Maochen Wei,†,‡ Jing Deng,†,‡ Kun Feng,†,‡ Boyang Yu,† and Yijun Chen*,†,‡,§
Laboratory of Chemical Biology and Jiangsu Provincial Key Laboratory of Molecular Targeted Antitumor Drug Research, China Pharmaceutical University, Nanjing, People’s Republic of China, and Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey
Polymerase chain reaction (PCR) is a basic technique with
wide applications in molecular biology. Despite the development
of different methods with various modifications,
the amplification of GC-rich DNA fragments is
frequently troublesome due to the formation of complex
secondary structure and poor denaturation. Given the fact
that GC-rich genes are closely related to transcriptional
regulation, transcriptional silencing, and disease progression,
we developed a PCR method combining a stepwise
procedure and a mixture of additives in the present work.
Our study demonstrated that the PCR method could
successfully amplify targeted DNA fragments up to 1.2
Kb with GC content as high as 83.5% from different
species. Compared to all currently available methods, our
work showed satisfactory, adaptable, fast and efficient
(SAFE) results on the amplification of GC-rich targets,
which provides a versatile and valuable tool for the
diagnosis of genetic disorders and for the study of functions
and regulations of various genes.
Most tumor-suppressor genes, housekeeping genes, and approximately
40% of tissue-specific genes in their promoter regions
contain high GC content,1 and 28% of genes in the human genome
are located in GC-rich regions.2 The GC-rich genes in these
regions are closely related to transcriptional regulation, transcriptional
silencing, and disease progression. Therefore, study of GCrich
regions is of great interest to biological and clinical investigations.
To study the function and regulation of various genes of
interest, amplification of related genes typically is an essential and
necessary step. Polymerase chain reaction (PCR) is a powerful
technique to amplify DNA fragments but needs specific adjustments
to amplify GC-rich DNA fragments (usually greater than
60%) due to complex secondary structures and poor denaturation
resulting in the formation of short and nonspecific DNA fragments
instead of the desired products.3-5
To amplify GC-rich templates, several approaches have been
attempted with different additives and PCR procedures. For
example, addition of chemical reagents, such as dimethylsulfoxide
(DMSO),6 glycerol,7 sulfoxide,8,9 betaine,10 and 7-deaza-dGTP11
and combinations of betaine and DMSO12-14 or DMSO, betaine,
and 7-deaza-dGTP,15 have shown promises to improve the amplification
of GC-rich templates to some extent. However, the
performance of these additives alone has been unsatisfactory
without further modification of the PCR procedures. On the other
hand, “Slowdown PCR”11 and “Two-Step PCR”16 exhibit superiority
in amplifying GC-rich sequences. Unfortunately, when dealing with
extremely GC-rich (greater than 80%) fragments, none of them
was able to provide adequate results. To the best of our
knowledge, the only successful example for amplifying target
DNA, which is located in the 5′ noncoding region of the Gas
subunit of heterotrimeric G protein (GNAS1) (GenBank Accession
No. M21139), with GC content of 83%, was a combination of
“Slowdown PCR” and 7-deaza-dGTP. However, this method did
not work on the amplification of the same gene longer than 250
bp.11 Thus, current PCR protocols have considerably limited the analyses of genotype and phenotype in the extremely GC-rich
regions, and there is a high demand for a new protocol to conquer
such a problem.