Influence of Base Stacking and Hydrogen Bonding on the Fluorescence of 2-Aminopurine and Pyrrolocytosine in Nucleic Acids†

Biochemistry ◽  
2006 ◽  
Vol 45 (30) ◽  
pp. 9145-9155 ◽  
Author(s):  
Samantha J. O. Hardman ◽  
Katherine C. Thompson
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acids ◽  
Base Stacking

scholarly journals Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

2021 ◽  
Author(s):  
Domenico Salerno ◽  
Francesco Mantegazza ◽  
Valeria Cassina ◽  
Matteo Cristofalo ◽  
Qing Shao ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Persistence Length ◽  
Base Stacking ◽  
Base Pairs ◽  
Left Handed ◽  
Negative Supercoiling ◽  
Mechanical Dynamics ◽  
Hydrogen Bonded

ABSTRACTSingle molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded A:T base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally. In addition, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing by DNA stretched and unwound by enzymatic activity. The intramolecular nature and ease of this transition likely prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length indicating it is much more contractile and prone to sharp bends and kinks. However, left-handed DAP DNA was twice as stiff as unmodified L-DNA. Thus, significantly doubly and triply hydrogen bonded segments have very distinct mechanical dynamics at physiological levels of negative supercoiling and tension.

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.

scholarly journals Guanine base stacking in G-quadruplex nucleic acids

2012 ◽  
Vol 41 (3) ◽  
pp. 2034-2046 ◽  
Author(s):  
Christopher Jacques Lech ◽  
Brahim Heddi ◽  
Anh Tuân Phan
Keyword(s):  
Nucleic Acids ◽  
Base Stacking ◽  
G Quadruplex ◽  
Guanine Base

scholarly journals A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity

2020 ◽  
Author(s):  
Kristen Scopino ◽  
Elliot Williams ◽  
Abdelrahman Elsayed ◽  
William A. Barr ◽  
Daniel Krizanc ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Bonding ◽  
18S Rrna ◽  
Protein Translation ◽  
Base Stacking ◽  
Codon Positions ◽  
Guanidinium Group ◽  
Dynamics Simulations ◽  
A Site ◽  
Interaction Surface

ABSTRACTGCN codons are over-represented in initial codons of ORFs of prokaryote and eukaryote mRNAs. We describe a ribosome rRNA-protein surface that interacts with an mRNA GCN codon when next-in-line for the ribosome A site. The interaction surface is comprised of the edges of two stacked rRNA bases: the Watson-Crick edge of 16S/18S rRNA C1054 and adjacent Hoogsteen edge of A1196 (Escherichia coli 16S rRNA numbering). Also part of the interaction surface, the planar guanidinium group of a conserved Arginine (R146 of yeast ribosomal protein Rps3) is stacked adjacent to A1196. On its other side, the interaction surface is anchored to the ribosome A site through base stacking of C1054 with the wobble anticodon base of the A-site tRNA. Using Molecular Dynamics simulations of a 495-residue subsystem of translocating ribosomes, we observe base pairing of C1054 to nucleotide G at position 1 of the next-in-line codon, consistent with previous cryo-EM observations, and hydrogen bonding of A1196 and R146 to C at position 2. Hydrogen bonding to both of these codon positions is significantly weakened when C at position 2 is changed to G, A or U. These sequence-sensitive mRNA-ribosome interactions at the C1054-A1196-R146 (CAR) surface potentially contribute to GCN-mediated regulation of protein translation.

scholarly journals Nonpolar nucleosides alter RNA Polymerase II NTP specificity by disrupting hydrogen bonding and base stacking

2012 ◽  
Vol 26 (S1) ◽  
Author(s):  
Matthew William Kellinger ◽  
Sebastien Ulrich ◽  
Eric T Kool ◽  
Dong Wang
Keyword(s):  
Hydrogen Bonding ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Base Stacking

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.

Crystal structures and conformations of 1-α-D-xylofuranosylcytosine and its protonated form (HCl salt)

1981 ◽  
Vol 59 (2) ◽  
pp. 238-245 ◽  
Author(s):  
Michael L. Post ◽  
Carol P. Huber ◽  
George I. Birnbaum ◽  
David Shugar
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Direct Method ◽  
Intramolecular Hydrogen Bonding ◽  
Protonated Form ◽  
X Ray Diffraction ◽  
Base Stacking ◽  
Torsion Angles ◽  
Cell Parameters ◽  
Intramolecular Hydrogen

The structures of 1-α-D-xylofuranosylcytosine, C9H13N3O5 (1), and its hydrochloride salt, C9H13N3O5•HCl (1•HCl), have been determined by X-ray diffraction from diffractometer data, using direct method techniques. Both compounds crystallize in the orthorhombic system with Z = 4. Space group and cell parameters are, for 1: P21212, a = 18.706, b = 8.127, c = 7.007 Å; and for 1 HCl::P21212, a = 16.800, b = 8.045, c = 8.897 Å. Refinement by block-diagonal least-squares calculations gave a final R of 0.033 on 873 reflections and 0.034 on 914 reflections for 1 and 1 HCl, respectively. The glycosyl torsion angles are in the anti domain, χCN = −25.1° (1) and −28.6° (1•HC1), and the sugar puckers are nearly pure [Formula: see text] and 3E (1•HCl) forms. The C(4′)—C(5′) rotamer is trans–gauche in both cases. No intramolecular hydrogen bonding occurs in the xylofuranosyl rings. Lattice packing in the crystal structures occurs via intermolecular hydrogen bonding, with base stacking in pairs about one of the 2-fold axes for the neutral form, and with no base-stacking interactions for the protonated form. The biological implications of the structure and conformation of α-nucleosides are examined.

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