Biology Reference
In-Depth Information
VIRTUAL ANGLES
In the hope of reducing the complexity of the polynucleotide backbone
configuration to a two-dimensional plot, various virtual angles have been
proposed during the past 30 years. Olson and Flory (1972) proposed to
consider two virtual bonds, one from P to C
5
' and the other from C
5
' to the
other P of the repeating nucleotide unit. They were therefore able to use a
two-dimensional representation of two virtual angles for the rotations
around these two virtual bonds. Duarte and Pyle (1998) suggested a slight
variation, using two virtual bonds from P to C
4
' and from C
4
' to the other P.
Whether a two-dimensional description can substitute the real situation of a
five- or six-dimensional space is open for discussion.
FUTURE ANALYSIS
While the polynucleotide configurations are more complicated than those of
polypeptides, it is essential to analyze them in complete detail regardless of
whether multi-dimensional space will be required. Once their periodic or
secondary structures are thoroughly understood, detailed comparison with
experimental data can provide valuable information about the three-
dimensional folding of DNA and RNA. In general, due to the presence of
five single bonds with some degree of freedom to rotate for each nucleotide,
the backbone structure of DNA and RNA may be quite flexible. With the
rapid development of experimental study of tertiary structures of RNA
molecules and short DNA segments, it may soon be possible to understand
how DNA is packaged tightly inside the -phage heads, into chromosomes
which can duplicate without tangling, etc.
REFERENCES
Donohue J and Trueblood KN (1960) Base pairing in DNA.
J. Mol. Biol.,
2
, 363-371.
Duarte CM and Pyle AM (1998) Stepping through an RNA structure: A novel approach to
conformational analysis.
J. Mol. Biol
.,
284
, 1465-1478.
Hoogsteen K (1963) The crystal and molecular structure of a hydrogen-bonded complex
between 1-methylthymine and 9-methyladenine.
Acta Cryst
.,
16
, 907-916.
Marzec CJ and Day LA (1993) An exact description of five-membered ring configurations. I.
Parameterization via an amplitude S, an angle the pseudorotation amplitude q and the
phase angle P, and the bond lengths.
J. Biomol. Struct. Dyn
.,
10
, 1091-1123.
Metzler DE (1977)
Biochemistry.
Academic Press, New York, NY.
