Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase

Alexandra Dimitri, Lei Jia, Vladimir Shafirovich, Nicholas E. Geacintov, Suse Broyde, David A. Scicchitano

Research output: Contribution to journalArticle

Abstract

Damage in transcribed DNA presents a challenge to the cell because it can partially or completely block the progression of an RNA polymerase, interfering with transcription and compromising gene expression. While blockage of RNA polymerase progression is thought to trigger the recruitment of transcription-coupled DNA repair (TCR), bypass of the lesion can also occur, either error-prone or error-free. Error-prone transcription is often referred to as transcriptional mutagenesis (TM). Elucidating why some lesions pose blocks to transcription elongation while others do not remains a challenging problem. As part of an effort to understand this, we studied transcription past a 5-guanidino-4-nitroimidazole (NI) lesion, using two structurally different RNA polymerases, human RNA polymerase II (hRNAPII) and bacteriophage T7 RNA polymerase (T7RNAP). The NI damage results from the oxidation of guanine in DNA by peroxynitrite, a well known, biologically important oxidant. It is of structural interest because it is a ring-opened and conformationally flexible guanine lesion. Our results show that NI acts as a partial block to T7RNAP while posing a major block to hRNAPII, which has a more constrained active site than T7RNAP. Lesion bypass by T7RNAP induces base misincorporations and deletions opposite the lesion (C > A > -1 deletion >G ⋙ U), but hRNAPII exhibits error-free transcription although lesion bypass is a rare event. We employed molecular modeling methods to explain the observed blockage or bypass accompanied by nucleotide incorporation opposite the lesion. The results of the modeling studies indicate that NI's multiple hydrogen-bonding capabilities and torsional flexibility are important determinants of its effect on transcription in both enzymes. These influence the kinetics of lesion bypass and may well play a role in TM and TCR in cells.

Original languageEnglish (US)
Pages (from-to)1276-1288
Number of pages13
JournalDNA Repair
Volume7
Issue number8
DOIs
StatePublished - Aug 2 2008

Fingerprint

RNA Phages
RNA Polymerase II
Transcription
DNA-Directed RNA Polymerases
Nitroimidazoles
DNA
Guanine
Mutagenesis
DNA Repair
Peroxynitrous Acid
Hydrogen Bonding
Oxidants
Catalytic Domain
Repair
Nucleotides
Gene Expression
Molecular modeling
bacteriophage T7 RNA polymerase
5-guanidino-4-nitroimidazole
Enzymes

Keywords

  • 5-Guanidino-4-nitroimidazole
  • DNA damage
  • Molecular modeling
  • RNA polymerase
  • Transcription

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase. / Dimitri, Alexandra; Jia, Lei; Shafirovich, Vladimir; Geacintov, Nicholas E.; Broyde, Suse; Scicchitano, David A.

In: DNA Repair, Vol. 7, No. 8, 02.08.2008, p. 1276-1288.

Research output: Contribution to journalArticle

@article{b8715c3cec274441af17c2d4ade5f00b,
title = "Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase",
abstract = "Damage in transcribed DNA presents a challenge to the cell because it can partially or completely block the progression of an RNA polymerase, interfering with transcription and compromising gene expression. While blockage of RNA polymerase progression is thought to trigger the recruitment of transcription-coupled DNA repair (TCR), bypass of the lesion can also occur, either error-prone or error-free. Error-prone transcription is often referred to as transcriptional mutagenesis (TM). Elucidating why some lesions pose blocks to transcription elongation while others do not remains a challenging problem. As part of an effort to understand this, we studied transcription past a 5-guanidino-4-nitroimidazole (NI) lesion, using two structurally different RNA polymerases, human RNA polymerase II (hRNAPII) and bacteriophage T7 RNA polymerase (T7RNAP). The NI damage results from the oxidation of guanine in DNA by peroxynitrite, a well known, biologically important oxidant. It is of structural interest because it is a ring-opened and conformationally flexible guanine lesion. Our results show that NI acts as a partial block to T7RNAP while posing a major block to hRNAPII, which has a more constrained active site than T7RNAP. Lesion bypass by T7RNAP induces base misincorporations and deletions opposite the lesion (C > A > -1 deletion >G ⋙ U), but hRNAPII exhibits error-free transcription although lesion bypass is a rare event. We employed molecular modeling methods to explain the observed blockage or bypass accompanied by nucleotide incorporation opposite the lesion. The results of the modeling studies indicate that NI's multiple hydrogen-bonding capabilities and torsional flexibility are important determinants of its effect on transcription in both enzymes. These influence the kinetics of lesion bypass and may well play a role in TM and TCR in cells.",
keywords = "5-Guanidino-4-nitroimidazole, DNA damage, Molecular modeling, RNA polymerase, Transcription",
author = "Alexandra Dimitri and Lei Jia and Vladimir Shafirovich and Geacintov, {Nicholas E.} and Suse Broyde and Scicchitano, {David A.}",
year = "2008",
month = "8",
day = "2",
doi = "10.1016/j.dnarep.2008.04.007",
language = "English (US)",
volume = "7",
pages = "1276--1288",
journal = "DNA Repair",
issn = "1568-7864",
publisher = "Elsevier",
number = "8",

