TY - JOUR
T1 - Sequence-Dependent Deviations of Constrained DNA from Canonical B-Form
AU - Kuchuk, Kfir
AU - Katrivas, Liat
AU - Kotlyar, Alexander
AU - Sivan, Uri
N1 - Publisher Copyright:
Copyright © 2019 American Chemical Society.
PY - 2019/9/11
Y1 - 2019/9/11
N2 - Decades of crystallographic and NMR studies have produced canonical structural models of short DNA. However, no experimental method so far has been able to test these models in vivo, where DNA is long and constrained by interactions with membranes, proteins, and other molecules. Here, we employ high-resolution frequency-modulation AFM to image single long poly(dA)-poly(dT), poly(dG)-poly(dC), and lambda DNA molecules interacting with an underlying substrate that emulates the effect of biological constraints on molecular structure. We find systematic sequence-dependent variations in groove dimensions, indicating that the structure of DNA subject to realistic interactions may differ profoundly from canonical models. These findings highlight the value of AFM as a unique, single molecule characterization tool.
AB - Decades of crystallographic and NMR studies have produced canonical structural models of short DNA. However, no experimental method so far has been able to test these models in vivo, where DNA is long and constrained by interactions with membranes, proteins, and other molecules. Here, we employ high-resolution frequency-modulation AFM to image single long poly(dA)-poly(dT), poly(dG)-poly(dC), and lambda DNA molecules interacting with an underlying substrate that emulates the effect of biological constraints on molecular structure. We find systematic sequence-dependent variations in groove dimensions, indicating that the structure of DNA subject to realistic interactions may differ profoundly from canonical models. These findings highlight the value of AFM as a unique, single molecule characterization tool.
KW - AFM
KW - DNA
KW - single molecule biophysics
UR - http://www.scopus.com/inward/record.url?scp=85072134312&partnerID=8YFLogxK
U2 - 10.1021/acs.nanolett.9b02863
DO - 10.1021/acs.nanolett.9b02863
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AN - SCOPUS:85072134312
SN - 1530-6984
VL - 19
SP - 6600
EP - 6603
JO - Nano Letters
JF - Nano Letters
IS - 9
ER -