Helical periodicity of (PNA)2.(DNA) triplexes in strand displacement complexes.
To study the helical structure in a P-loop formed by an invasion of oligopyrimidine peptide nucleic acid (PNA) into DNA duplex, bent DNA fragments containing a homopurine.homopyrimidine sequence between two bent DNA loci were prepared. As the spacer DNA length between the two bent loci varied by 1 bp over one helical turn, the electrophoretic mobility, reflecting the overall extent of DNA bending, was modulated sinusoidally in non-denaturing 5% polyacrylamide gel. When the bent DNA fragments differing in the spacer DNA length were preincubated with an oligopyrimidine PNA, the gel mobilities were changed due to a P-loop formation. By analyzing the gel mobility data with variations of the P-loop size, average helical parameters at the P-loop structure were determined. (PNA)2. (DNA) triplex within a P-loop had the helical periodicities of 15. 6(0.2) bp per turn at 20 degrees C and 17.4(0.7) bp per turn at 10 degrees C. In addition, the results indicate that a helical unwinding by 57(7) degrees at 20 degrees C and 37(13) degrees at 10 degrees C is present at the two junctions between a P-loop and its adjacent DNA duplex.
Kim
J H
JH
Department of Biochemistry, College of Science, Yonsei University, Seoul 120-749, Korea.
Kim
K H
KH
Møllegaard
N E
NE
Nielsen
P E
PE
Koo
H S
HS
D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004587:Electrophoresis, Agar Gel; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011687:Purines / Q000737:chemistry / Q000378:metabolism; D011743:Pyrimidines / Q000737:chemistry / Q000378:metabolism; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism; D013696:Temperature
D004277:DNA, Single-Stranded; D020135:Peptide Nucleic Acids; D011687:Purines; D011743:Pyrimidines; C051802:triplex DNA; D004247:DNA; D015719:Single-Strand Specific DNA and RNA Endonucleases