Probing Hydrogen Bonding in a DNA Triple Helix Using Protium−Deuterium Fractionation Factors

2003 ◽  
Vol 125 (22) ◽  
pp. 6626-6627 ◽  
Author(s):  
Daniel Coman ◽  
Irina M. Russu
Keyword(s):  
Hydrogen Bonding ◽  
Triple Helix ◽  
Dna Triple Helix ◽  
Fractionation Factors

scholarly journals Site-specific inhibition ofEcoRI restriction/modification enzymes by a DNA triple helix

1990 ◽  
Vol 18 (1) ◽  
pp. 157-161 ◽  
Author(s):  
Jeffery C. Hanvey ◽  
Mitsuhiro Shimizu ◽  
Robert D. Wells
Keyword(s):  
Triple Helix ◽  
Specific Inhibition ◽  
Site Specific ◽  
Dna Triple Helix ◽  
Restriction Modification

Proton Exchange and Base Pair Opening in a DNA Triple Helix†

Biochemistry ◽  
2001 ◽  
Vol 40 (37) ◽  
pp. 11065-11072 ◽  
Author(s):  
Stephen W. Powell ◽  
Lihong Jiang ◽  
Irina M. Russu
Keyword(s):  
Base Pair ◽  
Triple Helix ◽  
Proton Exchange ◽  
Dna Triple Helix ◽  
Base Pair Opening

scholarly journals Stability of an RNA•DNA–DNA triple helix depends on base triplet composition and length of the RNA third strand

2019 ◽  
Vol 47 (14) ◽  
pp. 7213-7222 ◽  
Author(s):  
Charlotte N Kunkler ◽  
Jacob P Hulewicz ◽  
Sarah C Hickman ◽  
Matthew C Wang ◽  
Phillip J McCown ◽  
...  
Keyword(s):  
Relative Stability ◽  
Triple Helix ◽  
Multiple Factors ◽  
Dna And Rna ◽  
Helix Formation ◽  
Canonical Base ◽  
Triple Helix Formation ◽  
Triple Helices ◽  
Dna Triple Helix ◽  
The Stability

AbstractRecent studies suggest noncoding RNAs interact with genomic DNA, forming an RNA•DNA–DNA triple helix that regulates gene expression. However, base triplet composition of pyrimidine motif RNA•DNA–DNA triple helices is not well understood beyond the canonical U•A–T and C•G–C base triplets. Using native gel-shift assays, the relative stability of 16 different base triplets at a single position, Z•X–Y (where Z = C, U, A, G and X–Y = A–T, G–C, T–A, C–G), in an RNA•DNA–DNA triple helix was determined. The canonical U•A–T and C•G–C base triplets were the most stable, while three non-canonical base triplets completely disrupted triple-helix formation. We further show that our RNA•DNA–DNA triple helix can tolerate up to two consecutive non-canonical A•G–C base triplets. Additionally, the RNA third strand must be at least 19 nucleotides to form an RNA•DNA–DNA triple helix but increasing the length to 27 nucleotides does not increase stability. The relative stability of 16 different base triplets in DNA•DNA–DNA and RNA•RNA–RNA triple helices was distinctly different from those in RNA•DNA–DNA triple helices, showing that base triplet stability depends on strand composition being DNA and/or RNA. Multiple factors influence the stability of triple helices, emphasizing the importance of experimentally validating formation of computationally predicted triple helices.

Symmetry and molecular structure of a DNA triple helix: d(T)n.cntdot.d(A)n.cntdot.d(T)n

Biochemistry ◽  
1993 ◽  
Vol 32 (2) ◽  
pp. 455-462 ◽  
Author(s):  
G. Raghunathan ◽  
H. Todd Miles ◽  
V. Sasisekharan
Keyword(s):  
Molecular Structure ◽  
Triple Helix ◽  
Dna Triple Helix
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