helix twist and in base pair roll, slide and propeller twist (Figure 2.19). The extent of variation from base
to base is much less than for the corresponding DNA hexanucleotide and seems to be dominated by the
need of the structure to achieve very nearly optimal base stacking. This picture supports experimental
studies that indicate that base stacking and hydrogen bonding are equally important as determinants of
RNA helix stability.
Antisense RNAis defined as a short RNA transcript that lacks coding capacity, but has a high degree
of complementarity to another RNA, which enables the two to hybridise.^48 The consequence is that such
anti-sense, or complementary, RNA can act as a repressor of the normal function or expression of the tar-
geted RNA. Such species have been detected in prokaryotic cells with suggested functions concerning
RNA-primed replication of plasmid DNA, transcription of bacterial genes, and messenger translation in
bacteria and bacteriophages. Quite clearly, such regulation of gene expression depends on the integrity of
RNA duplexes.
A crucial cellular ‘security’machinery that also depends on double-stranded RNA is RNA interference
or RNAi(see Section 5.7.2).49–51This mechanism has evolved to protect cells from hostile genes as well
as to regulate the activity of normal genes during growth and development. Tiny RNAs that are termed
short interfering RNAs (siRNAs) or micro RNAs (miRNAs), depending on their origin, are capable of
down-regulating gene expression by binding to complementary mRNAs, resulting either in mRNA elimin-
ation or arrest of translation. Although only discovered some 13 years ago in plants, RNA interference has
now been found to be ubiquitous in all eukaryotes. The extraordinary specificity of RNAi and the sim-
plicity of administering double-stranded RNAs to organisms with fully sequenced genomes (i.e. C. ele-
gans, D. melanogasterand X. lavis) render RNAi a method of choice for functional genomics. As with
potential applications of the anti-sense strategy for therapeutic purposes, the success of RNAi as a drug
will depend on breakthroughs in cellular uptake and delivery.
2.4.3 RNADNA Duplexes
Helices that have one strand of RNA and one of DNA are very important species in biology.
They are formed when reverse transcriptase makes a DNA complement to the viral RNA.
They occur when RNA polymerase transcribes DNA into complementary messenger RNA.
They are a feature in DNA replication of the short primer sequences in Okazaki fragments (Section
6.6.4).
Anti-sense DNA is a single-stranded oligodeoxynucleotide designed to bind to a short complementary
segment of a target nucleic acid (RNA or single-stranded DNA) with the potential for regulation of
gene expression (Section 5.7.1).
Such hybrids are formed in vitroby annealing together two strands with complementary sequences, such
as poly(rA)poly(dT) and poly(rI)poly(dC). These two hetero-duplexes adopt the A-conformation common
to RNA and DNA, the former giving an 11-fold helix typical of A-RNA and the latter a 12-fold helix char-
acteristic of A-RNA.
A self-complementary decamer r(GCG)d(TATACGC) also generates a hybrid duplex with Watson–Crick
base pairs. It has a helix rotation of 330° with a step-rise of 2. 6Å and C-3-endosugar pucker typical of
A-DNA and A-RNA (see Table 2.1). The thermodynamic stability of RNADNA hybrids relative to the
corresponding DNADNA duplexes is a function of the deoxypyrimidine content in the DNA strands of
the former.^52 Hybrids with DNA strands containing 70–100% pyrimidines are more stable to thermal
de-naturation than their DNADNA counterparts, whereas those with less than 30% deoxypyrimidines are
less stable than the DNAs. A pyrimidine content of ca.50% is the ‘break-even’ point.
The greater stability in some cases of RNADNA hetero-duplexes over DNADNA homo-duplexes is the
basis of the construction of antisense DNA oligomers.53–56These are intended to enter the cell where they
can pair with, and so inactivate, complementary mRNA sequences. Additional desirable features such as
membrane permeability and resistance to enzymatic degradation have focused attention on oligonucleotides
DNA and RNA Structure 59