Investigating the secondary structures for long oligonucleotides using attenuated-total-reflection surface-enhanced Raman spectroscopy

K. C. Chiu*, J. N. Yih, L. Y. Yu, Shean-Jen Chen

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

This study utilizes a surface-enhanced Raman spectroscopy (SERS) based on the attenuated-total-reflection method to investigate the secondary structures of long oligonucleotides and their influence on the DNA hybridization. It is found that the ring-breathing modes of adenine, thyrnine, guanine, and cytosine in Raman fingerprint associated with three 60mer oligonucleotides with prominent secondary structures are lower than those observed for the two oligonucleotides with no obvious secondary structures. It is also determined that increasing the DNA hybridization temperature from 35 °C to 45°C reduces secondary structure effects. The kinetics of biomolecular interaction analysis can be performed by using surface plasmons resonance biosensor, but the structural information of the oligonucleotides can not observed directly. The SERS spectrum provides the structural information of the oligonucleotides with the help of a silver colloidal nanoparticle monolayer by control of the size and distribution of the nanoparticles adapted as a Raman active substrate. Also, the detection limit of the DNA Raman signal has been successfully improved to reach sub-micro molarity of DNA concentration.

Original languageEnglish
Title of host publicationPlasmonics
Subtitle of host publicationMetallic Nanostructures and their Optical Properties IV
DOIs
StatePublished - 30 Nov 2006
EventPlasmonics: Metallic Nanostructures and their Optical Properties IV - San Diego, CA, United States
Duration: 13 Aug 200616 Aug 2006

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
Volume6323
ISSN (Print)0277-786X

Conference

ConferencePlasmonics: Metallic Nanostructures and their Optical Properties IV
CountryUnited States
CitySan Diego, CA
Period13/08/0616/08/06

Keywords

  • DNA secondary structure
  • Metal nanoparticles
  • Structural change
  • Surface plasmons
  • Surface-enhanced Raman scattering

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