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Technology Seminar (7 Dec 2011)


Technology Seminar

7 December 2011 (Wed)

Room 7-03, 7/F

The Hong Kong Jockey Club Building for Interdisciplinary Research
5 Sassoon Road, Pokfulam, Hong Kong


Dr. Scott Rose

Director of Molecular Genetics, Integrated DNA Technologies (IDT)

  Part 1: Genotyping with Locked Nucleic Acid (LNA) Fluorescent Probes  
  Time: 10:30 am – 11:30 am  

Oligonucleotides containing LNA modifications have enhanced melting temperatures, and are typically much shorter than a standard all DNA oligonucleotide.   An LNA base is similar to an RNA base, but the ribose ring is constrained by a methylene bridge between the 2’ and 4’ carbons.   Upon hybridization to a DNA target sequence containing a single base mismatch, these oligonucleotides show an increased destabilization (delta Tm).   This property can be exploited in qPCR based SNP assays to accurately genotype samples with exquisite sensitivity by achieving probes with differences in melting temperature between a match and mismatch sequence of 10 to 15 degrees Celsius.  Detailed analysis of the thermodynamics of the interactions of LNA containing oligonucleotides hybridized to match and mismatched DNA sequences at IDT has resulted in improved design of highly sensitive SNP assays using fluorescently labeled LNA probes.
  Tea Break: 11:30 am – 11:40 am, Refreshment to be served.  
  Part 2: Recent Advances in the Synthesis and Use of Long Oligonucleotides in Synthetic Biology  
  Time: 11:40 am – 12:40 pm  

The ability using synthetic oligonucleotides to build artificial genes was elegantly demonstrated with the cloning of the human insulin gene by Goeddel in 1979, who employed a simple anneal and ligate assembly method.  Gene synthesis methods today usually employ PCR to assemble long sequences from short 40-60 base long oligos.  This kind of enzymatic assembly works well for most sequences but usually fails when the sequence includes repeat domains or regions of low complexity. IDT has pioneered methods to synthesize extremely long oligonucleotides called UltramersTM.  Ultramer synthesis employs special, proprietary solid supports and optimized chemistry / reaction conditions that result in a coupling efficiency which averages >99.5% and permits high fidelity synthesis of 200 mers or longer.  Using proprietary ESI-LC-MS techniques, we can perform mass spectrometry QC on oligos up to 200 bases in length.  Use of these high qualities, ultra long synthetic building blocks enable assembly of difficult gene sequences containing repeats and homopolymeric runs that previously could not be made.  Additionally, UltramersTM are extremely useful for rapidly mutagenizing, or adding complex sequences to existing cloned sequences, or in the de novo assembly of libraries.

Kind Reminder: Please take off your lab coat before coming to the seminar.

Co-organized with Integrated DNA Technologies (IDT) Inc.
For enquiries, please call 2831-5500 or write to This e-mail address is being protected from spambots. You need JavaScript enabled to view it