Two-Dimensional 1H NMR Studies of 32-Base-Pair Synthetic Immobile Holliday Junctions: Complete Assignments of the Labile Protons and Identification of the Base-Pairing Scheme

Shiow meei Chen, Fred Heffron, Walter J. Chazin

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The labile protons of two 32-base-pair, four-arm models of immobile Holliday junctions have been studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Overlap of resonances in the imino-imino region of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitates the use of a multi-pathway approach for obtaining sequence-specific assignments wherein all possible NOE connectivities to the labile protons are utilized, including those from the 2H of adenine, 5CH3 of thymine, and 5H of cytosine. Resonance assignments are obtained for all slowly exchanging imino and cytosine amino protons. Base-pairing up to and including the junction point is found in all four arms of both Holliday junctions. Several cross-arm NOE connectivities are identified and can be used to infer the geometry of the helical stacking domains. The two Holliday junctions studied, which differ only by the exchange of two base pairs at the branch point, appear to have opposite arm stacking geometries. These assignments form an important part of the critical background for detailed NMR analysis of Holliday junction structure and dynamics.

Original languageEnglish (US)
Pages (from-to)319-326
Number of pages8
JournalBiochemistry
Volume32
Issue number1
DOIs
StatePublished - Jan 1 1993
Externally publishedYes

Fingerprint

Cruciform DNA
Base Pairing
Protons
Magnetic Resonance Spectroscopy
Cytosine
Nuclear magnetic resonance
Thymine
Geometry
Adenine
Nuclear magnetic resonance spectroscopy

ASJC Scopus subject areas

  • Biochemistry

Cite this

Two-Dimensional 1H NMR Studies of 32-Base-Pair Synthetic Immobile Holliday Junctions : Complete Assignments of the Labile Protons and Identification of the Base-Pairing Scheme. / Chen, Shiow meei; Heffron, Fred; Chazin, Walter J.

In: Biochemistry, Vol. 32, No. 1, 01.01.1993, p. 319-326.

Research output: Contribution to journalArticle

@article{516de5e2d6da41d2a40f9593d443f21a,
title = "Two-Dimensional 1H NMR Studies of 32-Base-Pair Synthetic Immobile Holliday Junctions: Complete Assignments of the Labile Protons and Identification of the Base-Pairing Scheme",
abstract = "The labile protons of two 32-base-pair, four-arm models of immobile Holliday junctions have been studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Overlap of resonances in the imino-imino region of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitates the use of a multi-pathway approach for obtaining sequence-specific assignments wherein all possible NOE connectivities to the labile protons are utilized, including those from the 2H of adenine, 5CH3 of thymine, and 5H of cytosine. Resonance assignments are obtained for all slowly exchanging imino and cytosine amino protons. Base-pairing up to and including the junction point is found in all four arms of both Holliday junctions. Several cross-arm NOE connectivities are identified and can be used to infer the geometry of the helical stacking domains. The two Holliday junctions studied, which differ only by the exchange of two base pairs at the branch point, appear to have opposite arm stacking geometries. These assignments form an important part of the critical background for detailed NMR analysis of Holliday junction structure and dynamics.",
author = "Chen, {Shiow meei} and Fred Heffron and Chazin, {Walter J.}",
year = "1993",
month = "1",
day = "1",
doi = "10.1021/bi00052a040",
language = "English (US)",
volume = "32",
pages = "319--326",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "1",

}

TY - JOUR

T1 - Two-Dimensional 1H NMR Studies of 32-Base-Pair Synthetic Immobile Holliday Junctions

T2 - Complete Assignments of the Labile Protons and Identification of the Base-Pairing Scheme

AU - Chen, Shiow meei

AU - Heffron, Fred

AU - Chazin, Walter J.

PY - 1993/1/1

Y1 - 1993/1/1

N2 - The labile protons of two 32-base-pair, four-arm models of immobile Holliday junctions have been studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Overlap of resonances in the imino-imino region of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitates the use of a multi-pathway approach for obtaining sequence-specific assignments wherein all possible NOE connectivities to the labile protons are utilized, including those from the 2H of adenine, 5CH3 of thymine, and 5H of cytosine. Resonance assignments are obtained for all slowly exchanging imino and cytosine amino protons. Base-pairing up to and including the junction point is found in all four arms of both Holliday junctions. Several cross-arm NOE connectivities are identified and can be used to infer the geometry of the helical stacking domains. The two Holliday junctions studied, which differ only by the exchange of two base pairs at the branch point, appear to have opposite arm stacking geometries. These assignments form an important part of the critical background for detailed NMR analysis of Holliday junction structure and dynamics.

AB - The labile protons of two 32-base-pair, four-arm models of immobile Holliday junctions have been studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Overlap of resonances in the imino-imino region of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitates the use of a multi-pathway approach for obtaining sequence-specific assignments wherein all possible NOE connectivities to the labile protons are utilized, including those from the 2H of adenine, 5CH3 of thymine, and 5H of cytosine. Resonance assignments are obtained for all slowly exchanging imino and cytosine amino protons. Base-pairing up to and including the junction point is found in all four arms of both Holliday junctions. Several cross-arm NOE connectivities are identified and can be used to infer the geometry of the helical stacking domains. The two Holliday junctions studied, which differ only by the exchange of two base pairs at the branch point, appear to have opposite arm stacking geometries. These assignments form an important part of the critical background for detailed NMR analysis of Holliday junction structure and dynamics.

UR - http://www.scopus.com/inward/record.url?scp=0027339077&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0027339077&partnerID=8YFLogxK

U2 - 10.1021/bi00052a040

DO - 10.1021/bi00052a040

M3 - Article

C2 - 8418851

AN - SCOPUS:0027339077

VL - 32

SP - 319

EP - 326

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 1

ER -