Properties of Double-Stranded Oligonucleotides Modified with Lipophilic Substituents

Abstract

We have synthesized a series of short, self-complementary oligonucleotide sequences modified at their 5'- and/or 3'- termini with a lipophilic dodecane (C12); these systems serve as models to assess the biophysical properties of double-stranded DNA (dsDNA) equipped with potentially stabilizing lipophilic substituents. Addition of C12 to the 5'-termini of self-complementary 10 nucleotide sequences increased their duplex melting temperatures (T(m)) by approximately 4-8 degrees C over their corresponding unmodified sequences. C12 functionalities added to both the 3'- and 5'-termini increased T(m) values by approximately 10-12 degrees C. The observed increases in T(m) correlated with greater duplex stabilities as determined by the free energy values (DeltaG) derived from T(m) plots. There is a greater degree of stabilization when C12 is positioned with a C.G base pair at the termini, and the stabilizing effect of lipophilic groups far exceeds the effect seen in adding an additional base pair to both ends of DNA. Stable, short dsDNA sequences are of potential interest in the development of transcription factor decoy oligonucleotides as possible therapeutic agents and/or biological tools. These results suggest that the stability of short dsDNA sequences are improved by lipophilic substituents and can be used as the basis for the design of dsDNAs with improved biological stabilities and function under physiological conditions.

Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications

“…54 Yet, there is no definite answer as to the minimal size of the hydrophobic part that will lead to aggregation of the LON (a dodecane chain may be too short though). 55 The types of aggregates formed from LONs are somewhat different from the pattern usually observed with classical surfactants. While classical single-chain and double-chain surfactants usually give predictable aggregated structures, no such simple trend is observed with LONs ( Figure 4).…”

Amphiphilic DNA Duplex Stabilized by a Hydrophobic Zipper

“…Chemical modifications of DNA with aliphatic functional groups have varying effects on the thermodynamic stability of double‐stranded DNA (dsDNA), depending on the chemical structure and locations of the introduced aliphatic groups 5–10. Modified DNAs containing aliphatic base surrogates in a face‐to‐face arrangement can provide increased duplex stability through their interstrand hydrophobic interactions 8–11. In an attempt to introduce a hydrophobic zipper into DNA, we focused our attention on a dodecyl phosphotriester linkage as a hydrophobic region (dod‐DNA, Figure 1).…”

A 5′‐Cap for DNA Probes Binding RNA Target Strands

“…[45] In the optimization phase of our study, we chose peptidic linkers (Scheme 1b) both for their flexibility, synthetic ease, and the modest lipophilicity of the chain. Some long chain alkanes can stabilize DNA:DNA duplexes, [46] but strongly lipophilic caps or linkers can lead to hydrophobic dimerization, [47] and can complicate purification due to strong adsorption or micelle formation. Many affinity-increasing terminal substituents known from the literature are fairly lipophilic.…”