TITLE

Enhanced recognition of non-complementary hybridization by single-LNA-modified oligonucleotide probes

AUTHOR(S)
XianYu Piao; Ying Yan; Jing Yan; YiFu Guan
PUB. DATE
July 2009
SOURCE
Analytical & Bioanalytical Chemistry;Jul2009, Vol. 394 Issue 6, p1637
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Locked nucleic acid (LNA) is a deoxyribonucleotide analogue with an unusual ‘locked’ furanose conformation. LNA-modified oligonucleotide probes have demonstrated an enhanced binding affinity towards their complementary strands; however, their potential to discriminate non-complementary hybridization of mismatches has not been explored. In this study, we investigated the effect of the chemical nature of LNA nucleobases on the hybridization stability and the capability of LNA-modified oligonucleotides to discriminate the LNA:DNA mismatched base pairs. It was observed that LNA modification indeed improves the discrimination capability of oligonucleotides by increasing the melting temperature differences between the complementary duplexes and hybrids containing mismatches. Particularly, LNA purines offer a greater potential to recognize the mismatches than LNA pyrimidines and DNA purines. Real-time PCR experiments further confirmed that LNA modifications at the 3′-end are more effective. The results and conclusions in this study provide useful information for hybridization-based nucleic acid analysis where designing sound oligonucleotide probes is crucial to the success of the analyses. [Figure not available: see fulltext.]
ACCESSION #
42211586

 

Related Articles

  • Enzymatic synthesis of DNA strands containing α-L-LNA (α-L-configured locked nucleic acid) thymine nucleotides. Højland, Torben; Veedu, Rakesh N.; Vester, Birte; Wengel, Jesper // Artificial DNA;Jan2012, Vol. 3 Issue 1, p14 

    We describe the first enzymatic incorporation of an α-L-LNA nucleotide into an oligonucleotide. It was found that the 5'-triphosphate of α-L-LNA is a substrate for the DNA polymerases KOD, 9°Nm, Phusion and HIV RT. Three dispersed α-L- LNA thymine nucleotides can be incorporated into...

  • Microarrays for Pathogen Detection and Analysis. McLoughlin, Kevin S. // Briefings in Functional Genomics;Nov2011, Vol. 10 Issue 6, p342 

    DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples. These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies...

  • Generalized DNA Barcode Design Based on Hamming Codes. Bystrykh, Leonid V. // PLoS ONE;May2012, Vol. 7 Issue 5, p1 

    The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the...

  • Mathematical tools to optimize the design of oligonucleotide probes and primers. Noguera, Daniel; Wright, Erik; Camejo, Pamela; Yilmaz, L. // Applied Microbiology & Biotechnology;Dec2014, Vol. 98 Issue 23, p9595 

    The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or 'oligos' for short) shares many of the same...

  • Preparation of nanocones for immobilizing DNA probe by a low-temperature plasma plume. Guangliang Chen; Wenjun Zhao; Shihua Chen; Mingyan Zhou; Wenran Feng; Weichao Gu; Si-ze Yang // Applied Physics Letters;9/18/2006, Vol. 89 Issue 12, p121501 

    Using allylamine monomer, a matrix of nanocones was fabricated by applying a low-temperature plasma plume without any catalysts and template. This nanocone acted as an adhesion layer immobilizing DNA probe for DNA hybridization assay. A simple conceptual model to describe the growth of the...

  • DNA barcode ITS2 coupled with high resolution melting (HRM) analysis for taxonomic identification of Sideritis species growing in Greece. Kalivas, Apostolos; Ganopoulos, Ioannis; Xanthopoulou, Aliki; Chatzopoulou, Paschalina; Tsaftaris, Athanasios; Madesis, Panagiotis // Molecular Biology Reports;Aug2014, Vol. 41 Issue 8, p5147 

    Identification of genotypes in Sideritis is complicated owing to the morphological similarity and common occurrence of natural hybridisation within Sideritis species. Species- and genotype-specific DNA markers are very useful for plant identification, breeding and preservation programs. Herein,...

  • Detection of Non-Amplified Mycobacterium tuberculosis Genomic DNA Using Piezoelectric DNA-Based Biosensors. Kaewphinit, Thongchai; Santiwatanakul, Somchai; Promptmas, Chamras; Chansiri, Kosum // Sensors (14248220);2010, Vol. 10 Issue 3, p1846 

    Piezoelectric DNA-based biosensor technology was developed as a new method for detection of M. tuberculosis. This method consists of immobilizing a thiol-modified oligonucleotide probe on the gold electrode surface of a quartz crystal, using a self-assembled monolayer method. The advantage of...

  • Polymerase-Endonuclease Amplification Reaction (PEAR) for Large-Scale Enzymatic Production of Antisense Oligonucleotides. Xiaolong Wang; Deming Gou; Shuang-yong Xu // PLoS ONE;2010, Vol. 5 Issue 1, p1 

    Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain...

  • Interaction of Replication Protein A and Flap Endonuclease 1 with DNA Duplexes Containing a Nick or a Flap. Khlimankov, D. Yu.; Rechkunova, N. I.; Khodyreva, S. N.; Petruseva, I. O.; Nazarkina, Zh. K.; Belousova, E. A.; Lavrik, O. I. // Molecular Biology;Nov2002, Vol. 36 Issue 6, p849 

    Nicks and flaps are intermediates in various processes of DNA metabolism, including replication and repair. Photoaffinity modification was employed in studying the interaction of the replication protein A (RPA) and flap endonuclease 1 (FEN-1) with DNA duplexes similar to structures arising...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics