2-Aminopurine/cytosine base pair containing oligonucleotides: fluorescence spectroscopy studies on DNA-polyamide binding.
Studies on the binding of a triamide f-IPI (1) to its cognate sequence labeled with a 2-aminopurine (2AP or G( *)) group are described. ITC studies showed that f-IPI (1) bound to the cognate site (ACG( *)CGT) with only 3.5-fold lower affinity than binding to the unlabeled DNA (ACGCGT) (K(eq)=2 x 10(7) and 7 x 10(7)M(-1), respectively). Titration of f-IPI (1) to both sequences gave strong induced bands at 330 nm via circular dichroism studies. The compound also gave comparable DeltaT(m) values of 5.0 and 7.8 degrees C, respectively. These techniques also proved that the sequence selectivity of f-IPI (1) was uncompromised, as only limited binding to the non-cognate sequence ACCG( *)GT was observed. Fluorescence studies demonstrated a 2:1 ligand:DNA binding motif as anticipated, and indicated that the limit of detection for this technique was 20muM DNA concentration. The results demonstrate that 2-aminopurine is a sufficient substitute for guanine in a G.C base pair useful in DNA binding studies.
Sielaff
Alan
A
Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, MI 49423, USA.
Mackay
Hilary
H
Brown
Toni
T
Lee
Moses
M
D015075:2-Aminopurine / Q000737:chemistry*; D020029:Base Pairing; D001665:Binding Sites; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D009757:Nylons / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
D009757:Nylons; D009841:Oligonucleotides; D015075:2-Aminopurine; D003596:Cytosine; D004247:DNA