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Related Concept Videos

Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...
Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are slanted or...
¹³C NMR: ¹H–¹³C Decoupling01:04

¹³C NMR: ¹H–¹³C Decoupling

The probability of having two carbon-13 atoms next to each other is negligible because of the low natural abundance of carbon-13. Consequently, peak splitting due to carbon-carbon spin-spin coupling is not observed in spectra. However, protons up to three sigma bonds away split the carbon signal according to the n+1 rule, resulting in complicated spectra.
A broadband decoupling technique is used to simplify these complex, sometimes overlapping, signals. Broadband decoupling relies on a...
Double Resonance Techniques: Overview01:12

Double Resonance Techniques: Overview

Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...

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Spectroscopic Super-resolution Imaging of DNA Molecules using Intrinsic Contrast
09:19

Spectroscopic Super-resolution Imaging of DNA Molecules using Intrinsic Contrast

Published on: March 6, 2026

Hybridization in ssDNA films--a multi-technique spectroscopy study.

Caitlin Howell1, Jianli Zhao, Patrick Koelsch

  • 1Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.

Physical Chemistry Chemical Physics : PCCP
|July 28, 2011
PubMed
Summary

Researchers used advanced spectroscopy to study DNA hybridization on surfaces. Densely packed DNA films showed lower hybridization, while less dense films showed more, with significant molecular orientation changes observed.

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Area of Science:

  • Surface science
  • Spectroscopy
  • Biophysics

Background:

  • Studying DNA hybridization on surfaces is crucial for biosensor development.
  • Understanding the impact of DNA film density and length on hybridization is key.
  • Characterizing molecular orientation at interfaces provides insights into binding events.

Purpose of the Study:

  • To investigate DNA hybridization on Au(111) surfaces using multiple spectroscopic techniques.
  • To correlate ssDNA film properties (density, length) with hybridization efficiency.
  • To monitor molecular orientation changes during DNA hybridization at interfaces.

Main Methods:

  • Utilized X-ray photoelectron spectroscopy (XPS), high-resolution XPS, NEXAFS, and SFG spectroscopy.
  • Employed thiolated thymine homo-oligonucleotides and thymine-adenine diblock-oligonucleotides as probe systems.
  • Analyzed ssDNA films before and after hybridization with target molecules.

Main Results:

  • Shorter, densely packed ssDNA films yielded fewer hybrids compared to longer, less dense films.
  • Diblock-oligonucleotide films showed reduced hybridization yield, potentially due to internal hybrid formation.
  • Significant orientational changes of ssDNA molecules were observed and monitored upon hybridization.

Conclusions:

  • A combination of XPS, NEXAFS, and SFG spectroscopy effectively monitors DNA hybridization and orientation at interfaces.
  • Film density and oligonucleotide structure significantly influence hybridization efficiency.
  • The study provides molecular-level insights into hybrid formation at solid-liquid interfaces.