Crystallization and self-assembly of shape-complementary sequence-defined peptoids

2021 ◽  
Author(s):  
Sunting Xuan ◽  
Xi Jiang ◽  
Nitash P. Balsara ◽  
Ronald N. Zuckermann
Keyword(s):  
Protein Binding ◽  
Self Assembly ◽  
Biological Systems ◽  
Base Pairing ◽  
Complementary Sequence ◽  
Binding Interactions ◽  
Crystal Lattices ◽  
Shape Complementarity ◽  
Dna Base

Shape complementarity between polymers is a hallmark of biological systems (e.g. DNA base pairing and protein binding interactions). Here we explore the role of shape complementarity between sequence-defined N-alkyl peptoids in crystal lattices.

scholarly journals Yeast Mre11 and Rad1 Proteins Define a Ku-Independent Mechanism To Repair Double-Strand Breaks Lacking Overlapping End Sequences

2003 ◽  
Vol 23 (23) ◽  
pp. 8820-8828 ◽  
Author(s):  
Jia-Lin Ma ◽  
Eun Mi Kim ◽  
James E. Haber ◽  
Sang Eun Lee
Keyword(s):  
Gamma Ray ◽  
Constitutive Expression ◽  
Double Strand Breaks ◽  
Base Pairing ◽  
End Joining ◽  
Complementary Sequence ◽  
Strand Breaks ◽  
End Sequences ◽  
Chromosome Iii

ABSTRACT End joining of double-strand breaks (DSBs) requires Ku proteins and frequently involves base pairing between complementary terminal sequences. To define the role of terminal base pairing in end joining, two oppositely oriented HO endonuclease cleavage sites separated by 2.0 kb were integrated into yeast chromosome III, where constitutive expression of HO endonuclease creates two simultaneous DSBs with no complementary end sequence. Lack of complementary sequence in their 3′ single-strand overhangs facilitates efficient repair events distinctly different from when the 3′ ends have a 4-bp sequence base paired in various ways to create 2- to 3-bp insertions. Repair of noncomplementary ends results in a set of nonrandom deletions of up to 302 bp, annealed by imperfect microhomology of about 8 to 10 bp at the junctions. This microhomology-mediated end joining (MMEJ) is Ku independent, but strongly dependent on Mre11, Rad50, and Rad1 proteins and partially dependent on Dnl4 protein. The MMEJ also occurs when Rad52 is absent, but the extent of deletions becomes more limited. The increased gamma ray sensitivity of rad1Δ rad52Δ yku70Δ strains compared to rad52Δ yku70Δ strains suggests that MMEJ also contributes to the repair of DSBs induced by ionizing radiation.

The role of self-assembly in biological systems: evidence from iridescent colloidal sporopollenin in Selaginella megaspore walls

1994 ◽  
Vol 345 (1312) ◽  
pp. 163-173 ◽  
Keyword(s):  
Self Assembly ◽  
Colloidal Crystal ◽  
Biological Systems ◽  
Spore Wall ◽  
The Self ◽  
Detailed Explanation ◽  
Stored Information ◽  
Organismal Development ◽  
Adjacent Wall

Iridescent exines have previously been reported in both fossil and modern megaspores of selaginellalean affinity. This striking feature has been shown to result from a colloidal crystal configuration of the exine units in at least part of the wall. This paper discusses the mechanics of formation of the colloidal crystal and of the adjacent wall layers (by depletion attraction), and provides a detailed explanation of the cause of the iridescence. Selaginella leaves and virus aggregates provide comparisons with the iridescent arrangement present in the spore wall. The self-assembly aspect of colloidal structures in biological systems is explored. Periods of selfassembly in organismal development may represent a saving in terms of stored information retrieval. Self-assembly, and its often chaotic behaviour, offer the prospect of large changes in organismal construction associated with relatively little change in the underlying genetic configuration.

Self‐Assembly of Perylenediimide–Single‐Strand‐DNA Conjugates: Employing Hydrophobic Interactions and DNA Base‐Pairing To Create a Diverse Structural Space

2017 ◽  
Vol 23 (43) ◽  
pp. 10328-10337 ◽  
Author(s):  
Ashutosh Kumar Mishra ◽  
Haim Weissman ◽  
Elisha Krieg ◽  
Kevin A. Votaw ◽  
Martin McCullagh ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hydrophobic Interactions ◽  
Single Strand ◽  
Base Pairing ◽  
Dna Conjugates ◽  
Dna Base ◽  
Structural Space

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Sticky ends in a self-assembling ABA triblock copolymer: the role of ureas in stimuli-responsive hydrogels

2019 ◽  
Vol 4 (1) ◽  
pp. 91-102 ◽  
Author(s):  
Ryan T. Shafranek ◽  
Joel D. Leger ◽  
Song Zhang ◽  
Munira Khalil ◽  
Xiaodan Gu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Viscoelastic Properties ◽  
Triblock Copolymer ◽  
Thermal Response ◽  
Stimuli Responsive ◽  
Self Assembling ◽  
Polymeric Hydrogels ◽  
Aba Triblock Copolymer ◽  
Responsive Hydrogels

Directed self-assembly in polymeric hydrogels allows tunability of thermal response and viscoelastic properties.

Shape Complementarity Modulated Self-Assembly of Nanoring and Nanosphere Hetero-nanostructures

2020 ◽  
Vol 142 (27) ◽  
pp. 11680-11684
Author(s):  
Na Li ◽  
Fan Wu ◽  
Zihong Han ◽  
Xiaofeng Wang ◽  
Yi Liu ◽  
...  
Keyword(s):  
Self Assembly ◽  
Shape Complementarity

scholarly journals Understanding the role of conjugation length on the self-assembly behaviour of oligophenyleneethynylenes

2021 ◽  
Author(s):  
Beatriz Matarranz ◽  
Goutam Ghosh ◽  
Ramesh Kandanelli ◽  
Angel Sampedro ◽  
Kalathil K. Kartha ◽  
...  
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Conjugation Length ◽  
The Relationship

We unravel the relationship between conjugation length and self-assembly behaviour of oligophenyleneethynylenes (OPEs).

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