Carbon nanotubes altering specificity of repeated PCR and DNA integrity properties.

We have investigated the impact of aqueous suspension of single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) on performance of repeated PCR, and discussed their thermal impact on DNA characteristics. Both SWCNTs and MWCNTs are found significantly enhancing the specificity of the repeated PCR and capable of inhibition of long DNA thermal degradation. SWCNTs performed a better specificity in repeated PCR than MWCNTs did.

Non-degenerate graphical representation of DNA sequences and its applications to phylogenetic analysis.

In this paper, we propose a new 3-D graphical representation of a DNA sequence and prove that it has two properties: (1) there is no circuit in the graph; (2) there exists a one-to-one correspondence between a DNA sequence and the graph. These properties guarantee it has nondegeneracy. Based on the 3-D graphical representation, we characterize a DNA sequence by a 12-dimensional vector whose components are normalized ALE-indexes of the corresponding L/L matrices.

A support vector machine based method to predict success for polymerase chain reactions.

Polymerase chain reaction (PCR) is one of the most popular molecular biological techniques and has been widely applied in many areas. However, PCR still faces challenges nowadays. During recent decades, the experimental procedure of PCR, including the primer design, was always the focus of attention, while little attention was paid to the analysis of the PCR template, and still nobody can accurately predict whether or not a DNA sequence can be simply amplified using conventional Taq DNA polymerase-based PCR protocol.

Enhanced amplification of GC-rich DNA with two organic reagents.

Amplification of GC-rich DNA sequences is still a difficult task worldwide. Two frequently seen and inexpensive reagents-ethylene glycol and 1,2-propanediol-were found to be more effective than betaine in the amplification of 104 randomly selected GC-rich human DNA sequences with GC contents of 60-80% and lengths of 700-800 bp.