scholarly journals Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation

2020 ◽  
Vol 124 (46) ◽  
pp. 10345-10352
Author(s):  
Martin Zacharias
Keyword(s):  
Base Pairing ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Base pairing and stacking contributions to double stranded DNA formation

2020 ◽  
Author(s):  
Martin Zacharias
Keyword(s):  
Base Pair ◽  
Nearest Neighbor ◽  
Base Pairing ◽  
Base Stacking ◽  
Dsdna Molecule ◽  
Double Stranded Dna ◽  
The Stability ◽  
Free Energy Contribution ◽  
Formed Hydrogen ◽  
Adenine Thymine

AbstractDouble-strand (ds)DNA formation and dissociation are of fundamental biological importance. The negatively DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base pair steps along the DNA and additional parameters due to DNA termini. In efforts to separate contributions it has been concluded that base-stacking dominates dsDNA stability whereas base-pairing contributes negligibly. Using a different model for dsDNA formation we re-analyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base pair steps that contain only guanine/cytosine, mixed steps and steps with only adenine/thymine follows the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with available stacking data and nearest-neighbor dsDNA parameters. It allows to assign a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of −0.72 kcal·mol-1 based entirely on experimental data.

scholarly journals Bending and Base-Stacking Interactions in Double-Stranded DNA

1999 ◽  
Vol 82 (22) ◽  
pp. 4560-4563 ◽  
Author(s):  
Zhou Haijun ◽  
Zhang Yang ◽  
Ou-Yang Zhong-can
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Selective recognition of human telomeric G-quadruplex with designed peptide via hydrogen bonding followed by base stacking interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40255-40262 ◽  
Author(s):  
Shikhar Tyagi ◽  
Sarika Saxena ◽  
Nikita Kundu ◽  
Taniya Sharma ◽  
Amlan Chakraborty ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Synthetic Peptide ◽  
High Selectivity ◽  
Selective Recognition ◽  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna ◽  
G Quadruplex ◽  
Guanine Base

A new synthetic peptide is presented. A Glu residue binds through H-bonding to a guanine-base and a Trp residue intercalates with K+ resulting in stabilization of a human telomeric G-quadruplex with high selectivity over a complementary c-rich strand and double-stranded DNA.

BENDING AND BASE-STACKING INTERACTIONS IN DOUBLE-STRANDED DNA

APPC 2000 ◽  
2001 ◽  
Author(s):  
HAIJUN ZHOU ◽  
YANG ZHANG ◽  
ZHONG-CAN OU-YANG
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

scholarly journals Effect of Molecular Crowding on DNA Polymerase Reactions along Unnatural DNA Templates

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4120
Author(s):  
Shuntaro Takahashi ◽  
Piet Herdwijn ◽  
Naoki Sugimoto
Keyword(s):  
Hydrogen Bonding ◽  
Bulk Solution ◽  
Molecular Crowding ◽  
Klenow Fragment ◽  
Base Pairing ◽  
Base Stacking ◽  
Dna Templates ◽  
Template Strand ◽  
Structural Improvement ◽  
Nucleotide Incorporation

Unnatural nucleic acids are promising materials to expand genetic information beyond the natural bases. During replication, substrate nucleotide incorporation should be strictly controlled for optimal base pairing with template strand bases. Base-pairing interactions occur via hydrogen bonding and base stacking, which could be perturbed by the chemical environment. Although unnatural nucleobases and sugar moieties have undergone extensive structural improvement for intended polymerization, the chemical environmental effect on the reaction is less understood. In this study, we investigated how molecular crowding could affect native DNA polymerization along various templates comprising unnatural nucleobases and sugars. Under non-crowding conditions, the preferred incorporation efficiency of pyrimidine deoxynucleotide triphosphates (dNTPs) by the Klenow fragment (KF) was generally high with low fidelity, whereas that of purine dNTPs was the opposite. However, under crowding conditions, the efficiency remained almost unchanged with varying preferences in each case. These results suggest that hydrogen bonding and base-stacking interactions could be perturbed by crowding conditions in the bulk solution and polymerase active center during transient base pairing before polymerization. This study highlights that unintended dNTP incorporation against unnatural nucleosides could be differentiated in cases of intracellular reactions.

Promotion of Single-Strand Invasion of PNA to Double-Stranded DNA by Pseudo-Complementary Base Pairing

2019 ◽  
Vol 92 (2) ◽  
pp. 330-335 ◽  
Author(s):  
Narumi Shigi ◽  
Yuki Mizuno ◽  
Hiroko Kunifuda ◽  
Kazunari Matsumura ◽  
Makoto Komiyama
Keyword(s):  
Single Strand ◽  
Base Pairing ◽  
Double Stranded Dna ◽  
Strand Invasion

Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking

2002 ◽  
Vol 24 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Stephen C. Harvey ◽  
Chunlin Wang ◽  
Stephane Teletchea ◽  
Richard Lavery
Keyword(s):  
Nucleic Acids ◽  
Molecular Mechanics ◽  
Base Pairing ◽  
Base Stacking
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