The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

Single molecule DNA experiments provide interesting data that allow a better understanding of the mechanical interactions between the strands and the nucleotides of this molecule. In some sense, these experiments complement the classical ones about DNA thermal denaturation. It is well known that the original Peyrard–Bishop (PB) model by means of a harmonic stacking potential and a nonlinear substrate potential has been able to predict the existence of a critical temperature of full denaturation of the molecule. In the present paper, driven by the findings of single molecule experiments, we substitute the original harmonic intra-strand stacking potential with a Duffing type potential. By elementary and analytical arguments, we show that with this choice it is possible to obtain a sharp transition in the classical domain wall solution of the PB model and the compactification of the classical solitary wave solutions of other models for the dynamics of DNA. We discuss why these solutions may improve our knowledge of the DNA dynamics in several directions.

Download Full-text

FURTHER STUDIES OF INFECTIOUS DNA EXTRACTED FROM MYCOBACTERIOPHAGES

Journal of Experimental Medicine ◽

10.1084/jem.123.2.327 ◽

1966 ◽

Vol 123 (2) ◽

pp. 327-340 ◽

Cited By ~ 12

Author(s):

Margret I. Sellers ◽

Tohru Tokunaga

Keyword(s):

Mycobacterium Smegmatis ◽

Base Composition ◽

Thermal Denaturation ◽

Buoyant Density ◽

Plaque Formation ◽

Double Stranded Dna ◽

Calf Thymus ◽

Phage Dna ◽

Dna Thermal Denaturation ◽

Adenine Thymine

Results of the previous investigation in which it was found that DNA extracted from D29 mycobacteriophage was infectious for Mycobacterium smegmatis 607, have been extended. DNA extracted from mycobacteriophage D4 and D32 produced plaques when plated on their respective hosts; D28 DNA, extracted in the same manner and tested under similar conditions, failed to show infectivity. Species barriers were not crossed by mycobacteriophage DNA; bacteria resistant to intact phage were not infected with the phage DNA. The efficiency of plating of the DNA is very much lower than that of intact phage; infection of a given host was not accomplished by DNA when titration for plaque formation by the intact phage was less than 109 PFU. The base composition of DNA extracted from the four mycobacteriophages and the three propagating hosts was very similar. The bases were paired, adenine with thymine and guanine with cytosine. A relatively higher per cent of guanine-cytosine than of adenine-thymine, was found. The buoyant density of each DNA in CsCl was linearly related to its guanine-cytosine content whereas with the exception of D28 DNA, thermal denaturation temperatures failed to show this relationship. However, the thermal transition profiles were characteristic of double stranded DNA. Additional evidence that D29 DNA forms complexes with basic proteins was obtained. Binding between calf thymus histone and between RNAase and D29 DNA readily occurs with a resultant loss in DNA infectivity. Trypsin and D29 DNA are only weakly reactive.

Download Full-text

Bending and Base-Stacking Interactions in Double-Stranded DNA

Physical Review Letters ◽

10.1103/physrevlett.82.4560 ◽

1999 ◽

Vol 82 (22) ◽

pp. 4560-4563 ◽

Cited By ~ 75

Author(s):

Zhou Haijun ◽

Zhang Yang ◽

Ou-Yang Zhong-can

Keyword(s):

Stacking Interactions ◽

Base Stacking ◽

Double Stranded Dna

Download Full-text

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

RSC Advances ◽

10.1039/c9ra08761c ◽

2019 ◽

Vol 9 (69) ◽

pp. 40255-40262 ◽

Cited By ~ 2

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.

Download Full-text

Thermal denaturation of fibrinogen visualized by single-molecule atomic force microscopy

Colloids and Surfaces B Biointerfaces ◽

10.1016/j.colsurfb.2018.04.037 ◽

2018 ◽

Vol 167 ◽

pp. 370-376 ◽

Cited By ~ 6

Author(s):

Nikolay A. Barinov ◽

Anna D. Protopopova ◽

Evgeniy V. Dubrovin ◽

Dmitry V. Klinov

Keyword(s):

Atomic Force Microscopy ◽

Single Molecule ◽

Thermal Denaturation ◽

Force Microscopy ◽

Atomic Force

Download Full-text

BENDING AND BASE-STACKING INTERACTIONS IN DOUBLE-STRANDED DNA

APPC 2000 ◽

10.1142/9789812811523_0107 ◽

2001 ◽

Author(s):

