Base-sequence specificity of Hoechst 33258 and DAPI binding to five (A/T)4 DNA sites with kinetic evidence for more than one high-affinity Hoechst 33258-AATT complex

2002 ◽  
Vol 315 (5) ◽  
pp. 1049-1061 ◽  
Author(s):  
Sophia Y. Breusegem ◽  
Robert M. Clegg ◽  
Frank G. Loontiens
Keyword(s):  
Base Sequence ◽  
Sequence Specificity ◽  
Hoechst 33258 ◽  
High Affinity

scholarly journals AID Associates with Single-Stranded DNA with High Affinity and a Long Complex Half-Life in a Sequence-Independent Manner

2006 ◽  
Vol 27 (1) ◽  
pp. 20-30 ◽  
Author(s):  
Mani Larijani ◽  
Alexander P. Petrov ◽  
Oxana Kolenchenko ◽  
Maribel Berru ◽  
Sergey N. Krylov ◽  
...  
Keyword(s):  
Half Life ◽  
Dissociation Constants ◽  
Hot Spot ◽  
Scaffolding Protein ◽  
Sequence Specificity ◽  
Independent Manner ◽  
Single Stranded Dna ◽  
Stem Loop ◽  
High Affinity

ABSTRACT Activation-induced cytidine deaminase (AID) initiates secondary antibody diversification processes by deaminating cytidines on single-stranded DNA. AID preferentially mutates cytidines preceded by W(A/T)R(A/G) dinucleotides, a sequence specificity that is evolutionarily conserved from bony fish to humans. To uncover the biochemical mechanism of AID, we compared the catalytic and binding kinetics of AID on WRC (a hot-spot motif, where W equals A or T and R equals A or G) and non-WRC motifs. We show that although purified AID preferentially deaminates WRC over non-WRC motifs to the same degree observed in vivo, it exhibits similar binding affinities to either motif, indicating that its sequence specificity is not due to preferential binding of WRC motifs. AID preferentially deaminates bubble substrates of five to seven nucleotides rather than larger bubbles and preferentially binds to bubble-type rather than to single-stranded DNA substrates, suggesting that the natural targets of AID are either transcription bubbles or stem-loop structures. Importantly, AID displays remarkably high affinity for single-stranded DNA as indicated by the low dissociation constants and long half-life of complex dissociation that are typical of transcription factors and single-stranded DNA binding protein. These findings suggest that AID may persist on immunoglobulin and other target sequences after deamination, possibly acting as a scaffolding protein to recruit other factors.

Molecular mechanics calculations on the complexes between analogues of Hoechst 33258 and d(CGCGAAT-TCGCG)2: influence of bulky group substitution on base pair preference of DNA minor groove binders

1995 ◽  
Vol 73 (6) ◽  
pp. 878-884 ◽  
Author(s):  
Ding-Kwo Chang ◽  
Shu-Fang Cheng ◽  
Ting-Lin Chien
Keyword(s):  
Molecular Mechanics ◽  
Base Pair ◽  
Minor Groove ◽  
Sequence Specificity ◽  
Hoechst 33258 ◽  
Molecular Mechanics Calculations ◽  
Dna Minor Groove ◽  
Minor Groove Binders ◽  
Detailed Structural Analysis ◽  
Groove Binders

Molecular mechanics calculations were performed on the three structures of the complexes formed by the derivatives of Hoechst 33258 and dodecameric DNA duplex d(CGCGAATTCGCG)2. Formation and docking energies of these complexes were compared. It was found that the CG site that is 3′ to the central AATT region can be tolerated by the drugs. This is probably due to the presence of the bulky piperazine ring and, more pronouncedly, by alkylated analogues of the drug that prefer the wider minor groove formed by the GC base pair region of B-DNA. The argument of bulkiness of the piperazine moiety as the origin of enhancement of GC affinity is supported by detailed structural analysis of the intermolecular interface and widening of the DNA minor groove at the binding site. Implications of the results are discussed. Keywords: minor groove binder, docking energy, sequence specificity.

Base sequence specificity of three 2-chloroethylnitrosoureas

1990 ◽  
Vol 40 (6) ◽  
pp. 1201-1209 ◽  
Author(s):  
William T. Briscoe ◽  
Steven P. Anderson ◽  
Hubert E. May
Keyword(s):  
Base Sequence ◽  
Sequence Specificity

Acquisition of Myogenic Specificity through Replacement of One Amino Acid of MASH-1 and Introduction of an Additional alpha -Helical Turn

1999 ◽  
Vol 380 (6) ◽  
Author(s):  
C. Dezan ◽  
D. Meierhans ◽  
A.G.E. Künne ◽  
R.K. Allemann
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Sequence Specificity ◽  
High Affinity ◽  
E Box ◽  
Helical Turn

AbstractThe homologous transcription factors Myf-5, MyoD, myogenin, MRF-4, and MASH-1 bind with high affinity and modest sequence specificity to DNA containing an E-box (CANNTG). This similarity of the

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