Structure of three-way dna junctions. 2. effects of extra bases and mismatches

Luda S. Shlyakhtenko, Ettore Appella, Rodney E. Harrington, Igor Kutyavin, Yuri L. Lyubchenko

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.

Original languageEnglish (US)
Pages (from-to)131-143
Number of pages13
JournalJournal of Biomolecular Structure and Dynamics
Volume12
Issue number1
DOIs
StatePublished - Aug 1994

Fingerprint

Nucleotides
DNA
Cyclization
Base Pairing

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Structure of three-way dna junctions. 2. effects of extra bases and mismatches. / Shlyakhtenko, Luda S.; Appella, Ettore; Harrington, Rodney E.; Kutyavin, Igor; Lyubchenko, Yuri L.

In: Journal of Biomolecular Structure and Dynamics, Vol. 12, No. 1, 08.1994, p. 131-143.

Research output: Contribution to journalArticle

Shlyakhtenko, Luda S. ; Appella, Ettore ; Harrington, Rodney E. ; Kutyavin, Igor ; Lyubchenko, Yuri L. / Structure of three-way dna junctions. 2. effects of extra bases and mismatches. In: Journal of Biomolecular Structure and Dynamics. 1994 ; Vol. 12, No. 1. pp. 131-143.
@article{9854d0bca2714393b76f00e5c748e139,
title = "Structure of three-way dna junctions. 2. effects of extra bases and mismatches",
abstract = "The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.",
author = "Shlyakhtenko, {Luda S.} and Ettore Appella and Harrington, {Rodney E.} and Igor Kutyavin and Lyubchenko, {Yuri L.}",
year = "1994",
month = "8",
doi = "10.1080/07391102.1994.10508092",
language = "English (US)",
volume = "12",
pages = "131--143",
journal = "Journal of Biomolecular Structure and Dynamics",
issn = "0739-1102",
publisher = "Adenine Press",
number = "1",

}

TY - JOUR

T1 - Structure of three-way dna junctions. 2. effects of extra bases and mismatches

AU - Shlyakhtenko, Luda S.

AU - Appella, Ettore

AU - Harrington, Rodney E.

AU - Kutyavin, Igor

AU - Lyubchenko, Yuri L.

PY - 1994/8

Y1 - 1994/8

N2 - The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.

AB - The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.

UR - http://www.scopus.com/inward/record.url?scp=0028019454&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0028019454&partnerID=8YFLogxK

U2 - 10.1080/07391102.1994.10508092

DO - 10.1080/07391102.1994.10508092

M3 - Article

C2 - 7848563

AN - SCOPUS:0028019454

VL - 12

SP - 131

EP - 143

JO - Journal of Biomolecular Structure and Dynamics

JF - Journal of Biomolecular Structure and Dynamics

SN - 0739-1102

IS - 1

ER -