Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions.
The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Douglas
D
Iverson
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Crystal
C
Serrano
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Ann Marie
AM
Brahan
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.
Arik
A
Shams
Department of Chemistry, New York University, New York, NY, USA.
Filbert
F
Totsingan
Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA. Electronic address: Anthony.Bell@usm.edu.
Anthony J
AJ
Bell
D000818:Animals; D001483:Base Sequence; D044704:DNA, A-Form / Q000737:chemistry* / Q000378:metabolism*; D059371:DNA, B-Form / Q000737:chemistry* / Q000378:metabolism*; D024243:HMGB1 Protein / Q000378:metabolism*; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism*; D011485:Protein Binding; D051381:Rats
D044704:DNA, A-Form; D059371:DNA, B-Form; D024243:HMGB1 Protein; D020135:Peptide Nucleic Acids; D008274:Magnesium
A-DNA helices; B-DNA helices; Four-way junctions; High mobility group proteins (HMG); Peptide nucleic acids (PNAs)