VOL. 5, No. 1/2, July 2009

Y. S. Kim, et al. [2009] Med. Hypotheses Res. 5: 1‒18.

Genetic Code is Composed of Pyrimidine-Purine DNA
Segments as a Basic Unit Displaying DNA Base Pair

Yeon Sook Kim, Dae Sung Lee, Dae Gwan Lee, Suk Keun Lee*, Sun
Jin Choi, In Sun Song, Sang Shin Lee, Young Joon Lee, Yun Woo Lee,
Sang Chul Park and Je Geun Chi

Department of Oral Pathology, College of Dentistry, Kangnung National University,
Gangneung, Korea; Department of Biochemistry, and Department of Pathology, Seoul
National University College of Medicine, Seoul, 110-799, Korea; Institute of Molecular
Genetics, Gangneung, Korea; Department of dental Hygiene, College of Health, Cheongju
University, Cheongju, Korea.

Abstract. DNA base pair hybridization composed of a pyrimidine (Py) and a purine
(Pu) shows characteristic electrostatic polarity by hydrogen bonds between Py and Pu. As
this electrostatic charge of hydrogen bond is not neutralized between hydrogen donor and
acceptor, it can induce a base pair polarity of each nucleotide, and also affect a polarity from
the 5’ to 3’ direction in each DNA strand. Although many Py and Pu sequences are arranged
in DNA duplex in a complex manner, we hypothesize that a PynPun sequence is a basic
pyrimidine-purine DNA segment (Pyu DNA segment), contrast to the PunPyn sequence (the
Puy DNA segment). A series of short DNA segments, 6-30 bp different pairs of synthesized
oligonuleotides, were analyzed by EtdBr-intercalated electrophorersis assay and reverse
phase HPLC. The annealing of primers composed of Pyu or Puy sequences were also
evaluated by the optimized PCR. Resultantly, the DNAs composed of Pyu DNA segment
were more strongly intercalated by EtdBr than those composed of Puy DNA segment. And
more, in PCR the primers composed of Pyu sequences produced more object DNA than
those composed of Puy sequences. Here, we show that the Pyu DNA segment is a basic unit
of the genetic code, which can produce more specific hybridization and more stable DNA
duplex than Puy DNA segment.

* Correspondence: Dr. Suk Keun Lee, Department of Oral Pathology, College of
Dentistry, Kangnung National University, Gangneung Korea. Tel: +82 33-640-2228. Fax: +82
33-642-6410, E-mail: