Fluorescence Measurements of Duplex DNA Oligomers under Conditions Conducive for Forming M−DNA (a Metal−DNA Complex)

2007 ◽  
Vol 111 (33) ◽  
pp. 10040-10052 ◽  
Author(s):  
Bryan Q. Spring ◽  
Robert M. Clegg
Keyword(s):  
Duplex Dna ◽  
Dna Oligomers ◽  
Fluorescence Measurements ◽  
Dna Complex

RNase H1 Can Catalyze RNA/DNA Hybrid Formation and Cleavage with Stable Hairpin or Duplex DNA Oligomers†

Biochemistry ◽  
1998 ◽  
Vol 37 (15) ◽  
pp. 5154-5161 ◽  
Author(s):  
Jing Li ◽  
Roger M. Wartell
Keyword(s):  
Duplex Dna ◽  
Dna Oligomers ◽  
Hybrid Formation

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.

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

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.

Studies on the Interaction of Dna-Ligands with Modified Parallel-Stranded Duplex-Dna Oligomers

1998 ◽  
Vol 17 (9-11) ◽  
pp. 1539-1545 ◽  
Author(s):  
I. Förtsch ◽  
E. Birch-Hirschfeld ◽  
T. M. Jovin ◽  
A. Stelzner ◽  
C. Zimmer
Keyword(s):  
Duplex Dna ◽  
Dna Oligomers

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

scholarly journals Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation

2017 ◽  
Vol 114 (21) ◽  
pp. 5443-5448 ◽  
Author(s):  
Vladimir Mekler ◽  
Leonid Minakhin ◽  
Konstantin Severinov
Keyword(s):  
Dna Sequences ◽  
Rna Binding ◽  
Proximal Region ◽  
Target Sequence ◽  
Duplex Dna ◽  
Rna Molecules ◽  
Guide Rna ◽  
Double Stranded Dna ◽  
Protospacer Adjacent Motif ◽  
Dna Complex

The prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (Cas9) endonuclease cleaves double-stranded DNA sequences specified by guide RNA molecules and flanked by a protospacer adjacent motif (PAM) and is widely used for genome editing in various organisms. The RNA-programmed Cas9 locates the target site by scanning genomic DNA. We sought to elucidate the mechanism of initial DNA interrogation steps that precede the pairing of target DNA with guide RNA. Using fluorometric and biochemical assays, we studied Cas9/guide RNA complexes with model DNA substrates that mimicked early intermediates on the pathway to the final Cas9/guide RNA–DNA complex. The results show that Cas9/guide RNA binding to PAM favors separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guide RNA. The duplex destabilization is mediated, in part, by Cas9/guide RNA affinity for unpaired segments of nontarget strand DNA close to PAM. Furthermore, our data indicate that the entry of double-stranded DNA beyond a short threshold distance from PAM into the Cas9/single-guide RNA (sgRNA) interior is hindered. We suggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proximal region during early steps of Cas9/guide RNA–DNA complex formation, thus additionally destabilizing the protospacer duplex. The mechanism that emerges from our analysis explains how the Cas9/sgRNA complex is able to locate the correct target sequence efficiently while interrogating numerous nontarget sequences associated with correct PAMs.

scholarly journals Structural Transitions Of a Helicase-Partial Duplex DNA Complex during ATP Hydrolysis Cycle

2009 ◽  
Vol 96 (3) ◽  
pp. 415a
Author(s):  
Hamza Balci ◽  
Sinan Arslan ◽  
Sua Myong ◽  
Taekjip Ha
Keyword(s):  
Atp Hydrolysis ◽  
Duplex Dna ◽  
Structural Transitions ◽  
Dna Complex

Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

2008 ◽  
Vol 6 (5) ◽  
pp. 916 ◽  
Author(s):  
Avik Ghosh ◽  
Abraham Joy ◽  
Gary B. Schuster ◽  
Thierry Douki ◽  
Jean Cadet
Keyword(s):  
Duplex Dna ◽  
Dna Oligomers
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