CA runs increase DNA flexibility in the complex of lambda Cro protein with the OR3 site.
The alternating pyrimidine-purine elements CA, CAC, and CACA are anisotropically flexible, as deduced from gel circularization assays on point mutations and single-base mismatches in the OR3 site of lambda phage alone and in the specific complex with the Cro protein. These sequences evidently promote DNA bending in the specific binding region of the complex and may also facilitate overwinding in the central nonbinding region. Effects for CACA are exceptionally large and suggest that an alternative DNA structure may occur in this element.
Lyubchenko
Y L
YL
Department of Biochemistry, University of Nevada-Reno 89557.
Shlyakhtenko
L S
LS
Appella
E
E
Harrington
R E
RE
D000225:Adenine; D010582:Bacteriophage lambda / Q000378:metabolism*; D001483:Base Sequence; D002942:Circular Dichroism; D003596:Cytosine; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D012097:Repressor Proteins / Q000378:metabolism*; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000378:metabolism; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004279:DNA, Viral; D004268:DNA-Binding Proteins; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins; D014157:Transcription Factors; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D003596:Cytosine; D000225:Adenine