Nearest-Neighbor Thermodynamics of Internal A·C Mismatches in DNA:  Sequence Dependence and pH Effects

Biochemistry ◽  
1998 ◽  
Vol 37 (26) ◽  
pp. 9435-9444 ◽  
Author(s):  
Hatim T. Allawi ◽  
John SantaLucia
Keyword(s):  
Dna Sequence ◽  
Nearest Neighbor ◽  
Ph Effects ◽  
Sequence Dependence

DFT study of DNA sequence dependence at the level of dinucleoside monophosphates

2011 ◽  
Vol 975 (1-3) ◽  
pp. 69-75 ◽  
Author(s):  
V.I. Poltev ◽  
V.M. Anisimov ◽  
V.I. Danilov ◽  
D. Garcia ◽  
A. Deriabina ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dft Study ◽  
Sequence Dependence ◽  
Dinucleoside Monophosphates

scholarly journals The DNA Sequence-dependence of Nucleosome Positioningin vivoandin vitro

2010 ◽  
Vol 27 (6) ◽  
pp. 713-724 ◽  
Author(s):  
Andrew Travers ◽  
Edwige Hiriart ◽  
Mark Churcher ◽  
Micaela Caserta ◽  
Ernesto Di Mauro
Keyword(s):  
Dna Sequence ◽  
Sequence Dependence

scholarly journals DNA sequence preferences of GAL4 and PPR1: how a subset of Zn2 Cys6 binuclear cluster proteins recognizes DNA.

1996 ◽  
Vol 16 (7) ◽  
pp. 3773-3780 ◽  
Author(s):  
S D Liang ◽  
R Marmorstein ◽  
S C Harrison ◽  
M Ptashne
Keyword(s):  
Crystal Structure ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Tight Binding ◽  
Recognition Sequence ◽  
Sequence Dependence ◽  
Network Of Hydrogen Bonds ◽  
Dna Binding Assay ◽  
Related Proteins

Biophysical and genetic experiments have defined how the Saccharomyces cerevisiae protein GAL4 and a subset of related proteins recognize specific DNA sequences. We assessed DNA sequence preferences of GAL4 and a related protein, PPR1, in an in vitro DNA binding assay. For GAL4, the palindromic CGG triplets at the ends of the 17-bp recognition site are essential for tight binding, whereas the identities of the internal 11 bp are much less important, results consistent with the GAL4-DNA crystal structure. Small reductions in affinity due to mutations at the center-most 5 bp are consistent with the idea that an observed constriction in the minor groove in the crystalline GAL4-DNA complex is sequence dependent. The crystal structure suggests that this sequence dependence is due to phosphate contacts mediated by arginine 51, as part of a network of hydrogen bonds. Here we show that the mutant protein GAL4(1-100)R51A fails to discriminate sites with alterations in the center of the site from the wild-type site. PPR1, a relative of GAL4, also recognizes palindromic CGG triplets at the ends of its 12-bp recognition sequence. The identities of the internal 6 bp do not influence the binding of PPR1. We also show that the PPR1 site consists of a 12-bp duplex rather than 16 bp as reported previously: the two T residues immediately 5' to the CGG sequence in each half site, although highly conserved, are not important for binding by PPR1. Thus, GAL4 and PPR1 share common CGG half sites, but they prefer DNA sequences with the palindromic CGG separated by the appropriate number of base pairs, 11 for GAL4 and 6 for PPR1.

scholarly journals Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence

2020 ◽  
Vol 48 (20) ◽  
pp. 11602-11614
Author(s):  
Youbin Mo ◽  
Nicholas Keller ◽  
Damian delToro ◽  
Neeti Ananthaswamy ◽  
Stephen C Harvey ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Motor Function ◽  
Optical Tweezers ◽  
Single Molecule ◽  
Dna Sequences ◽  
Viral Genome ◽  
Bacteriophage T4 ◽  
Repeated Measurements ◽  
Genome Packaging ◽  
Sequence Dependence

Abstract Many viruses employ ATP-powered motors during assembly to translocate DNA into procapsid shells. Previous reports raise the question if motor function is modulated by substrate DNA sequence: (i) the phage T4 motor exhibits large translocation rate fluctuations and pauses and slips; (ii) evidence suggests that the phage phi29 motor contacts DNA bases during translocation; and (iii) one theoretical model, the ‘B-A scrunchworm’, predicts that ‘A-philic’ sequences that transition more easily to A-form would alter motor function. Here, we use single-molecule optical tweezers measurements to compare translocation of phage, plasmid, and synthetic A-philic, GC rich sequences by the T4 motor. We observed no significant differences in motor velocities, even with A-philic sequences predicted to show higher translocation rate at high applied force. We also observed no significant changes in motor pausing and only modest changes in slipping. To more generally test for sequence dependence, we conducted correlation analyses across pairs of packaging events. No significant correlations in packaging rate, pausing or slipping versus sequence position were detected across repeated measurements with several different DNA sequences. These studies suggest that viral genome packaging is insensitive to DNA sequence and fluctuations in packaging motor velocity, pausing and slipping are primarily stochastic temporal events.

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