}

TY - JOUR

T1 - Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase

AU - Dimitri, Alexandra

AU - Jia, Lei

AU - Shafirovich, Vladimir

AU - Geacintov, Nicholas E.

AU - Broyde, Suse

AU - Scicchitano, David A.

PY - 2008/8/2

Y1 - 2008/8/2

N2 - Damage in transcribed DNA presents a challenge to the cell because it can partially or completely block the progression of an RNA polymerase, interfering with transcription and compromising gene expression. While blockage of RNA polymerase progression is thought to trigger the recruitment of transcription-coupled DNA repair (TCR), bypass of the lesion can also occur, either error-prone or error-free. Error-prone transcription is often referred to as transcriptional mutagenesis (TM). Elucidating why some lesions pose blocks to transcription elongation while others do not remains a challenging problem. As part of an effort to understand this, we studied transcription past a 5-guanidino-4-nitroimidazole (NI) lesion, using two structurally different RNA polymerases, human RNA polymerase II (hRNAPII) and bacteriophage T7 RNA polymerase (T7RNAP). The NI damage results from the oxidation of guanine in DNA by peroxynitrite, a well known, biologically important oxidant. It is of structural interest because it is a ring-opened and conformationally flexible guanine lesion. Our results show that NI acts as a partial block to T7RNAP while posing a major block to hRNAPII, which has a more constrained active site than T7RNAP. Lesion bypass by T7RNAP induces base misincorporations and deletions opposite the lesion (C > A > -1 deletion >G ⋙ U), but hRNAPII exhibits error-free transcription although lesion bypass is a rare event. We employed molecular modeling methods to explain the observed blockage or bypass accompanied by nucleotide incorporation opposite the lesion. The results of the modeling studies indicate that NI's multiple hydrogen-bonding capabilities and torsional flexibility are important determinants of its effect on transcription in both enzymes. These influence the kinetics of lesion bypass and may well play a role in TM and TCR in cells.

AB - Damage in transcribed DNA presents a challenge to the cell because it can partially or completely block the progression of an RNA polymerase, interfering with transcription and compromising gene expression. While blockage of RNA polymerase progression is thought to trigger the recruitment of transcription-coupled DNA repair (TCR), bypass of the lesion can also occur, either error-prone or error-free. Error-prone transcription is often referred to as transcriptional mutagenesis (TM). Elucidating why some lesions pose blocks to transcription elongation while others do not remains a challenging problem. As part of an effort to understand this, we studied transcription past a 5-guanidino-4-nitroimidazole (NI) lesion, using two structurally different RNA polymerases, human RNA polymerase II (hRNAPII) and bacteriophage T7 RNA polymerase (T7RNAP). The NI damage results from the oxidation of guanine in DNA by peroxynitrite, a well known, biologically important oxidant. It is of structural interest because it is a ring-opened and conformationally flexible guanine lesion. Our results show that NI acts as a partial block to T7RNAP while posing a major block to hRNAPII, which has a more constrained active site than T7RNAP. Lesion bypass by T7RNAP induces base misincorporations and deletions opposite the lesion (C > A > -1 deletion >G ⋙ U), but hRNAPII exhibits error-free transcription although lesion bypass is a rare event. We employed molecular modeling methods to explain the observed blockage or bypass accompanied by nucleotide incorporation opposite the lesion. The results of the modeling studies indicate that NI's multiple hydrogen-bonding capabilities and torsional flexibility are important determinants of its effect on transcription in both enzymes. These influence the kinetics of lesion bypass and may well play a role in TM and TCR in cells.

KW - 5-Guanidino-4-nitroimidazole

KW - DNA damage

KW - Molecular modeling

KW - RNA polymerase

KW - Transcription

UR - http://www.scopus.com/inward/record.url?scp=46649117840&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=46649117840&partnerID=8YFLogxK

U2 - 10.1016/j.dnarep.2008.04.007

DO - 10.1016/j.dnarep.2008.04.007

M3 - Article

VL - 7

SP - 1276

EP - 1288

JO - DNA Repair

JF - DNA Repair

SN - 1568-7864

IS - 8

ER -