PMID- 36615321
OWN - NLM
STAT- MEDLINE
DCOM- 20230110
LR  - 20230111
IS  - 1420-3049 (Electronic)
IS  - 1420-3049 (Linking)
VI  - 28
IP  - 1
DP  - 2022 Dec 23
TI  - Factors Impacting Invader-Mediated Recognition of Double-Stranded DNA.
LID - 10.3390/molecules28010127 [doi]
LID - 127
AB  - The development of chemically modified oligonucleotides enabling robust, 
      sequence-unrestricted recognition of complementary chromosomal DNA regions has 
      been an aspirational goal for scientists for many decades. While several 
      groove-binding or strand-invading probes have been developed towards this end, 
      most enable recognition of DNA only under limited conditions (e.g., homopurine or 
      short mixed-sequence targets, low ionic strength, fully modified probe strands). 
      Invader probes, i.e., DNA duplexes modified with +1 interstrand zippers of 
      intercalator-functionalized nucleotides, are predisposed to recognize DNA targets 
      due to their labile nature and high affinity towards complementary DNA. Here, we 
      set out to gain further insight into the design parameters that impact the 
      thermal denaturation properties and binding affinities of Invader probes. Towards 
      this end, ten Invader probes were designed, and their biophysical properties and 
      binding to model DNA hairpins and chromosomal DNA targets were studied. A 
      Spearman's rank-order correlation analysis of various parameters was then 
      performed. Densely modified Invader probes were found to result in efficient 
      recognition of chromosomal DNA targets with excellent binding specificity in the 
      context of denaturing or non-denaturing fluorescence in situ hybridization (FISH) 
      experiments. The insight gained from the initial phase of this study informed 
      subsequent probe optimization, which yielded constructs displaying improved 
      recognition of chromosomal DNA targets. The findings from this study will 
      facilitate the design of efficient Invader probes for applications in the life 
      sciences.
FAU - Shepard, Caroline P
AU  - Shepard CP
AD  - Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
FAU - Emehiser, Raymond G
AU  - Emehiser RG
AD  - Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
FAU - Karmakar, Saswata
AU  - Karmakar S
AD  - Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
FAU - Hrdlicka, Patrick J
AU  - Hrdlicka PJ
AD  - Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
LA  - eng
GR  - P20 GM103408/GM/NIGMS NIH HHS/United States
GR  - IF13-001, IF14-012, IGEM-004/Higher Education Research Council, Idaho State Board 
      of Education/
PT  - Journal Article
DEP - 20221223
PL  - Switzerland
TA  - Molecules
JT  - Molecules (Basel, Switzerland)
JID - 100964009
RN  - 9007-49-2 (DNA)
RN  - 0 (Oligonucleotides)
RN  - 0 (Nucleotides)
RN  - 0 (DNA, Complementary)
RN  - 0 (DNA Probes)
SB  - IM
MH  - In Situ Hybridization, Fluorescence
MH  - *DNA/chemistry
MH  - *Oligonucleotides/chemistry
MH  - Nucleotides
MH  - DNA, Complementary
MH  - DNA Probes
PMC - PMC9821881
OTO - NOTNLM
OT  - DNA
OT  - DNA recognition
OT  - FISH
OT  - SNP
OT  - chromosomes
OT  - fluorescence
OT  - karyotyping
OT  - oligonucleotides
OT  - pyrene
OT  - strand invasion
COIS- PJH is an inventor on patents pertaining to Invader probes, which have been 
      issued to the University Idaho.
EDAT- 2023/01/09 06:00
MHDA- 2023/01/11 06:00
PMCR- 2022/12/23
CRDT- 2023/01/08 01:33
PHST- 2022/10/29 00:00 [received]
PHST- 2022/12/16 00:00 [revised]
PHST- 2022/12/20 00:00 [accepted]
PHST- 2023/01/08 01:33 [entrez]
PHST- 2023/01/09 06:00 [pubmed]
PHST- 2023/01/11 06:00 [medline]
PHST- 2022/12/23 00:00 [pmc-release]
AID - molecules28010127 [pii]
AID - molecules-28-00127 [pii]
AID - 10.3390/molecules28010127 [doi]
PST - epublish
SO  - Molecules. 2022 Dec 23;28(1):127. doi: 10.3390/molecules28010127.