Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons

To take full advantage of locked nucleic acid (LNA) based molecular beacons (LNA-MBs) for a variety of applications including analysis of complex samples and intracellular monitoring, we have systematically synthesized a series of DNA/LNA chimeric MBs and studied the effect of DNA/LNA ratio in MBs o...

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Main Authors:	Yang, Chaoyong James, Wang, Lin, Wu, Yanrong, Kim, Youngmi, Medley, Colin D., Lin, Hui, Tan, Weihong
Format:	Online
Language:	English
Published:	Oxford University Press 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919502/

id	pubmed-1919502
recordtype	oai_dc
spelling	pubmed-19195022007-07-24 Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons Yang, Chaoyong James Wang, Lin Wu, Yanrong Kim, Youngmi Medley, Colin D. Lin, Hui Tan, Weihong Molecular Biology To take full advantage of locked nucleic acid (LNA) based molecular beacons (LNA-MBs) for a variety of applications including analysis of complex samples and intracellular monitoring, we have systematically synthesized a series of DNA/LNA chimeric MBs and studied the effect of DNA/LNA ratio in MBs on their thermodynamics, hybridization kinetics, protein binding affinity and enzymatic resistance. It was found that the LNA bases in a MB stem sequence had a significant effect on the stability of the hair-pin structure. The hybridization rates of LNA-MBs were significantly improved by lowering the DNA/LNA ratio in the probe, and most significantly, by having a shared-stem design for the LNA-MB to prevent sticky-end pairing. It was found that only MB sequences with DNA/LNA alternating bases or all LNA bases were able to resist nonspecific protein binding and DNase I digestion. Additional results showed that a sequence consisting of a DNA stretch less than three bases between LNA bases was able to block RNase H function. This study suggested that a shared-stem MB with a 4 base-pair stem and alternating DNA/LNA bases is desirable for intracellular applications as it ensures reasonable hybridization rates, reduces protein binding and resists nuclease degradation for both target and probes. These findings have implications on the design of LNA molecular probes for intracellular monitoring application, disease diagnosis and basic biological studies. Oxford University Press 2007-06 2007-06-08 /pmc/articles/PMC1919502/ /pubmed/17557813 http://dx.doi.org/10.1093/nar/gkm358 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Yang, Chaoyong James Wang, Lin Wu, Yanrong Kim, Youngmi Medley, Colin D. Lin, Hui Tan, Weihong
spellingShingle	Yang, Chaoyong James Wang, Lin Wu, Yanrong Kim, Youngmi Medley, Colin D. Lin, Hui Tan, Weihong Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
author_facet	Yang, Chaoyong James Wang, Lin Wu, Yanrong Kim, Youngmi Medley, Colin D. Lin, Hui Tan, Weihong
author_sort	Yang, Chaoyong James
title	Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
title_short	Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
title_full	Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
title_fullStr	Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
title_full_unstemmed	Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
title_sort	synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons
description	To take full advantage of locked nucleic acid (LNA) based molecular beacons (LNA-MBs) for a variety of applications including analysis of complex samples and intracellular monitoring, we have systematically synthesized a series of DNA/LNA chimeric MBs and studied the effect of DNA/LNA ratio in MBs on their thermodynamics, hybridization kinetics, protein binding affinity and enzymatic resistance. It was found that the LNA bases in a MB stem sequence had a significant effect on the stability of the hair-pin structure. The hybridization rates of LNA-MBs were significantly improved by lowering the DNA/LNA ratio in the probe, and most significantly, by having a shared-stem design for the LNA-MB to prevent sticky-end pairing. It was found that only MB sequences with DNA/LNA alternating bases or all LNA bases were able to resist nonspecific protein binding and DNase I digestion. Additional results showed that a sequence consisting of a DNA stretch less than three bases between LNA bases was able to block RNase H function. This study suggested that a shared-stem MB with a 4 base-pair stem and alternating DNA/LNA bases is desirable for intracellular applications as it ensures reasonable hybridization rates, reduces protein binding and resists nuclease degradation for both target and probes. These findings have implications on the design of LNA molecular probes for intracellular monitoring application, disease diagnosis and basic biological studies.
publisher	Oxford University Press
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919502/
_version_	1611398280215789568

Synthesis and investigation of deoxyribonucleic acid/locked nucleic acid chimeric molecular beacons

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