited on the APTES-treated surface, the morphology of the nicked DNA changed significantly.…”

Preparation of Well‐Defined DNA Samples for Reproducible Nanospectroscopic Measurements

“…TERS exploits the near‐field enhancement generated by excitation of surface plasmons at the laser‐irradiated apex of a metal or metallized SPM tip . A few research groups have applied TERS to study nucleic acids . The technique was applied to read and identify DNA bases and was proposed as a potential method to determine DNA base sequences .…”

“…The molecular structure of individual double strand breaks (DSBs) was characterized using TERS by Lipiec et al Based on spectral data, it was found that DSBs result from cleavage at the 3′ and 5′ bonds of the deoxyribose unit upon exposure to UV C radiation . TERS was also used in DNA conformation studies . The most common form of the DNA, which is present in physiological salt concentrations (neutral pH), is B‐conformation.…”

“…The third form of DNA has a strikingly different, left‐handed helical structure . TERS was already applied in order to confirm spectroscopically that cation‐deposited DNA undergoes a partial B‐ to A‐form conformational transition upon drying . Molecular spectroscopies such as Raman and infrared spectroscopy are powerful tools for studying DNA conformation .…”

Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy

“…But the molecules in 2D remain stiffer, even for lengths shorter than 3400 bp [2-5, 7, 8]. Moreover, transition from B-DNA to A-DNA during the imaging in the dry air can also cause DNA stiffer [33][34][35][36]. To avoid this structural transition, DNA molecules in fig 1 were scanned in solution and biological conditions.…”