Sticking and Stacking: Persistent Ordering of Fragmented DNA Analogs

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2018 Aug 11

PMID 30093389

Authors

Rudolf Podgornik

Affiliations

Soon will be listed here.

References

Mariani P, Spinozzi F, Federiconi F, Amenitsch H, Spindler L, Drevensek-Olenik I . Small angle X-ray scattering analysis of deoxyguanosine 5'-monophosphate self-assembing in solution: nucleation and growth of G-quadruplexes. J Phys Chem B. 2009; 113(22):7934-44. DOI: 10.1021/jp809734p. View

Lindsay S, Lee S, Powell J, Weidlich T, DEMARCO C, Lewen G . The origin of the A to B transition in DNA fibers and films. Biopolymers. 1988; 27(6):1015-43. DOI: 10.1002/bip.360270610. View

Minsky A . Information content and complexity in the high-order organization of DNA. Annu Rev Biophys Biomol Struct. 2004; 33:317-42. DOI: 10.1146/annurev.biophys.33.110502.133328. View

Yasar S, Podgornik R, Valle-Orero J, Johnson M, Parsegian V . Continuity of states between the cholesteric → line hexatic transition and the condensation transition in DNA solutions. Sci Rep. 2014; 4:6877. PMC: 4220286. DOI: 10.1038/srep06877. View

Smith G, Fraccia T, Todisco M, Zanchetta G, Zhu C, Hayden E . Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity. Proc Natl Acad Sci U S A. 2018; 115(33):E7658-E7664. PMC: 6099888. DOI: 10.1073/pnas.1721369115. View

Bellini T, Cerbino R, Zanchetta G . DNA-based soft phases. Top Curr Chem. 2011; 318:225-79. DOI: 10.1007/128_2011_230. View

Parsegian V, Rand R, Fuller N, Rau D . Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol. 1986; 127:400-16. DOI: 10.1016/0076-6879(86)27032-9. View

Livolant F, Levelut A, Doucet J, Benoit J . The highly concentrated liquid-crystalline phase of DNA is columnar hexagonal. Nature. 1989; 339(6227):724-6. DOI: 10.1038/339724a0. View

Fudenberg G, Mirny L . Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev. 2012; 22(2):115-24. PMC: 3697851. DOI: 10.1016/j.gde.2012.01.006. View

10.

Garces R, Podgornik R, Lorman V . Antipolar and Anticlinic Mesophase Order in Chromatin Induced by Nucleosome Polarity and Chirality Correlations. Phys Rev Lett. 2015; 114(23):238102. DOI: 10.1103/PhysRevLett.114.238102. View

11.

Zavadlav J, Podgornik R, Praprotnik M . Order and interactions in DNA arrays: Multiscale molecular dynamics simulation. Sci Rep. 2017; 7(1):4775. PMC: 5500594. DOI: 10.1038/s41598-017-05109-2. View

12.

Fraccia T, Smith G, Bethge L, Zanchetta G, Nava G, Klussmann S . Liquid Crystal Ordering and Isotropic Gelation in Solutions of Four-Base-Long DNA Oligomers. ACS Nano. 2016; 10(9):8508-16. DOI: 10.1021/acsnano.6b03622. View

13.

Leforestier A, Livolant F . Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: evidence for a discotic columnar hexagonal phase. Biophys J. 1997; 73(4):1771-6. PMC: 1181077. DOI: 10.1016/S0006-3495(97)78207-9. View

14.

Mariani P, Ciuchi F, Saturni L . Helix-specific interactions induce condensation of guanosine four-stranded helices in concentrated salt solutions. Biophys J. 1998; 74(1):430-5. PMC: 1299395. DOI: 10.1016/S0006-3495(98)77800-2. View

15.

Podgornik R, Strey H, Gawrisch K, Rau D, Rupprecht A, Parsegian V . Bond orientational order, molecular motion, and free energy of high-density DNA mesophases. Proc Natl Acad Sci U S A. 1996; 93(9):4261-6. PMC: 39523. DOI: 10.1073/pnas.93.9.4261. View

16.

Nakata M, Zanchetta G, Chapman B, Jones C, Cross J, Pindak R . End-to-end stacking and liquid crystal condensation of 6 to 20 base pair DNA duplexes. Science. 2007; 318(5854):1276-9. DOI: 10.1126/science.1143826. View