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Title: Oligonucleotide–Peptide Complexes: Phase Control by Hybridization

Abstract

When oppositely charged polymers are mixed, counterion release drives phase separation; understanding this process is a key unsolved problem in polymer science and biophysical chemistry, particularly for nucleic acids, polyanions whose biological functions are intimately related to their high charge density. In the cell, complexation by basic proteins condenses DNA into chromatin, and membraneless organelles formed by liquid-liquid phase separation of RNA and proteins perform vital functions and have been linked to disease. Electrostatic interactions are also the primary method used for assembly of nanoparticles to deliver therapeutic nucleic acids into cells. This paper describes complexation experiments with oligonucleotides and cationic peptides spanning a wide range of polymer lengths, concentrations, and structures, including RNA and methylphosphonate backbones. We find that the phase of the complexes is controlled by the hybridization state of the nucleic acid, with double-stranded nucleic acids forming solid precipitates while single-stranded oligonucleotides form liquid coacervates, apparently due to their lower charge density. Adding salt "melts" precipitates into coacervates, and oligonucleotides in coacervates remain competent for sequence-specific hybridization and phase change, suggesting the possibility of environmentally responsive complexes and nanoparticles for therapeutic or sensing applications.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [1];  [3];  [1];  [4];  [5]
  1. Univ. of Chicago, IL (United States). Inst. for Molecular Engineering
  2. Univ. of Chicago, IL (United States). Dept. of Chemistry
  3. Univ. of Central Florida, Orlando, FL (United States). Dept. of Materials Science and Engineering
  4. Univ. of Puerto Rico at Rio Piedras, San Juan, PR (United States). Dept. of Biological Sciences
  5. Univ. of Chicago, IL (United States). Inst. for Molecular Engineering; Argonne National Lab. (ANL), Argonne, IL (United States). Inst. for Molecular Engineering
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division
OSTI Identifier:
1461292
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of the American Chemical Society
Additional Journal Information:
Journal Volume: 140; Journal Issue: 5; Journal ID: ISSN 0002-7863
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 36 MATERIALS SCIENCE

Citation Formats

Vieregg, Jeffrey R., Lueckheide, Michael, Marciel, Amanda B., Leon, Lorraine, Bologna, Alex J., Rivera, Josean Reyes, and Tirrell, Matthew V. Oligonucleotide–Peptide Complexes: Phase Control by Hybridization. United States: N. p., 2018. Web. doi:10.1021/jacs.7b03567.
Vieregg, Jeffrey R., Lueckheide, Michael, Marciel, Amanda B., Leon, Lorraine, Bologna, Alex J., Rivera, Josean Reyes, & Tirrell, Matthew V. Oligonucleotide–Peptide Complexes: Phase Control by Hybridization. United States. doi:10.1021/jacs.7b03567.
Vieregg, Jeffrey R., Lueckheide, Michael, Marciel, Amanda B., Leon, Lorraine, Bologna, Alex J., Rivera, Josean Reyes, and Tirrell, Matthew V. Tue . "Oligonucleotide–Peptide Complexes: Phase Control by Hybridization". United States. doi:10.1021/jacs.7b03567. https://www.osti.gov/servlets/purl/1461292.
@article{osti_1461292,
title = {Oligonucleotide–Peptide Complexes: Phase Control by Hybridization},
author = {Vieregg, Jeffrey R. and Lueckheide, Michael and Marciel, Amanda B. and Leon, Lorraine and Bologna, Alex J. and Rivera, Josean Reyes and Tirrell, Matthew V.},
abstractNote = {When oppositely charged polymers are mixed, counterion release drives phase separation; understanding this process is a key unsolved problem in polymer science and biophysical chemistry, particularly for nucleic acids, polyanions whose biological functions are intimately related to their high charge density. In the cell, complexation by basic proteins condenses DNA into chromatin, and membraneless organelles formed by liquid-liquid phase separation of RNA and proteins perform vital functions and have been linked to disease. Electrostatic interactions are also the primary method used for assembly of nanoparticles to deliver therapeutic nucleic acids into cells. This paper describes complexation experiments with oligonucleotides and cationic peptides spanning a wide range of polymer lengths, concentrations, and structures, including RNA and methylphosphonate backbones. We find that the phase of the complexes is controlled by the hybridization state of the nucleic acid, with double-stranded nucleic acids forming solid precipitates while single-stranded oligonucleotides form liquid coacervates, apparently due to their lower charge density. Adding salt "melts" precipitates into coacervates, and oligonucleotides in coacervates remain competent for sequence-specific hybridization and phase change, suggesting the possibility of environmentally responsive complexes and nanoparticles for therapeutic or sensing applications.},
doi = {10.1021/jacs.7b03567},
journal = {Journal of the American Chemical Society},
issn = {0002-7863},
number = 5,
volume = 140,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 18 works
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Figures / Tables:

Figure 1 Figure 1: Oligonucleotides and poly(L)lysine (pLys) form phase-separated complexes upon mixing. A) 22 nt single-stranded DNA and 50 aa pLys form liquid droplets when mixed at 2.5 mM amine and phosphate concentration. 22 bp double-stranded DNA and 50 aa pLys form solid precipitates when mixed under the same conditions. Imagesmore » taken 4 hours after mixing. B) Quantification of non-complexed DNA shows that the complexes appear nearly neutral (black line) regardless of bulk charge ratio and polymer length: [N]/[P] ≡ [pLys amines] / [DNA phosphates]. Total charge ([amine] + [phosphate]) is fixed at 5 mM. Solution DNA values are normalized to 1 at [pLys] = 0 and 0 at [DNA] = 0. C) Phase separation is consistent across a wide range of polyanion : polycation concentration ratios ([N]/[P] = 1 shown in Panel A).« less

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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.