HAIJUN ZHOU ◽

YANG ZHANG ◽

ZHONG-CAN OU-YANG

Keyword(s):

Stacking Interactions ◽

Base Stacking ◽

Double Stranded Dna

Download Full-text

Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates

Nucleic Acids Research ◽

10.1093/nar/gkz810 ◽

2019 ◽

Vol 47 (21) ◽

pp. 11225-11237 ◽

Cited By ~ 4

Author(s):

Chaoyou Xue ◽

James M Daley ◽

Xiaoyu Xue ◽

Justin Steinfeld ◽

Youngho Kwon ◽

...

Keyword(s):

Single Molecule ◽

Molecular Mechanisms ◽

Genetic Disorder ◽

Protein A ◽

Base Pairs ◽

Single Stranded Dna ◽

Double Stranded Dna ◽

Blm Helicase ◽

Dna Replication And Repair ◽

Regulatory Effects

Abstract Bloom helicase (BLM) and its orthologs are essential for the maintenance of genome integrity. BLM defects represent the underlying cause of Bloom Syndrome, a rare genetic disorder that is marked by strong cancer predisposition. BLM deficient cells accumulate extensive chromosomal aberrations stemming from dysfunctions in homologous recombination (HR). BLM participates in several HR stages and helps dismantle potentially harmful HR intermediates. However, much remains to be learned about the molecular mechanisms of these BLM-mediated regulatory effects. Here, we use DNA curtains to directly visualize the activity of BLM helicase on single molecules of DNA. Our data show that BLM is a robust helicase capable of rapidly (∼70–80 base pairs per second) unwinding extensive tracts (∼8–10 kilobases) of double-stranded DNA (dsDNA). Importantly, we find no evidence for BLM activity on single-stranded DNA (ssDNA) that is bound by replication protein A (RPA). Likewise, our results show that BLM can neither associate with nor translocate on ssDNA that is bound by the recombinase protein RAD51. Moreover, our data reveal that the presence of RAD51 also blocks BLM translocation on dsDNA substrates. We discuss our findings within the context of potential regulator roles for BLM helicase during DNA replication and repair.

Download Full-text

Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1518028112 ◽

2015 ◽

Vol 112 (50) ◽

pp. E6852-E6861 ◽

Cited By ~ 23

Author(s):

Behzad Rad ◽

Anthony L. Forget ◽

Ronald J. Baskin ◽

Stephen C. Kowalczykowski

Keyword(s):

Single Molecule ◽

Fluorescent Sensor ◽

Holliday Junctions ◽

Dna Unwinding ◽

Recq Helicase ◽

Dna Breaks ◽

Dna Helicases ◽

Double Stranded Dna ◽

Functional Forms ◽

And Migration

DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40–60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.

Download Full-text

Direct Observation of Large Temperature Fluctuations during DNA Thermal Denaturation

Physical Review Letters ◽

10.1103/physrevlett.96.038102 ◽

2006 ◽

Vol 96 (3) ◽

Cited By ~ 12

Author(s):

K. S. Nagapriya ◽

A. K. Raychaudhuri ◽

Dipankar Chatterji

Keyword(s):

Direct Observation ◽

Thermal Denaturation ◽

Temperature Fluctuations ◽

Large Temperature ◽

Dna Thermal Denaturation

Download Full-text

Investigation of the binding modes between AIE-active molecules and dsDNA by single molecule force spectroscopy

Nanoscale ◽

10.1039/c5nr01247c ◽

2015 ◽

Vol 7 (19) ◽

pp. 8939-8945 ◽

Cited By ~ 21

Author(s):

Ying Chen ◽

Ke Ma ◽

Ting Hu ◽

Bo Jiang ◽

Bin Xu ◽

...

Keyword(s):

Single Molecule ◽

Force Spectroscopy ◽

Binding Modes ◽

Single Molecule Force Spectroscopy ◽

Aggregation Induced Emission ◽

Double Stranded Dna

The binding modes between double-stranded DNA (dsDNA) and typical AIE (aggregation-induced emission)-active molecules were investigated using AFM-based single molecule force spectroscopy.

Download Full-text