Long-Distance Radical Cation Migration through A/T Base Pairs in DNA:  An Experimental Test of Theory

2001 ◽  
Vol 105 (45) ◽  
pp. 11057-11059 ◽  
Author(s):  
Valerie Sartor ◽  
Edna Boone ◽  
Gary B. Schuster
Keyword(s):  
Radical Cation ◽  
Experimental Test ◽  
Base Pairs ◽  
Long Distance ◽  
Cation Migration

Long-Distance Radical Cation Migration in Z-Form DNA

2001 ◽  
Vol 123 (27) ◽  
pp. 6696-6697 ◽  
Author(s):  
Ibrahim M. Abdou ◽  
Valerie Sartor ◽  
Huachuan Cao ◽  
Gary B. Schuster
Keyword(s):  
Radical Cation ◽  
Long Distance ◽  
Cation Migration

Long-Distance Radical Cation Hopping in DNA:  The Effect of Thymine−Hg(II)−Thymine Base Pairs

2007 ◽  
Vol 9 (10) ◽  
pp. 1843-1846 ◽  
Author(s):  
Joshy Joseph ◽  
Gary B. Schuster
Keyword(s):  
Radical Cation ◽  
Base Pairs ◽  
Long Distance

scholarly journals Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae

2007 ◽  
Vol 27 (15) ◽  
pp. 5575-5586 ◽  
Author(s):  
Krista C. Dobi ◽  
Fred Winston
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Activation ◽  
Target Gene ◽  
Core Promoter ◽  
Striking Difference ◽  
Base Pairs ◽  
Long Distance ◽  
Factors Affecting ◽  
Promoter Specificity

ABSTRACT Most fundamental aspects of transcription are conserved among eukaryotes. One striking difference between yeast Saccharomyces cerevisiae and metazoans, however, is the distance over which transcriptional activation occurs. In S. cerevisiae, upstream activation sequences (UASs) are generally located within a few hundred base pairs of a target gene, while in Drosophila and mammals, enhancers are often several kilobases away. To study the potential for long-distance activation in S. cerevisiae, we constructed and analyzed reporters in which the UAS-TATA distance varied. Our results show that UASs lose the ability to activate normal transcription as the UAS-TATA distance increases. Surprisingly, transcription does initiate, but proximally to the UAS, regardless of its location. To identify factors affecting long-distance activation, we screened for mutants allowing activation of a reporter when the UAS-TATA distance is 799 bp. These screens identified four loci, SIN4, SPT2, SPT10, and HTA1-HTB1, with sin4 mutations being the strongest. Our results strongly suggest that long-distance activation in S. cerevisiae is normally limited by Sin4 and other factors and that this constraint plays a role in ensuring UAS-core promoter specificity in the compact S. cerevisiae genome.

Effect of positively charged backbone groups on radical cation migration and reaction in duplex DNA

2011 ◽  
Vol 89 (3) ◽  
pp. 326-330 ◽  
Author(s):  
Sriram Kanvah ◽  
Gary B. Schuster
Keyword(s):  
Radical Cation ◽  
Dna Analysis ◽  
Duplex Dna ◽  
Charge Migration ◽  
Electron Hole ◽  
Dna Oligomers ◽  
Phosphodiester Backbone ◽  
Cation Migration ◽  
Covalently Linked ◽  
Positively Charged

A series of DNA oligomers were prepared that contain guanidinium linkages (positively charged) positioned selectively in place of and among the normal negatively charged phosphodiester backbone groups of duplex DNA. One-electron oxidation of these DNA oligomers by UV irradiation of a covalently linked anthraquinone group generates a radical cation (electron “hole”) that migrates by hopping through the DNA and is trapped at reactive sites, GG steps, to form mutated bases that are detected by strand cleavage after subsequent piperidine treatment of the irradiated DNA. Analysis of the strand cleavage pattern reveals that guanidinium substitution in these oligomers does not measurably affect the charge migration rate but it does inhibit reaction at nearby guanines.

External electric field promotes proton transfer in the radical cation of adenine–thymine

2016 ◽  
Vol 30 (21) ◽  
pp. 1650276 ◽  
Author(s):  
Guiqing Zhang ◽  
Shijie Xie
Keyword(s):  
Electric Field ◽  
Proton Transfer ◽  
External Electric Field ◽  
Radical Cation ◽  
Base Pair ◽  
Low Temperatures ◽  
Room Temperature ◽  
Theoretical Calculations ◽  
Base Pairs ◽  
Adenine Thymine

According to [Formula: see text] measurements, it has been predicted that proton transfer would not occur in the radical cation of adenine–thymine (A:T). However, recent theoretical calculations indicate that proton transfer takes place in the base pair in water below the room temperature. We have performed simulations of proton transfer in the cation of B-DNA stack composed of 10 A:T base pairs in water from 20 K to 300 K. Proton transfer occurs below the room temperature, meanwhile it could also be observed at the room temperature under the external electric field. Another case that interests us is that proton transfer bounces back after [Formula: see text][Formula: see text]300 fs from the appearance of proton transfer at low temperatures.

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