Early Interrogation and Recognition of DNA Sequence by Indirect Readout

Elizabeth J. Little, Andrea C. Babic, Nancy C Horton

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.

Original languageEnglish (US)
Pages (from-to)1828-1837
Number of pages10
JournalStructure
Volume16
Issue number12
DOIs
StatePublished - Dec 12 2008

Fingerprint

Recombinational DNA Repair
DNA
Enzymes
Proteins
GTYRAC-specific type II deoxyribonucleases

Keywords

  • DNA

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Early Interrogation and Recognition of DNA Sequence by Indirect Readout. / Little, Elizabeth J.; Babic, Andrea C.; Horton, Nancy C.

In: Structure, Vol. 16, No. 12, 12.12.2008, p. 1828-1837.

Research output: Contribution to journalArticle

Little, Elizabeth J. ; Babic, Andrea C. ; Horton, Nancy C. / Early Interrogation and Recognition of DNA Sequence by Indirect Readout. In: Structure. 2008 ; Vol. 16, No. 12. pp. 1828-1837.
@article{fed9f808d3594a549182686fd294c922,
title = "Early Interrogation and Recognition of DNA Sequence by Indirect Readout",
abstract = "Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.",
keywords = "DNA",
author = "Little, {Elizabeth J.} and Babic, {Andrea C.} and Horton, {Nancy C}",
year = "2008",
month = "12",
day = "12",
doi = "10.1016/j.str.2008.09.009",
language = "English (US)",
volume = "16",
pages = "1828--1837",
journal = "Structure with Folding & design",
issn = "0969-2126",
publisher = "Cell Press",
number = "12",

}

TY - JOUR

T1 - Early Interrogation and Recognition of DNA Sequence by Indirect Readout

AU - Little, Elizabeth J.

AU - Babic, Andrea C.

AU - Horton, Nancy C

PY - 2008/12/12

Y1 - 2008/12/12

N2 - Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.

AB - Control of replication, transcription, recombination and repair requires proteins capable of finding particular DNA sequences in a background of a large excess of nonspecific sequences. Such recognition can involve direct readout, with direct contacts to the bases of DNA, or in some cases through the less well-characterized indirect readout mechanisms. In order to measure the relative contributions of direct and indirect readout by a sequence specific endonuclease, HincII, a mutant enzyme deficient in a direct contact, was characterized, and surprisingly showed no loss of sequence specificity. The three dimensional crystal structure shows the loss of most of the direct readout contacts to the DNA, possibly capturing an early stage in target site recognition using predominately indirect readout to prescreen sites before full sequence interrogation.

KW - DNA

UR - http://www.scopus.com/inward/record.url?scp=57049101786&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=57049101786&partnerID=8YFLogxK

U2 - 10.1016/j.str.2008.09.009

DO - 10.1016/j.str.2008.09.009

M3 - Article

VL - 16

SP - 1828

EP - 1837

JO - Structure with Folding & design

JF - Structure with Folding & design

SN - 0969-2126

IS - 12

ER -