The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation

Donald M. Gray, Kenneth H. Johnson, Marilyn R. Vaughan, Patricia A. Morris, John C. Sutherland, Robert L. Ratliff

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

CD spectra were obtained for eight synthetic double‐stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A‐C) · d(G‐T)] and poly[d(A‐G) · d(C‐T)], (b) poly[d(A‐C‐C) · d(G‐G‐T)] and poly[d(A‐C‐G) · d(C‐G‐T)], and (c) poly[d(A) · d(T)], poly[d(A‐T) · d(A‐T)], poly[d(A‐A‐T) · d(A‐T‐T)], and poly[d(A‐A‐T‐T) · d(A‐A‐T‐T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)‐containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right‐handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)‐rich polymers and was absent from two first‐neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)‐rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.

Original languageEnglish (US)
Pages (from-to)317-323
Number of pages7
JournalBiopolymers
Volume29
Issue number2
DOIs
StatePublished - Jan 1 1990
Externally publishedYes

Fingerprint

DNA sequences
Vacuum
Conformations
Polymers
Isomers
Wavelength
Dilatation and Curettage
DNA
Base Pairing
2'-deoxythymidylyl-(3'-5')-2'-deoxyadenosine

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

Cite this

The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation. / Gray, Donald M.; Johnson, Kenneth H.; Vaughan, Marilyn R.; Morris, Patricia A.; Sutherland, John C.; Ratliff, Robert L.

In: Biopolymers, Vol. 29, No. 2, 01.01.1990, p. 317-323.

Research output: Contribution to journalArticle

Gray, Donald M. ; Johnson, Kenneth H. ; Vaughan, Marilyn R. ; Morris, Patricia A. ; Sutherland, John C. ; Ratliff, Robert L. / The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation. In: Biopolymers. 1990 ; Vol. 29, No. 2. pp. 317-323.
@article{2347a3c4fac640ada46b8d19ab4f82c6,
title = "The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation",
abstract = "CD spectra were obtained for eight synthetic double‐stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A‐C) · d(G‐T)] and poly[d(A‐G) · d(C‐T)], (b) poly[d(A‐C‐C) · d(G‐G‐T)] and poly[d(A‐C‐G) · d(C‐G‐T)], and (c) poly[d(A) · d(T)], poly[d(A‐T) · d(A‐T)], poly[d(A‐A‐T) · d(A‐T‐T)], and poly[d(A‐A‐T‐T) · d(A‐A‐T‐T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)‐containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right‐handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)‐rich polymers and was absent from two first‐neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)‐rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.",
author = "Gray, {Donald M.} and Johnson, {Kenneth H.} and Vaughan, {Marilyn R.} and Morris, {Patricia A.} and Sutherland, {John C.} and Ratliff, {Robert L.}",
year = "1990",
month = "1",
day = "1",
doi = "10.1002/bip.360290204",
language = "English (US)",
volume = "29",
pages = "317--323",
journal = "Biopolymers",
issn = "0006-3525",
publisher = "John Wiley and Sons Inc.",
number = "2",

}

TY - JOUR

T1 - The vacuum UV CD bands of repeating DNA sequences are dependent on sequence and conformation

AU - Gray, Donald M.

AU - Johnson, Kenneth H.

AU - Vaughan, Marilyn R.

AU - Morris, Patricia A.

AU - Sutherland, John C.

AU - Ratliff, Robert L.

PY - 1990/1/1

Y1 - 1990/1/1

N2 - CD spectra were obtained for eight synthetic double‐stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A‐C) · d(G‐T)] and poly[d(A‐G) · d(C‐T)], (b) poly[d(A‐C‐C) · d(G‐G‐T)] and poly[d(A‐C‐G) · d(C‐G‐T)], and (c) poly[d(A) · d(T)], poly[d(A‐T) · d(A‐T)], poly[d(A‐A‐T) · d(A‐T‐T)], and poly[d(A‐A‐T‐T) · d(A‐A‐T‐T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)‐containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right‐handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)‐rich polymers and was absent from two first‐neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)‐rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.

AB - CD spectra were obtained for eight synthetic double‐stranded DNA polymers down to at least 175 nm in the vacuum uv. Three sets of sequence isomers were studied: (a) poly[d(A‐C) · d(G‐T)] and poly[d(A‐G) · d(C‐T)], (b) poly[d(A‐C‐C) · d(G‐G‐T)] and poly[d(A‐C‐G) · d(C‐G‐T)], and (c) poly[d(A) · d(T)], poly[d(A‐T) · d(A‐T)], poly[d(A‐A‐T) · d(A‐T‐T)], and poly[d(A‐A‐T‐T) · d(A‐A‐T‐T)]. There were significant differences in the CD spectra at short wavelengths among each set of sequence isomers. The (G · C)‐containing sequences had the largest vacuum uv bands, which were positive and in the wavelength range of 180–191 nm. There were no large negative bands at longer wavelengths, consistent with the polymers all being in right‐handed conformations. Among the set of sequences containing only A · T base pairs, poly[d(A) · d(T)] had the largest vacuum uv CD band, which was at 190 nm. This CD band was not present in the spectra of the other (A · T)‐rich polymers and was absent from two first‐neighbor estimations of the poly[d(A) · d(T)] spectrum obtained from the other three sequences. We concluded that the sequence dependence of the vacuum uv spectra of the (A · T)‐rich polymers was due in part of the fact that poly[d(A) · d(T)] exists in a noncanonical B conformation.

UR - http://www.scopus.com/inward/record.url?scp=0025100839&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025100839&partnerID=8YFLogxK

U2 - 10.1002/bip.360290204

DO - 10.1002/bip.360290204

M3 - Article

C2 - 2331501

AN - SCOPUS:0025100839

VL - 29

SP - 317

EP - 323

JO - Biopolymers

JF - Biopolymers

SN - 0006-3525

IS - 2

ER -