ANALYSIS OF THE STRUCTURE AND STABILITY OF A BACKBONE-MODIFIED OLIGONUCLEOTIDE - IMPLICATIONS FOR AVOIDING PRODUCT INHIBITION IN CATALYTIC TEMPLATE-DIRECTED SYNTHESIS
Pz. Luo et al., ANALYSIS OF THE STRUCTURE AND STABILITY OF A BACKBONE-MODIFIED OLIGONUCLEOTIDE - IMPLICATIONS FOR AVOIDING PRODUCT INHIBITION IN CATALYTIC TEMPLATE-DIRECTED SYNTHESIS, Journal of the American Chemical Society, 120(13), 1998, pp. 3019-3031
The structural and thermodynamic origins of the destabilization of a b
ackbone-modified DNA duplex 1, formed between d(CpGpT(N)TpGpC), contai
ning a single aminoethyl group (-CH2-CH2-NH2+-) in place of the phosph
odiester (-O-PO2--O-) linkage of the central TT dimer, and d(GpCpApApC
pG) are investigated. Analyses for the corresponding native duplex and
two other related structural analogues of duplex 1 have been compared
. Duplex 1 shows a cooperative thermal melting transition that is cons
istent with a two-state process. At a 2 mM concentration, the melting
temperature of duplex 1 is reduced by 17 degrees C from the native dup
lex, and this decrease in stability is further assigned to an unfavora
ble decrease in enthalpy of 7 kcal mol(-1) and a favorable increase in
entropy of 15 eu mol(-1) NMR structural analysis shows that the modif
ied duplex 1 still adopts a canonical B-DNA conformation with Watson-C
rick base pairing preserved; however, the CH2 group that replaces the
native PO2- group in the modified backbone is flexible and free to col
lapse onto a hydrophobic core formed by the base edges and sugar rings
of the flanking TT/AA nucleosides of the duplex. This conformation is
significantly different from the maximally solvent-exposed orientatio
n of the native phosphate in DNA. The entropic origin of the 15 eu mol
(-1) difference between the native and the modified duplex 1 is attrib
uted to the hydrophobic interaction between the collapsed ethylamine L
inkage with the hydrophobic core of duplex 1. This assignment is furth
er supported by a favorable comparison between the observed change in
entropy and the estimated value for the hydrophobic interaction around
the modified region. This estimated value is based on recent experime
ntal measurement of the hydrophobic interaction between aliphatic grou
ps and nucleic acids as well as ethylamine solvent transfer data. The
overall decrease in the stability of duplex 1 results from a decrease
in base stacking and hydrogen-bonding interactions between the base pa
irs. A model is, therefore, proposed to explain how the change in the
local backbone conformation could disrupt the long-range cooperativity
of DNA duplex formation upon backbone modifications. These studies pr
ovide an approach for identifying the factors that control the stabili
ty of the nucleic acid duplex structures containing backbone modificat
ions, with direct implication for designing antisense oligonucleotides
and template-directed reactions containing non-native phosphodiester
linkages.