ABSTRACT
A number of 5'-and 3'-glycoconjugates of the oligonucleotide (5')d(TGGGAG)(3') have been synthesized, exploiting fully automated, online phosphoramidite-based solid phase strategy, as potential anti-HIV-1 agents. The thermodynamic stability of the resulting quadruplexes has been investigated by thermal denaturation studies, via a detailed CD Q1 analysis.
Subject(s)
Anti-HIV Agents/chemistry , Glycoconjugates/chemistry , HIV-1 , Oligodeoxyribonucleotides/chemistry , Anti-HIV Agents/chemical synthesis , Glycoconjugates/chemical synthesis , Guanosine/genetics , Oligodeoxyribonucleotides/chemical synthesis , Sugar Phosphates/chemistryABSTRACT
Targeting double-stranded DNA with homopyrimidine PNAs results in strand displacement complexes PNA/DNA/PNA rather than PNA/DNA/DNA triplex structures. Not much is known about the binding properties of DNA-PNA chimeras. A 16-mer 5'-DNA-3'-p-(N)PNA(C) has been investigated for its ability to hybridize a complementary duplex DNA by DSC, CD, and molecular modeling studies. The obtained results showed the formation of a triplex structure having similar, if not slightly higher, stability compared to the same all-DNA complex.
Subject(s)
Chimera , DNA/chemistry , Nucleic Acid Conformation , Peptide Nucleic Acids/chemistry , Chemical Phenomena , Chemistry, Physical , Circular Dichroism , DNA/chemical synthesis , DNA/metabolism , Hydrogen Bonding , Hydrogen-Ion Concentration , Models, Molecular , Molecular Structure , Oligodeoxyribonucleotides/chemical synthesis , Peptide Nucleic Acids/chemical synthesis , Peptide Nucleic Acids/metabolism , Pyrimidine Nucleotides/chemistry , Temperature , ThermodynamicsABSTRACT
A systematic study to evaluate the ability of 5'-DNA-3'-p-(N)-PNA-(C) chimeras to form triple helix structures has been undertaken. Preliminary results carried out on a 16-mer chimera with three PNA monomers at the 3'-end showed the formation of a stable DNA-PNA/DNA/DNA triplex, having similar conformational behaviour to a canonical DNA/DNA/DNA triplex.
Subject(s)
DNA/chemistry , Oligodeoxyribonucleotides/chemistry , Peptide Nucleic Acids/chemistry , Binding Sites , Chimera , Circular Dichroism , Nucleic Acid ConformationABSTRACT
The stability of a 16-mer DNA triple helix containing a 3-N(ferrocenemethyl)-thymidine residue in the third strand has been investigated in comparison with the unmodified triplex of the same sequence. A complete physico-chemical characterization of the two triple helices on changing the pH by means of calorimetry, circular dichroism and molecular modeling is therefore reported. The thermodynamic parameters were obtained in the pH range 5.5-7.2 by differential scanning calorimetry (DSC). For both triplexes the T(m) and Delta H degrees (T(m)) values increase on decreasing the pH. In the pH range 7.2-6.0 the triplex containing the ferrocenemethyl nucleoside is less stable than the unmodified one, whereas the modified triplex becomes more stable at pH 5.5. Such difference in stability at each pH value is overwhelmingly enthalpic in origin. CD spectra show conformational changes on decreasing the pH for both the triplexes. By spectroscopic pH titration the apparent pK(a) values of the cytosines in the two triplexes could be estimated, with the cytosines in the TFO containing the ferrocenemethyl residue having lower apparent pK(a) values. These results are consistent with the calorimetric data, showing a decrease of the thermodynamic parameters in the pH range 7.2-6.0 and an increase at pH 5.5 for the ferrocenylated triplex with respect to the unmodified one. The thermodynamic and spectroscopic data are also discussed in relation to molecular models.
