Calculating sequence-dependent melting stability of duplex DNA oligomers and multiplex sequence analysis by graphs

2001 ◽  
pp. 165-192 ◽  
Author(s):  
Albert S Benight ◽  
Petr Pančoška ◽  
Richard Owczarzy ◽  
Peter M Vallone ◽  
Jaroslav Nešetřil ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Duplex Dna ◽  
Dna Oligomers ◽  
Sequence Dependent

Predicting sequence-dependent melting stability of short duplex DNA oligomers

Biopolymers ◽  
1997 ◽  
Vol 44 (3) ◽  
pp. 217-239 ◽  
Author(s):  
Richard Owczarzy ◽  
Peter M. Vallone ◽  
Frank J. Gallo ◽  
Teodoro M. Paner ◽  
Michael J. Lane ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Dna Oligomers ◽  
Sequence Dependent

Studies of DNA dumbbells VII: Evaluation of the next-nearest-neighbor sequence-dependent interactions in duplex DNA

Biopolymers ◽  
1999 ◽  
Vol 52 (1) ◽  
pp. 29-56 ◽  
Author(s):  
Richard Owczarzy ◽  
Peter M. Vallone ◽  
Robert F. Goldstein ◽  
Albert S. Benight
Keyword(s):  
Nearest Neighbor ◽  
Duplex Dna ◽  
Sequence Dependent

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.

scholarly journals Thermodynamic and Structural Analysis of DNA Damage Architectures Related to Replication

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Nicholas J. Amato ◽  
Christopher N. Mwai ◽  
Timothy C. Mueser ◽  
Amanda C. Bryant-Friedrich
Keyword(s):  
Dna Damage ◽  
Nucleic Acid ◽  
Strand Break ◽  
Duplex Dna ◽  
Hydrogen Atoms ◽  
Scanning Calorimetry ◽  
Dna Oligomers ◽  
Physiological Processes ◽  
Thermal Melting ◽  
The Impact

Damaged DNA, generated by the abstraction of one of five hydrogen atoms from the 2′-deoxyribose ring of the nucleic acid, can contain a variety of lesions, some of which compromise physiological processes. Recently, DNA damage, resulting from the formation of a C3′-thymidinyl radical in DNA oligomers, was found to be dependent on nucleic acid structure. Architectures relevant to DNA replication were observed to generate larger amounts of strand-break and 1-(2′-deoxy-β-D-threo-pentofuranosyl)thymidine formation than that observed for duplex DNA. To understand how this damage can affect the integrity of DNA, the impact of C3′-thymidinyl radical derived lesions on DNA stability and structure was characterized using biophysical methods. DNA architectures evaluated include duplex DNA (dsDNA), single 3′ or 5′-overhangs (OvHgs), and forks. Thermal melting analysis and differential scanning calorimetry measurements indicate that an individual 3′-OvHg is more destabilizing than a 5′-OvHg. The presence of a terminal 3′ or 5′ phosphate decreases theΔG25to the same extent, while the effect of the phosphate at the ss-dsDNA junction of OvHgs is dependent on sequence. Additionally, the effect of 1-(2′-deoxy-β-D-threo-pentofuranosyl)thymidine is found to depend on DNA architecture and proximity to the 3′ end of the damaged strand.

Sign in / Sign up

Export Citation Format

Share Document